Starting phenix.real_space_refine on Sun Aug 24 05:45:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e98_27959/08_2025/8e98_27959.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e98_27959/08_2025/8e98_27959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e98_27959/08_2025/8e98_27959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e98_27959/08_2025/8e98_27959.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e98_27959/08_2025/8e98_27959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e98_27959/08_2025/8e98_27959.map" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.097 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: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 10935 2.51 5 N 2961 2.21 5 O 3245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17208 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 4109 Classifications: {'peptide': 648} Incomplete info: {'truncation_to_alanine': 273} Link IDs: {'PTRANS': 27, 'TRANS': 620} Chain breaks: 2 Unresolved non-hydrogen bonds: 1080 Unresolved non-hydrogen angles: 1352 Unresolved non-hydrogen dihedrals: 887 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'ASN:plan1': 26, 'ARG:plan': 26, 'HIS:plan': 11, 'GLU:plan': 38, 'GLN:plan1': 16, 'PHE:plan': 8, 'TRP:plan': 2, 'ASP:plan': 22, 'TYR:plan': 9} Unresolved non-hydrogen planarities: 674 Chain: "B" Number of atoms: 3965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 3965 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 260} Link IDs: {'PTRANS': 38, 'TRANS': 603} Chain breaks: 2 Unresolved non-hydrogen bonds: 1059 Unresolved non-hydrogen angles: 1357 Unresolved non-hydrogen dihedrals: 882 Unresolved non-hydrogen chiralities: 89 Planarities with less than four sites: {'PHE:plan': 13, 'GLN:plan1': 20, 'ARG:plan': 32, 'ASP:plan': 19, 'GLU:plan': 24, 'ASN:plan1': 7, 'HIS:plan': 14, 'TYR:plan': 6, 'TRP:plan': 7} Unresolved non-hydrogen planarities: 667 Chain: "C" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 4464 Classifications: {'peptide': 655} Incomplete info: {'truncation_to_alanine': 188} Link IDs: {'PTRANS': 29, 'TRANS': 625} Chain breaks: 1 Unresolved non-hydrogen bonds: 753 Unresolved non-hydrogen angles: 918 Unresolved non-hydrogen dihedrals: 624 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ARG:plan': 22, 'GLU:plan': 39, 'GLN:plan1': 13, 'ASN:plan1': 19, 'TRP:plan': 1, 'HIS:plan': 7, 'ASP:plan': 18, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 512 Chain: "D" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 4427 Classifications: {'peptide': 638} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PTRANS': 39, 'TRANS': 598} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 532 Unresolved non-hydrogen angles: 652 Unresolved non-hydrogen dihedrals: 440 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 14, 'PHE:plan': 4, 'ARG:plan': 22, 'ASP:plan': 16, 'GLU:plan': 20, 'ASN:plan1': 5, 'HIS:plan': 8, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 380 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.42, per 1000 atoms: 0.20 Number of scatterers: 17208 At special positions: 0 Unit cell: (130.968, 144.664, 135.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 3245 8.00 N 2961 7.00 C 10935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS B 317 " distance=2.03 Simple disulfide: pdb=" SG CYS B 426 " - pdb=" SG CYS B 453 " distance=2.03 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.05 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 82 " - pdb=" SG CYS D 317 " distance=2.04 Simple disulfide: pdb=" SG CYS D 426 " - pdb=" SG CYS D 453 " distance=2.04 Simple disulfide: pdb=" SG CYS D 433 " - pdb=" SG CYS D 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 798 " distance=2.03 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A 902 " - " ASN A 771 " " NAG A 903 " - " ASN A 471 " " NAG B 901 " - " ASN B 337 " " NAG C 902 " - " ASN C 771 " " NAG C 903 " - " ASN C 350 " " NAG C 904 " - " ASN C 276 " " NAG D 901 " - " ASN D 337 " " NAG F 1 " - " ASN B 685 " " NAG G 1 " - " ASN C 61 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 731.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4786 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 29 sheets defined 37.0% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 37 through 53 removed outlier: 3.718A pdb=" N MET A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 85 removed outlier: 3.926A pdb=" N SER A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.694A pdb=" N THR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 159 removed outlier: 4.265A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.904A pdb=" N LEU A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.604A pdb=" N ALA A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 296 removed outlier: 4.051A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 527 removed outlier: 4.083A pdb=" N TYR A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 695 removed outlier: 3.654A pdb=" N ILE A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 699 through 709 removed outlier: 4.082A pdb=" N HIS A 709 " --> pdb=" O HIS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 723 removed outlier: 3.815A pdb=" N ILE A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.582A pdb=" N GLU A 739 " --> pdb=" O VAL A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 783 removed outlier: 3.724A pdb=" N GLY A 783 " --> pdb=" O SER A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 73 through 89 Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 145 through 160 removed outlier: 3.530A pdb=" N GLN B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 removed outlier: 3.577A pdb=" N ARG B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.617A pdb=" N GLN B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 242 removed outlier: 4.159A pdb=" N GLU B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VAL B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 306 removed outlier: 3.745A pdb=" N GLN B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 335 removed outlier: 3.734A pdb=" N TYR B 332 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 379 Processing helix chain 'B' and resid 457 through 470 Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 687 through 696 removed outlier: 3.573A pdb=" N ASN B 691 " --> pdb=" O SER B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 703 removed outlier: 4.153A pdb=" N HIS B 700 " --> pdb=" O TYR B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 721 removed outlier: 3.637A pdb=" N THR B 716 " --> pdb=" O GLU B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 739 Processing helix chain 'B' and resid 748 through 752 Processing helix chain 'B' and resid 768 through 783 removed outlier: 4.275A pdb=" N ALA B 772 " --> pdb=" O HIS B 768 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 775 " --> pdb=" O ARG B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 794 Processing helix chain 'C' and resid 36 through 53 removed outlier: 3.903A pdb=" N GLN C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 85 Processing helix chain 'C' and resid 104 through 114 removed outlier: 3.810A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 146 removed outlier: 3.618A pdb=" N HIS C 146 " --> pdb=" O PRO C 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 143 through 146' Processing helix chain 'C' and resid 147 through 158 removed outlier: 3.537A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 187 removed outlier: 4.039A pdb=" N ALA C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN C 177 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG C 179 " --> pdb=" O ALA C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 removed outlier: 3.820A pdb=" N LEU C 208 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.851A pdb=" N ILE C 254 " --> pdb=" O GLU C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 removed outlier: 4.118A pdb=" N TYR C 261 " --> pdb=" O ASN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 297 removed outlier: 3.530A pdb=" N SER C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N HIS C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 327 Processing helix chain 'C' and resid 457 through 470 Processing helix chain 'C' and resid 500 through 508 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.825A pdb=" N GLN C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 695 removed outlier: 3.989A pdb=" N ILE C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 707 removed outlier: 3.565A pdb=" N THR C 701 " --> pdb=" O VAL C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 768 through 783 Processing helix chain 'C' and resid 783 through 793 removed outlier: 3.533A pdb=" N ASP C 787 " --> pdb=" O GLY C 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 51 Processing helix chain 'D' and resid 73 through 88 Processing helix chain 'D' and resid 104 through 116 removed outlier: 3.671A pdb=" N LEU D 108 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 161 removed outlier: 3.989A pdb=" N GLU D 159 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR D 160 " --> pdb=" O VAL D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 187 removed outlier: 3.589A pdb=" N ARG D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 218 removed outlier: 3.771A pdb=" N THR D 212 " --> pdb=" O PRO D 208 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'D' and resid 284 through 308 removed outlier: 3.561A pdb=" N GLN D 306 " --> pdb=" O SER D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 335 Processing helix chain 'D' and resid 456 through 470 Processing helix chain 'D' and resid 492 through 500 Processing helix chain 'D' and resid 513 through 520 removed outlier: 3.837A pdb=" N ILE D 519 " --> pdb=" O GLU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 687 through 696 Processing helix chain 'D' and resid 696 through 703 Processing helix chain 'D' and resid 712 through 721 removed outlier: 3.541A pdb=" N THR D 716 " --> pdb=" O GLU D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 737 removed outlier: 3.842A pdb=" N TYR D 735 " --> pdb=" O ALA D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 784 removed outlier: 3.985A pdb=" N ALA D 772 " --> pdb=" O HIS D 768 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 775 " --> pdb=" O ARG D 771 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA D 776 " --> pdb=" O ALA D 772 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP D 783 " --> pdb=" O GLN D 779 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY D 784 " --> pdb=" O PHE D 780 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 794 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 removed outlier: 7.357A pdb=" N ALA A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.411A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 193 through 197 removed outlier: 6.334A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 268 through 271 removed outlier: 3.524A pdb=" N GLY A 268 " --> pdb=" O MET A 354 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY A 365 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 473 through 478 removed outlier: 3.520A pdb=" N ILE A 400 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 512 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ALA A 515 " --> pdb=" O GLY A 761 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLY A 761 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU A 517 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP A 731 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 528 through 529 removed outlier: 4.360A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 409 through 412 Processing sheet with id=AA9, first strand: chain 'B' and resid 64 through 68 removed outlier: 6.279A pdb=" N VAL B 32 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL B 67 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL B 34 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 200 removed outlier: 7.197A pdb=" N PHE B 165 " --> pdb=" O ASP B 197 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N VAL B 199 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL B 167 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA B 164 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL B 225 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA B 166 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N TYR B 227 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE B 168 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL B 276 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LEU B 273 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU B 363 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 360 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 405 through 406 removed outlier: 3.654A pdb=" N ALA B 406 " --> pdb=" O MET B 505 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 414 through 417 removed outlier: 3.607A pdb=" N GLU B 417 " --> pdb=" O CYS B 453 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS B 453 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 452 " --> pdb=" O CYS B 433 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 725 through 728 removed outlier: 7.072A pdb=" N THR B 529 " --> pdb=" O THR B 756 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N THR B 756 " --> pdb=" O THR B 529 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 59 through 66 removed outlier: 7.916A pdb=" N VAL C 87 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 194 through 197 removed outlier: 6.842A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 219 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 248 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 268 through 270 removed outlier: 6.927A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 473 through 478 removed outlier: 7.039A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AC1, first strand: chain 'C' and resid 486 through 489 Processing sheet with id=AC2, first strand: chain 'C' and resid 527 through 528 removed outlier: 3.651A pdb=" N MET C 762 " --> pdb=" O GLU C 528 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 535 through 536 Processing sheet with id=AC4, first strand: chain 'C' and resid 730 through 732 removed outlier: 3.817A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 64 through 68 removed outlier: 6.193A pdb=" N VAL D 32 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL D 67 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL D 34 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA D 33 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE D 93 " --> pdb=" O LEU D 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 197 through 201 Processing sheet with id=AC7, first strand: chain 'D' and resid 274 through 277 removed outlier: 3.576A pdb=" N GLY D 373 " --> pdb=" O VAL D 360 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA D 362 " --> pdb=" O MET D 371 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N MET D 371 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 379 " --> pdb=" O GLU D 376 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 337 through 340 removed outlier: 3.672A pdb=" N TRP D 340 " --> pdb=" O ARG D 343 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER D 346 " --> pdb=" O VAL D 354 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 415 through 417 removed outlier: 3.627A pdb=" N GLU D 417 " --> pdb=" O CYS D 453 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 431 " --> pdb=" O CYS D 454 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU D 475 " --> pdb=" O PRO D 432 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG D 434 " --> pdb=" O LEU D 475 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR D 407 " --> pdb=" O TYR D 476 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET D 505 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 762 " --> pdb=" O ALA D 506 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 486 through 487 Processing sheet with id=AD2, first strand: chain 'D' and resid 532 through 534 722 hydrogen bonds defined for protein. 2073 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.92 - 1.24: 2639 1.24 - 1.56: 14828 1.56 - 1.88: 102 1.88 - 2.21: 0 2.21 - 2.53: 1 Bond restraints: 17570 Sorted by residual: bond pdb=" CB PRO B 356 " pdb=" CG PRO B 356 " ideal model delta sigma weight residual 1.492 2.527 -1.035 5.00e-02 4.00e+02 4.28e+02 bond pdb=" CG PRO B 356 " pdb=" CD PRO B 356 " ideal model delta sigma weight residual 1.503 0.919 0.584 3.40e-02 8.65e+02 2.95e+02 bond pdb=" CG PRO B 448 " pdb=" CD PRO B 448 " ideal model delta sigma weight residual 1.503 1.097 0.406 3.40e-02 8.65e+02 1.43e+02 bond pdb=" N PRO B 356 " pdb=" CD PRO B 356 " ideal model delta sigma weight residual 1.473 1.560 -0.087 1.40e-02 5.10e+03 3.91e+01 bond pdb=" CA PRO B 356 " pdb=" CB PRO B 356 " ideal model delta sigma weight residual 1.533 1.448 0.086 1.42e-02 4.96e+03 3.64e+01 ... (remaining 17565 not shown) Histogram of bond angle deviations from ideal: 0.00 - 19.01: 24205 19.01 - 38.01: 3 38.01 - 57.02: 1 57.02 - 76.02: 0 76.02 - 95.03: 1 Bond angle restraints: 24210 Sorted by residual: angle pdb=" CB PRO B 356 " pdb=" CG PRO B 356 " pdb=" CD PRO B 356 " ideal model delta sigma weight residual 106.10 11.07 95.03 3.20e+00 9.77e-02 8.82e+02 angle pdb=" N PRO B 448 " pdb=" CD PRO B 448 " pdb=" CG PRO B 448 " ideal model delta sigma weight residual 103.20 70.54 32.66 1.50e+00 4.44e-01 4.74e+02 angle pdb=" CA PRO B 448 " pdb=" CB PRO B 448 " pdb=" CG PRO B 448 " ideal model delta sigma weight residual 104.50 67.02 37.48 1.90e+00 2.77e-01 3.89e+02 angle pdb=" N PRO B 356 " pdb=" CA PRO B 356 " pdb=" CB PRO B 356 " ideal model delta sigma weight residual 103.25 87.38 15.87 1.05e+00 9.07e-01 2.29e+02 angle pdb=" CB PRO B 448 " pdb=" CG PRO B 448 " pdb=" CD PRO B 448 " ideal model delta sigma weight residual 106.10 146.46 -40.36 3.20e+00 9.77e-02 1.59e+02 ... (remaining 24205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.99: 9874 25.99 - 51.98: 471 51.98 - 77.96: 74 77.96 - 103.95: 48 103.95 - 129.94: 23 Dihedral angle restraints: 10490 sinusoidal: 3069 harmonic: 7421 Sorted by residual: dihedral pdb=" CA GLN B 355 " pdb=" C GLN B 355 " pdb=" N PRO B 356 " pdb=" CA PRO B 356 " ideal model delta harmonic sigma weight residual 180.00 141.00 39.00 0 5.00e+00 4.00e-02 6.08e+01 dihedral pdb=" CB CYS C 79 " pdb=" SG CYS C 79 " pdb=" SG CYS C 308 " pdb=" CB CYS C 308 " ideal model delta sinusoidal sigma weight residual -86.00 -23.16 -62.84 1 1.00e+01 1.00e-02 5.22e+01 dihedral pdb=" CB CYS A 79 " pdb=" SG CYS A 79 " pdb=" SG CYS A 308 " pdb=" CB CYS A 308 " ideal model delta sinusoidal sigma weight residual -86.00 -146.53 60.53 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 10487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2760 0.086 - 0.172: 265 0.172 - 0.258: 6 0.258 - 0.344: 5 0.344 - 0.430: 1 Chirality restraints: 3037 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 685 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 3034 not shown) Planarity restraints: 3134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 131 " -0.110 5.00e-02 4.00e+02 1.56e-01 3.89e+01 pdb=" N PRO B 132 " 0.269 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 685 " -0.010 2.00e-02 2.50e+03 5.15e-02 3.31e+01 pdb=" CG ASN B 685 " 0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN B 685 " -0.059 2.00e-02 2.50e+03 pdb=" ND2 ASN B 685 " 0.059 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 438 " 0.081 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO C 439 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO C 439 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 439 " 0.061 5.00e-02 4.00e+02 ... (remaining 3131 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 578 2.70 - 3.25: 17096 3.25 - 3.80: 25285 3.80 - 4.35: 28136 4.35 - 4.90: 49599 Nonbonded interactions: 120694 Sorted by model distance: nonbonded pdb=" O LEU C 325 " pdb=" OG SER C 328 " model vdw 2.155 3.040 nonbonded pdb=" O VAL A 684 " pdb=" OG SER A 687 " model vdw 2.226 3.040 nonbonded pdb=" ND2 ASN C 70 " pdb=" O ARG D 318 " model vdw 2.230 3.120 nonbonded pdb=" O ASN B 73 " pdb=" OG SER B 76 " model vdw 2.250 3.040 nonbonded pdb=" O SER A 55 " pdb=" OG SER A 55 " model vdw 2.255 3.040 ... (remaining 120689 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 'A' and ((resid 25 through 26 and (name N or name CA or name C or name O \ or name CB )) or resid 27 through 34 or (resid 35 through 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 through 82 or (resid 83 and (n \ ame N or name CA or name C or name O or name CB )) or resid 84 through 158 or (r \ esid 159 and (name N or name CA or name C or name O or name CB )) or resid 160 t \ hrough 331 or (resid 332 and (name N or name CA or name C or name O or name CB ) \ ) or resid 333 through 358 or (resid 359 through 361 and (name N or name CA or n \ ame C or name O or name CB )) or resid 362 through 398 or (resid 399 and (name N \ or name CA or name C or name O or name CB )) or resid 400 through 411 or (resid \ 412 and (name N or name CA or name C or name O or name CB )) or resid 413 throu \ gh 414 or (resid 415 and (name N or name CA or name C or name O or name CB )) or \ resid 416 through 418 or (resid 419 and (name N or name CA or name C or name O \ or name CB )) or resid 420 through 421 or (resid 422 through 423 and (name N or \ name CA or name C or name O or name CB )) or resid 424 through 486 or (resid 487 \ through 497 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 98 through 508 or (resid 509 through 510 and (name N or name CA or name C or nam \ e O or name CB )) or resid 511 through 524 or (resid 525 and (name N or name CA \ or name C or name O or name CB )) or resid 526 through 527 or (resid 528 and (na \ me N or name CA or name C or name O or name CB )) or resid 529 through 535 or (r \ esid 536 and (name N or name CA or name C or name O or name CB )) or resid 537 t \ hrough 666 or (resid 667 through 669 and (name N or name CA or name C or name O \ or name CB )) or resid 670 through 678 or (resid 679 and (name N or name CA or n \ ame C or name O or name CB )) or resid 680 or (resid 681 through 682 and (name N \ or name CA or name C or name O or name CB )) or resid 683 through 684 or (resid \ 685 and (name N or name CA or name C or name O or name CB )) or resid 686 throu \ gh 693 or (resid 694 through 699 and (name N or name CA or name C or name O or n \ ame CB )) or resid 700 through 702 or (resid 703 through 710 and (name N or name \ CA or name C or name O or name CB )) or resid 711 or (resid 712 and (name N or \ name CA or name C or name O or name CB )) or resid 713 through 717 or (resid 718 \ through 728 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 29 through 735 or (resid 736 through 740 and (name N or name CA or name C or nam \ e O or name CB )) or resid 741 through 751 or (resid 752 and (name N or name CA \ or name C or name O or name CB )) or resid 753 through 754 or (resid 755 and (na \ me N or name CA or name C or name O or name CB )) or resid 756 through 762 or (r \ esid 763 and (name N or name CA or name C or name O or name CB )) or resid 764 t \ hrough 777 or (resid 778 and (name N or name CA or name C or name O or name CB ) \ ) or resid 779 through 780 or (resid 781 and (name N or name CA or name C or nam \ e O or name CB )) or resid 782 through 788 or (resid 789 through 790 and (name N \ or name CA or name C or name O or name CB )) or resid 791 through 903)) selection = (chain 'C' and (resid 25 through 27 or (resid 28 through 29 and (name N or name \ CA or name C or name O or name CB )) or resid 30 through 32 or (resid 33 and (na \ me N or name CA or name C or name O or name CB )) or resid 34 through 37 or (res \ id 38 through 45 and (name N or name CA or name C or name O or name CB )) or res \ id 46 through 52 or (resid 53 and (name N or name CA or name C or name O or name \ CB )) or resid 54 through 57 or (resid 58 through 63 and (name N or name CA or \ name C or name O or name CB )) or resid 64 through 67 or (resid 68 and (name N o \ r name CA or name C or name O or name CB )) or resid 69 or (resid 70 through 75 \ and (name N or name CA or name C or name O or name CB )) or resid 76 through 77 \ or (resid 78 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 9 through 80 or (resid 81 and (name N or name CA or name C or name O or name CB \ )) or resid 82 through 87 or (resid 88 through 89 and (name N or name CA or name \ C or name O or name CB )) or resid 90 through 100 or (resid 101 through 102 and \ (name N or name CA or name C or name O or name CB )) or resid 103 through 108 o \ r (resid 109 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 10 through 113 or (resid 114 through 116 and (name N or name CA or name C or nam \ e O or name CB )) or resid 117 through 120 or (resid 121 and (name N or name CA \ or name C or name O or name CB )) or resid 122 or (resid 123 through 124 and (na \ me N or name CA or name C or name O or name CB )) or resid 125 or (resid 126 thr \ ough 127 and (name N or name CA or name C or name O or name CB )) or resid 128 t \ hrough 130 or (resid 131 and (name N or name CA or name C or name O or name CB ) \ ) or resid 132 through 134 or (resid 135 and (name N or name CA or name C or nam \ e O or name CB )) or resid 136 or (resid 137 through 138 and (name N or name CA \ or name C or name O or name CB )) or resid 139 through 146 or (resid 147 and (na \ me N or name CA or name C or name O or name CB )) or resid 148 through 151 or (r \ esid 152 through 157 and (name N or name CA or name C or name O or name CB )) or \ resid 158 through 161 or (resid 162 through 163 and (name N or name CA or name \ C or name O or name CB )) or resid 164 or (resid 165 and (name N or name CA or n \ ame C or name O or name CB )) or resid 166 or (resid 167 through 172 and (name N \ or name CA or name C or name O or name CB )) or (resid 173 through 188 and (nam \ e N or name CA or name C or name O or name CB )) or resid 189 through 191 or (re \ sid 192 through 193 and (name N or name CA or name C or name O or name CB )) or \ resid 194 or (resid 195 through 198 and (name N or name CA or name C or name O o \ r name CB )) or resid 199 through 204 or (resid 205 through 206 and (name N or n \ ame CA or name C or name O or name CB )) or resid 207 or (resid 208 through 216 \ and (name N or name CA or name C or name O or name CB )) or resid 217 through 21 \ 8 or (resid 219 through 221 and (name N or name CA or name C or name O or name C \ B )) or resid 222 through 224 or (resid 225 through 229 and (name N or name CA o \ r name C or name O or name CB )) or resid 230 or (resid 231 through 238 and (nam \ e N or name CA or name C or name O or name CB )) or resid 239 through 245 or (re \ sid 246 through 248 and (name N or name CA or name C or name O or name CB )) or \ resid 249 through 253 or (resid 254 and (name N or name CA or name C or name O o \ r name CB )) or resid 255 through 256 or (resid 257 through 262 and (name N or n \ ame CA or name C or name O or name CB )) or resid 263 through 265 or (resid 266 \ through 267 and (name N or name CA or name C or name O or name CB )) or resid 26 \ 8 or (resid 269 through 273 and (name N or name CA or name C or name O or name C \ B )) or (resid 274 through 277 and (name N or name CA or name C or name O or nam \ e CB )) or resid 278 through 279 or (resid 280 through 281 and (name N or name C \ A or name C or name O or name CB )) or resid 282 or (resid 283 through 285 and ( \ name N or name CA or name C or name O or name CB )) or resid 286 or (resid 287 t \ hrough 291 and (name N or name CA or name C or name O or name CB )) or resid 292 \ through 294 or (resid 295 through 303 and (name N or name CA or name C or name \ O or name CB )) or resid 304 through 313 or (resid 314 and (name N or name CA or \ name C or name O or name CB )) or resid 315 through 319 or (resid 320 through 3 \ 26 and (name N or name CA or name C or name O or name CB )) or resid 327 through \ 329 or (resid 330 through 332 and (name N or name CA or name C or name O or nam \ e CB )) or resid 333 through 336 or (resid 337 and (name N or name CA or name C \ or name O or name CB )) or resid 338 or (resid 339 through 343 and (name N or na \ me CA or name C or name O or name CB )) or (resid 344 through 349 and (name N or \ name CA or name C or name O or name CB )) or resid 350 or (resid 351 and (name \ N or name CA or name C or name O or name CB )) or resid 352 or (resid 353 throug \ h 361 and (name N or name CA or name C or name O or name CB )) or resid 362 or ( \ resid 363 and (name N or name CA or name C or name O or name CB )) or resid 364 \ through 366 or (resid 367 and (name N or name CA or name C or name O or name CB \ )) or resid 368 through 378 or (resid 379 and (name N or name CA or name C or na \ me O or name CB )) or resid 380 through 385 or (resid 386 through 388 and (name \ N or name CA or name C or name O or name CB )) or resid 389 through 425 or (resi \ d 426 through 427 and (name N or name CA or name C or name O or name CB )) or re \ sid 428 through 440 or resid 448 through 519 or (resid 520 and (name N or name C \ A or name C or name O or name CB )) or resid 521 through 540 or (resid 541 and ( \ name N or name CA or name C or name O or name CB )) or resid 542 through 663 or \ (resid 664 through 665 and (name N or name CA or name C or name O or name CB )) \ or (resid 666 through 669 and (name N or name CA or name C or name O or name CB \ )) or resid 670 through 671 or (resid 672 through 674 and (name N or name CA or \ name C or name O or name CB )) or resid 675 through 694 or (resid 695 through 69 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 700 through \ 786 or (resid 787 and (name N or name CA or name C or name O or name CB )) or re \ sid 788 through 903)) } ncs_group { reference = (chain 'B' and (resid 31 through 53 or (resid 54 through 58 and (name N or name \ CA or name C or name O or name CB )) or resid 59 through 202 or (resid 203 and ( \ name N or name CA or name C or name O or name CB )) or resid 204 through 284 or \ (resid 285 through 291 and (name N or name CA or name C or name O or name CB )) \ or resid 292 through 305 or (resid 306 through 307 and (name N or name CA or nam \ e C or name O or name CB )) or resid 308 through 408 or (resid 409 through 411 a \ nd (name N or name CA or name C or name O or name CB )) or resid 412 through 416 \ or (resid 417 and (name N or name CA or name C or name O or name CB )) or resid \ 418 through 435 or (resid 436 and (name N or name CA or name C or name O or nam \ e CB )) or resid 437 or (resid 447 through 449 and (name N or name CA or name C \ or name O or name CB )) or resid 450 through 481 or (resid 482 and (name N or na \ me CA or name C or name O or name CB )) or resid 483 through 500 or (resid 501 a \ nd (name N or name CA or name C or name O or name CB )) or resid 502 through 537 \ or resid 659 through 667 or (resid 668 through 670 and (name N or name CA or na \ me C or name O or name CB )) or resid 671 through 698 or (resid 699 through 700 \ and (name N or name CA or name C or name O or name CB )) or resid 701 or (resid \ 702 through 703 and (name N or name CA or name C or name O or name CB )) or resi \ d 704 through 705 or (resid 706 through 709 and (name N or name CA or name C or \ name O or name CB )) or resid 710 through 723 or (resid 724 through 725 and (nam \ e N or name CA or name C or name O or name CB )) or resid 726 through 773 or (re \ sid 774 and (name N or name CA or name C or name O or name CB )) or resid 775 th \ rough 786 or (resid 787 through 788 and (name N or name CA or name C or name O o \ r name CB )) or resid 789 or (resid 790 and (name N or name CA or name C or name \ O or name CB )) or resid 791 through 901)) selection = (chain 'D' and ((resid 31 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 or (resid 38 through 39 and (name N or na \ me CA or name C or name O or name CB )) or resid 40 through 50 or (resid 51 and \ (name N or name CA or name C or name O or name CB )) or resid 52 through 64 or ( \ resid 65 and (name N or name CA or name C or name O or name CB )) or resid 66 or \ (resid 67 and (name N or name CA or name C or name O or name CB )) or resid 68 \ or (resid 69 through 73 and (name N or name CA or name C or name O or name CB )) \ or resid 74 through 77 or (resid 78 and (name N or name CA or name C or name O \ or name CB )) or resid 79 or (resid 80 through 81 and (name N or name CA or name \ C or name O or name CB )) or resid 82 through 89 or (resid 90 through 91 and (n \ ame N or name CA or name C or name O or name CB )) or resid 92 or (resid 93 thro \ ugh 111 and (name N or name CA or name C or name O or name CB )) or resid 112 th \ rough 113 or (resid 114 through 117 and (name N or name CA or name C or name O o \ r name CB )) or resid 118 or (resid 119 through 120 and (name N or name CA or na \ me C or name O or name CB )) or resid 121 or (resid 122 through 123 and (name N \ or name CA or name C or name O or name CB )) or resid 124 through 125 or (resid \ 126 through 131 and (name N or name CA or name C or name O or name CB )) or resi \ d 132 through 136 or (resid 137 through 142 and (name N or name CA or name C or \ name O or name CB )) or resid 143 or (resid 144 and (name N or name CA or name C \ or name O or name CB )) or resid 145 or (resid 146 through 162 and (name N or n \ ame CA or name C or name O or name CB )) or resid 163 through 164 or (resid 165 \ through 166 and (name N or name CA or name C or name O or name CB )) or resid 16 \ 7 or (resid 168 and (name N or name CA or name C or name O or name CB )) or resi \ d 169 through 170 or (resid 171 through 172 and (name N or name CA or name C or \ name O or name CB )) or resid 173 through 174 or (resid 175 through 178 and (nam \ e N or name CA or name C or name O or name CB )) or resid 179 through 181 or (re \ sid 182 through 197 and (name N or name CA or name C or name O or name CB )) or \ resid 198 through 212 or (resid 213 through 221 and (name N or name CA or name C \ or name O or name CB )) or resid 222 through 227 or (resid 228 and (name N or n \ ame CA or name C or name O or name CB )) or resid 229 or (resid 230 through 234 \ and (name N or name CA or name C or name O or name CB )) or resid 235 through 23 \ 8 or (resid 239 through 243 and (name N or name CA or name C or name O or name C \ B )) or resid 244 or (resid 245 through 246 and (name N or name CA or name C or \ name O or name CB )) or resid 247 through 249 or (resid 250 and (name N or name \ CA or name C or name O or name CB )) or resid 251 through 252 or (resid 253 and \ (name N or name CA or name C or name O or name CB )) or resid 254 through 258 or \ (resid 259 and (name N or name CA or name C or name O or name CB )) or resid 26 \ 0 through 262 or (resid 263 through 264 and (name N or name CA or name C or name \ O or name CB )) or resid 265 through 267 or (resid 268 and (name N or name CA o \ r name C or name O or name CB )) or resid 269 through 270 or (resid 271 and (nam \ e N or name CA or name C or name O or name CB )) or resid 272 or (resid 273 thro \ ugh 274 and (name N or name CA or name C or name O or name CB )) or resid 275 or \ (resid 276 and (name N or name CA or name C or name O or name CB )) or resid 27 \ 7 through 278 or (resid 279 and (name N or name CA or name C or name O or name C \ B )) or resid 280 through 282 or (resid 283 and (name N or name CA or name C or \ name O or name CB )) or resid 284 through 286 or (resid 287 through 291 and (nam \ e N or name CA or name C or name O or name CB )) or resid 292 or (resid 293 thro \ ugh 298 and (name N or name CA or name C or name O or name CB )) or resid 299 th \ rough 303 or (resid 304 through 307 and (name N or name CA or name C or name O o \ r name CB )) or resid 308 through 331 or (resid 332 through 336 and (name N or n \ ame CA or name C or name O or name CB )) or resid 337 or (resid 338 through 341 \ and (name N or name CA or name C or name O or name CB )) or (resid 342 through 3 \ 45 and (name N or name CA or name C or name O or name CB )) or resid 346 or (res \ id 347 and (name N or name CA or name C or name O or name CB )) or resid 348 thr \ ough 351 or (resid 352 through 355 and (name N or name CA or name C or name O or \ name CB )) or resid 356 or (resid 357 through 358 and (name N or name CA or nam \ e C or name O or name CB )) or resid 359 or (resid 360 through 371 and (name N o \ r name CA or name C or name O or name CB )) or resid 372 through 373 or (resid 3 \ 74 through 377 and (name N or name CA or name C or name O or name CB )) or resid \ 378 through 379 or (resid 380 and (name N or name CA or name C or name O or nam \ e CB )) or resid 381 or (resid 382 through 383 and (name N or name CA or name C \ or name O or name CB )) or resid 384 through 386 or (resid 387 and (name N or na \ me CA or name C or name O or name CB )) or resid 388 or (resid 389 through 390 a \ nd (name N or name CA or name C or name O or name CB )) or resid 391 or (resid 3 \ 99 and (name N or name CA or name C or name O or name CB )) or resid 400 or (res \ id 401 and (name N or name CA or name C or name O or name CB )) or resid 402 thr \ ough 422 or (resid 423 and (name N or name CA or name C or name O or name CB )) \ or resid 424 through 428 or (resid 429 and (name N or name CA or name C or name \ O or name CB )) or resid 430 through 433 or (resid 434 and (name N or name CA or \ name C or name O or name CB )) or resid 435 through 448 or (resid 449 and (name \ N or name CA or name C or name O or name CB )) or resid 450 through 454 or (res \ id 455 and (name N or name CA or name C or name O or name CB )) or resid 456 thr \ ough 514 or (resid 515 and (name N or name CA or name C or name O or name CB )) \ or resid 516 through 527 or (resid 528 and (name N or name CA or name C or name \ O or name CB )) or resid 529 through 679 or (resid 680 and (name N or name CA or \ name C or name O or name CB )) or resid 681 through 689 or (resid 690 and (name \ N or name CA or name C or name O or name CB )) or resid 691 through 692 or (res \ id 693 and (name N or name CA or name C or name O or name CB )) or resid 694 thr \ ough 796 or (resid 797 and (name N or name CA or name C or name O or name CB )) \ or resid 798 through 901)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.160 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 : 0.011 1.035 17599 Z= 0.306 Angle : 1.122 95.030 24281 Z= 0.533 Chirality : 0.048 0.430 3037 Planarity : 0.006 0.156 3125 Dihedral : 18.577 129.940 5665 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.89 % Favored : 92.07 % Rotamer: Outliers : 0.15 % Allowed : 26.96 % Favored : 72.89 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.17), residues: 2561 helix: 1.11 (0.18), residues: 841 sheet: -1.19 (0.27), residues: 400 loop : -2.15 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 467 TYR 0.017 0.001 TYR A 392 PHE 0.028 0.001 PHE C 753 TRP 0.016 0.001 TRP D 340 HIS 0.013 0.001 HIS D 377 Details of bonding type rmsd covalent geometry : bond 0.01066 (17570) covalent geometry : angle 1.09253 (24210) SS BOND : bond 0.00706 ( 13) SS BOND : angle 2.07179 ( 26) hydrogen bonds : bond 0.19296 ( 719) hydrogen bonds : angle 7.22428 ( 2073) Misc. bond : bond 0.00109 ( 1) link_BETA1-4 : bond 0.00746 ( 6) link_BETA1-4 : angle 3.07656 ( 18) link_NAG-ASN : bond 0.01000 ( 9) link_NAG-ASN : angle 7.15937 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 177 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 771 ARG cc_start: 0.7602 (mmm160) cc_final: 0.7326 (mmm160) outliers start: 2 outliers final: 0 residues processed: 178 average time/residue: 0.1206 time to fit residues: 33.1558 Evaluate side-chains 156 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 0.8980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.0970 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.0070 chunk 111 optimal weight: 0.0770 chunk 71 optimal weight: 5.9990 overall best weight: 0.6156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 270 GLN C 368 ASN ** D 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 HIS ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.157482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.123927 restraints weight = 44362.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.116002 restraints weight = 35655.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.116845 restraints weight = 30536.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.116641 restraints weight = 22736.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.116745 restraints weight = 20275.934| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 17599 Z= 0.124 Angle : 0.714 22.359 24281 Z= 0.344 Chirality : 0.047 0.458 3037 Planarity : 0.005 0.086 3125 Dihedral : 13.448 101.916 3053 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.74 % Allowed : 24.54 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.17), residues: 2561 helix: 1.14 (0.18), residues: 860 sheet: -1.09 (0.28), residues: 390 loop : -2.01 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 467 TYR 0.013 0.001 TYR A 392 PHE 0.011 0.001 PHE A 533 TRP 0.029 0.001 TRP B 793 HIS 0.005 0.001 HIS D 377 Details of bonding type rmsd covalent geometry : bond 0.00271 (17570) covalent geometry : angle 0.67486 (24210) SS BOND : bond 0.00451 ( 13) SS BOND : angle 2.40795 ( 26) hydrogen bonds : bond 0.04095 ( 719) hydrogen bonds : angle 5.45747 ( 2073) Misc. bond : bond 0.00030 ( 1) link_BETA1-4 : bond 0.01215 ( 6) link_BETA1-4 : angle 3.50016 ( 18) link_NAG-ASN : bond 0.00592 ( 9) link_NAG-ASN : angle 5.99787 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 172 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 GLU cc_start: 0.7784 (pp20) cc_final: 0.6916 (tt0) REVERT: A 694 ARG cc_start: 0.8149 (ttp80) cc_final: 0.7888 (ttm170) REVERT: B 356 PRO cc_start: 0.4415 (OUTLIER) cc_final: 0.4198 (Cg_exo) REVERT: B 494 MET cc_start: 0.7314 (mmt) cc_final: 0.6943 (mmt) REVERT: B 699 MET cc_start: 0.8618 (mpp) cc_final: 0.8245 (mpp) REVERT: C 746 LEU cc_start: 0.8531 (tp) cc_final: 0.8302 (tp) outliers start: 51 outliers final: 25 residues processed: 212 average time/residue: 0.1167 time to fit residues: 39.3496 Evaluate side-chains 187 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 356 PRO Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 448 PRO Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 791 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 124 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 180 optimal weight: 20.0000 chunk 99 optimal weight: 20.0000 chunk 19 optimal weight: 50.0000 chunk 199 optimal weight: 1.9990 chunk 86 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 213 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN C 770 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.150311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.113755 restraints weight = 44586.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.113295 restraints weight = 44283.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.113759 restraints weight = 34882.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.113438 restraints weight = 26953.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.113510 restraints weight = 26945.139| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 17599 Z= 0.333 Angle : 0.900 20.357 24281 Z= 0.452 Chirality : 0.054 0.493 3037 Planarity : 0.006 0.085 3125 Dihedral : 11.863 92.442 3053 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.29 % Favored : 90.59 % Rotamer: Outliers : 8.13 % Allowed : 22.93 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.17), residues: 2561 helix: 0.87 (0.18), residues: 870 sheet: -1.26 (0.27), residues: 402 loop : -2.19 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 139 TYR 0.030 0.003 TYR A 711 PHE 0.033 0.003 PHE C 533 TRP 0.042 0.003 TRP B 793 HIS 0.012 0.003 HIS D 377 Details of bonding type rmsd covalent geometry : bond 0.00789 (17570) covalent geometry : angle 0.86904 (24210) SS BOND : bond 0.00750 ( 13) SS BOND : angle 2.77386 ( 26) hydrogen bonds : bond 0.05829 ( 719) hydrogen bonds : angle 5.63523 ( 2073) Misc. bond : bond 0.00020 ( 1) link_BETA1-4 : bond 0.00603 ( 6) link_BETA1-4 : angle 3.02105 ( 18) link_NAG-ASN : bond 0.01049 ( 9) link_NAG-ASN : angle 6.11015 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 149 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 TRP cc_start: 0.6456 (t60) cc_final: 0.6148 (t60) REVERT: A 688 SER cc_start: 0.7412 (OUTLIER) cc_final: 0.6740 (t) REVERT: B 356 PRO cc_start: 0.4473 (OUTLIER) cc_final: 0.4235 (Cg_exo) REVERT: B 415 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7114 (mt) REVERT: B 436 GLN cc_start: 0.8277 (tt0) cc_final: 0.8071 (tt0) REVERT: B 494 MET cc_start: 0.7355 (mmt) cc_final: 0.6816 (mmt) REVERT: B 699 MET cc_start: 0.8307 (mpp) cc_final: 0.7938 (mpp) REVERT: C 109 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.8011 (m-80) REVERT: C 155 MET cc_start: 0.7938 (ttm) cc_final: 0.7723 (ttp) REVERT: C 354 MET cc_start: 0.7798 (tpp) cc_final: 0.7561 (mmm) REVERT: C 512 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8283 (ttp) REVERT: C 526 TYR cc_start: 0.6445 (OUTLIER) cc_final: 0.6105 (m-80) REVERT: C 746 LEU cc_start: 0.8268 (tp) cc_final: 0.7805 (tt) REVERT: D 108 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7753 (mm) REVERT: D 449 TYR cc_start: 0.5123 (OUTLIER) cc_final: 0.4400 (p90) outliers start: 111 outliers final: 67 residues processed: 241 average time/residue: 0.0972 time to fit residues: 38.3633 Evaluate side-chains 217 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 142 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 356 PRO Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 448 PRO Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 512 MET Chi-restraints excluded: chain C residue 526 TYR Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 731 TRP Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 375 TRP Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 449 TYR Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 773 ILE Chi-restraints excluded: chain D residue 791 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 146 optimal weight: 6.9990 chunk 251 optimal weight: 0.6980 chunk 227 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 80 optimal weight: 40.0000 chunk 85 optimal weight: 40.0000 chunk 9 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 HIS C 177 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.152426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.118916 restraints weight = 43997.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.112093 restraints weight = 42805.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.110948 restraints weight = 34390.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.111046 restraints weight = 27187.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.111165 restraints weight = 25317.980| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17599 Z= 0.164 Angle : 0.736 19.057 24281 Z= 0.358 Chirality : 0.049 0.527 3037 Planarity : 0.005 0.083 3125 Dihedral : 10.662 92.067 3053 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.30 % Favored : 92.66 % Rotamer: Outliers : 6.15 % Allowed : 25.93 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.17), residues: 2561 helix: 1.07 (0.18), residues: 879 sheet: -1.28 (0.27), residues: 402 loop : -2.07 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 771 TYR 0.014 0.001 TYR D 476 PHE 0.021 0.002 PHE A 533 TRP 0.044 0.001 TRP B 793 HIS 0.005 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00384 (17570) covalent geometry : angle 0.70279 (24210) SS BOND : bond 0.00458 ( 13) SS BOND : angle 2.67604 ( 26) hydrogen bonds : bond 0.03972 ( 719) hydrogen bonds : angle 5.11845 ( 2073) Misc. bond : bond 0.00002 ( 1) link_BETA1-4 : bond 0.00736 ( 6) link_BETA1-4 : angle 3.05283 ( 18) link_NAG-ASN : bond 0.00711 ( 9) link_NAG-ASN : angle 5.52354 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 156 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.6534 (ttt90) cc_final: 0.5725 (ttt90) REVERT: A 315 TRP cc_start: 0.6936 (t60) cc_final: 0.6366 (t60) REVERT: A 528 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6984 (tt0) REVERT: A 694 ARG cc_start: 0.8281 (ttp80) cc_final: 0.8064 (ttp80) REVERT: A 778 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7956 (ttpt) REVERT: B 415 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.7011 (mt) REVERT: B 436 GLN cc_start: 0.8462 (tt0) cc_final: 0.8242 (tt0) REVERT: B 494 MET cc_start: 0.7372 (mmt) cc_final: 0.6819 (mmt) REVERT: B 699 MET cc_start: 0.8660 (mpp) cc_final: 0.8244 (mpp) REVERT: B 723 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6545 (pp) REVERT: C 109 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.8007 (m-10) REVERT: C 502 MET cc_start: 0.8369 (mmm) cc_final: 0.8017 (mmm) REVERT: C 746 LEU cc_start: 0.8548 (tp) cc_final: 0.8202 (tt) REVERT: D 108 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7261 (mm) REVERT: D 377 HIS cc_start: 0.8193 (m90) cc_final: 0.7960 (m90) outliers start: 84 outliers final: 56 residues processed: 227 average time/residue: 0.1106 time to fit residues: 39.9639 Evaluate side-chains 211 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 149 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 778 LYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 356 PRO Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 448 PRO Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain B residue 763 MET Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 731 TRP Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 754 PHE Chi-restraints excluded: chain D residue 791 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 92 optimal weight: 50.0000 chunk 175 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 229 optimal weight: 9.9990 chunk 70 optimal weight: 50.0000 chunk 190 optimal weight: 0.7980 chunk 233 optimal weight: 6.9990 chunk 88 optimal weight: 30.0000 chunk 165 optimal weight: 0.0870 chunk 59 optimal weight: 5.9990 overall best weight: 3.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.149766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3760 r_free = 0.3760 target = 0.111771 restraints weight = 43918.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.108439 restraints weight = 38486.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.109649 restraints weight = 32102.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.109604 restraints weight = 28197.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.109711 restraints weight = 26857.651| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 17599 Z= 0.267 Angle : 0.803 17.909 24281 Z= 0.397 Chirality : 0.051 0.536 3037 Planarity : 0.005 0.083 3125 Dihedral : 10.026 82.413 3053 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.25 % Favored : 90.67 % Rotamer: Outliers : 7.40 % Allowed : 26.01 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.17), residues: 2561 helix: 0.99 (0.18), residues: 884 sheet: -1.39 (0.27), residues: 404 loop : -2.17 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 771 TYR 0.023 0.002 TYR D 476 PHE 0.028 0.002 PHE A 533 TRP 0.027 0.002 TRP B 793 HIS 0.010 0.002 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00636 (17570) covalent geometry : angle 0.77514 (24210) SS BOND : bond 0.00671 ( 13) SS BOND : angle 2.45303 ( 26) hydrogen bonds : bond 0.04801 ( 719) hydrogen bonds : angle 5.26537 ( 2073) Misc. bond : bond 0.00005 ( 1) link_BETA1-4 : bond 0.00812 ( 6) link_BETA1-4 : angle 2.87576 ( 18) link_NAG-ASN : bond 0.00894 ( 9) link_NAG-ASN : angle 5.51930 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 149 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 TRP cc_start: 0.6859 (t60) cc_final: 0.6344 (t60) REVERT: A 528 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7508 (pp20) REVERT: A 688 SER cc_start: 0.7196 (OUTLIER) cc_final: 0.6552 (t) REVERT: B 415 ILE cc_start: 0.7331 (OUTLIER) cc_final: 0.7036 (mt) REVERT: B 436 GLN cc_start: 0.8343 (tt0) cc_final: 0.8126 (tt0) REVERT: B 494 MET cc_start: 0.7259 (mmt) cc_final: 0.6861 (mmt) REVERT: B 699 MET cc_start: 0.8517 (mpp) cc_final: 0.8122 (mpp) REVERT: B 723 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6421 (pp) REVERT: C 109 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.8071 (m-10) REVERT: C 139 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7026 (mtt90) REVERT: C 478 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8093 (mp) REVERT: C 502 MET cc_start: 0.8285 (mmm) cc_final: 0.8039 (mmt) REVERT: C 526 TYR cc_start: 0.6700 (OUTLIER) cc_final: 0.6466 (m-80) REVERT: C 746 LEU cc_start: 0.8423 (tp) cc_final: 0.8077 (tt) REVERT: C 785 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.6658 (mmm) REVERT: D 108 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7653 (mm) REVERT: D 449 TYR cc_start: 0.5463 (OUTLIER) cc_final: 0.4641 (p90) outliers start: 101 outliers final: 71 residues processed: 231 average time/residue: 0.1039 time to fit residues: 38.3326 Evaluate side-chains 226 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 144 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 356 PRO Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 448 PRO Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain B residue 763 MET Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 526 TYR Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 731 TRP Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 785 MET Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 449 TYR Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 754 PHE Chi-restraints excluded: chain D residue 791 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 42 optimal weight: 0.9990 chunk 250 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 255 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 20 optimal weight: 50.0000 chunk 17 optimal weight: 2.9990 chunk 203 optimal weight: 0.5980 chunk 202 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.150792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.124144 restraints weight = 41916.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.114994 restraints weight = 47031.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.111954 restraints weight = 43516.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.112078 restraints weight = 41940.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.112970 restraints weight = 33583.317| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17599 Z= 0.149 Angle : 0.716 17.054 24281 Z= 0.347 Chirality : 0.048 0.548 3037 Planarity : 0.005 0.081 3125 Dihedral : 9.375 79.531 3053 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.34 % Favored : 92.62 % Rotamer: Outliers : 6.15 % Allowed : 26.89 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.17), residues: 2561 helix: 1.19 (0.18), residues: 881 sheet: -1.27 (0.27), residues: 396 loop : -2.01 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 771 TYR 0.017 0.001 TYR A 392 PHE 0.019 0.001 PHE A 533 TRP 0.047 0.001 TRP B 793 HIS 0.006 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00349 (17570) covalent geometry : angle 0.68770 (24210) SS BOND : bond 0.00447 ( 13) SS BOND : angle 2.22915 ( 26) hydrogen bonds : bond 0.03689 ( 719) hydrogen bonds : angle 4.93750 ( 2073) Misc. bond : bond 0.00005 ( 1) link_BETA1-4 : bond 0.00848 ( 6) link_BETA1-4 : angle 2.84303 ( 18) link_NAG-ASN : bond 0.00680 ( 9) link_NAG-ASN : angle 5.13720 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 159 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 TRP cc_start: 0.6911 (t60) cc_final: 0.6421 (t60) REVERT: A 528 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6935 (tt0) REVERT: A 688 SER cc_start: 0.7136 (OUTLIER) cc_final: 0.6540 (t) REVERT: B 415 ILE cc_start: 0.7281 (OUTLIER) cc_final: 0.7074 (mt) REVERT: B 436 GLN cc_start: 0.8431 (tt0) cc_final: 0.8201 (tt0) REVERT: B 494 MET cc_start: 0.7165 (mmt) cc_final: 0.6798 (mmt) REVERT: B 699 MET cc_start: 0.8632 (mpp) cc_final: 0.8260 (mpp) REVERT: B 723 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6445 (pp) REVERT: B 787 GLN cc_start: 0.7663 (tp-100) cc_final: 0.7185 (tp-100) REVERT: C 109 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.7947 (m-10) REVERT: C 166 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8254 (tt) REVERT: C 746 LEU cc_start: 0.8538 (tp) cc_final: 0.8337 (tt) REVERT: C 785 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.6565 (mmm) REVERT: D 108 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7465 (mm) REVERT: D 376 GLU cc_start: 0.7496 (tp30) cc_final: 0.7281 (tp30) REVERT: D 773 ILE cc_start: 0.8432 (pt) cc_final: 0.8165 (pt) outliers start: 84 outliers final: 63 residues processed: 231 average time/residue: 0.1075 time to fit residues: 39.6962 Evaluate side-chains 217 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 146 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 356 PRO Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 448 PRO Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 731 TRP Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 785 MET Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 754 PHE Chi-restraints excluded: chain D residue 791 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 116 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 209 optimal weight: 0.9980 chunk 226 optimal weight: 0.0040 chunk 202 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 255 optimal weight: 0.8980 chunk 215 optimal weight: 0.5980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 GLN ** D 218 GLN ** 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 = 0.4336 r_free = 0.4336 target = 0.152487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.125257 restraints weight = 42136.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.118287 restraints weight = 46653.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.115729 restraints weight = 39460.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.115544 restraints weight = 40845.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.116066 restraints weight = 31748.579| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17599 Z= 0.113 Angle : 0.691 16.379 24281 Z= 0.329 Chirality : 0.047 0.543 3037 Planarity : 0.005 0.078 3125 Dihedral : 8.609 73.867 3053 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.15 % Favored : 92.82 % Rotamer: Outliers : 4.18 % Allowed : 29.16 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.17), residues: 2561 helix: 1.28 (0.18), residues: 883 sheet: -1.28 (0.25), residues: 432 loop : -1.95 (0.18), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 771 TYR 0.017 0.001 TYR A 703 PHE 0.012 0.001 PHE A 408 TRP 0.026 0.001 TRP B 793 HIS 0.006 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00258 (17570) covalent geometry : angle 0.66474 (24210) SS BOND : bond 0.00645 ( 13) SS BOND : angle 1.86289 ( 26) hydrogen bonds : bond 0.03141 ( 719) hydrogen bonds : angle 4.71818 ( 2073) Misc. bond : bond 0.00005 ( 1) link_BETA1-4 : bond 0.00877 ( 6) link_BETA1-4 : angle 2.83345 ( 18) link_NAG-ASN : bond 0.00639 ( 9) link_NAG-ASN : angle 4.89056 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 159 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.6359 (ttt90) cc_final: 0.5430 (ttt90) REVERT: A 315 TRP cc_start: 0.6863 (t60) cc_final: 0.6391 (t60) REVERT: A 528 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7019 (tt0) REVERT: A 686 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7312 (pm20) REVERT: B 436 GLN cc_start: 0.8350 (tt0) cc_final: 0.8144 (tt0) REVERT: B 494 MET cc_start: 0.6939 (mmt) cc_final: 0.6651 (mmt) REVERT: B 699 MET cc_start: 0.8541 (mpp) cc_final: 0.8236 (mpp) REVERT: B 723 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6423 (pp) REVERT: C 109 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.7855 (m-10) REVERT: C 746 LEU cc_start: 0.8472 (tp) cc_final: 0.8219 (tt) REVERT: D 723 LEU cc_start: 0.6816 (tp) cc_final: 0.6609 (tp) REVERT: D 773 ILE cc_start: 0.8321 (pt) cc_final: 0.8092 (pt) outliers start: 57 outliers final: 41 residues processed: 205 average time/residue: 0.1075 time to fit residues: 34.5149 Evaluate side-chains 189 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 144 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 686 GLN Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 356 PRO Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 448 PRO Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 526 TYR Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 731 TRP Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 748 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 222 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 231 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 64 optimal weight: 40.0000 chunk 38 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 199 optimal weight: 0.5980 chunk 83 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 GLN ** D 218 GLN ** 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 = 0.4320 r_free = 0.4320 target = 0.151384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.124357 restraints weight = 42292.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.117602 restraints weight = 47619.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.116020 restraints weight = 40986.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.114786 restraints weight = 37238.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.115288 restraints weight = 33156.846| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17599 Z= 0.148 Angle : 0.707 16.061 24281 Z= 0.340 Chirality : 0.047 0.529 3037 Planarity : 0.005 0.077 3125 Dihedral : 8.199 71.479 3053 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.30 % Favored : 92.66 % Rotamer: Outliers : 5.86 % Allowed : 27.62 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.17), residues: 2561 helix: 1.38 (0.18), residues: 883 sheet: -1.31 (0.25), residues: 441 loop : -1.93 (0.18), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 467 TYR 0.015 0.001 TYR A 392 PHE 0.020 0.001 PHE A 533 TRP 0.024 0.001 TRP B 793 HIS 0.007 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00348 (17570) covalent geometry : angle 0.68040 (24210) SS BOND : bond 0.00416 ( 13) SS BOND : angle 2.21792 ( 26) hydrogen bonds : bond 0.03536 ( 719) hydrogen bonds : angle 4.74030 ( 2073) Misc. bond : bond 0.00007 ( 1) link_BETA1-4 : bond 0.00864 ( 6) link_BETA1-4 : angle 2.78798 ( 18) link_NAG-ASN : bond 0.00634 ( 9) link_NAG-ASN : angle 4.98378 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 146 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.6383 (ttt90) cc_final: 0.5964 (ttt90) REVERT: A 315 TRP cc_start: 0.6884 (t60) cc_final: 0.6430 (t60) REVERT: A 528 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6884 (tt0) REVERT: A 686 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7591 (pm20) REVERT: A 780 HIS cc_start: 0.8243 (OUTLIER) cc_final: 0.7928 (m-70) REVERT: B 415 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.7034 (mt) REVERT: B 436 GLN cc_start: 0.8377 (tt0) cc_final: 0.8143 (tt0) REVERT: B 494 MET cc_start: 0.6947 (mmt) cc_final: 0.6691 (mmt) REVERT: B 699 MET cc_start: 0.8586 (mpp) cc_final: 0.8241 (mpp) REVERT: B 723 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6433 (pp) REVERT: C 109 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.7658 (m-10) REVERT: C 139 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.6771 (mtt90) REVERT: C 166 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8198 (tt) REVERT: C 354 MET cc_start: 0.7886 (mmm) cc_final: 0.7273 (mpp) REVERT: C 478 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7990 (mp) REVERT: C 512 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8134 (ttp) REVERT: C 746 LEU cc_start: 0.8520 (tp) cc_final: 0.8277 (tt) REVERT: C 785 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6550 (mmm) outliers start: 80 outliers final: 62 residues processed: 212 average time/residue: 0.1056 time to fit residues: 35.7037 Evaluate side-chains 215 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 142 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 686 GLN Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 356 PRO Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 448 PRO Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 512 MET Chi-restraints excluded: chain C residue 526 TYR Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 731 TRP Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 785 MET Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 748 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 135 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 82 optimal weight: 0.0670 chunk 251 optimal weight: 9.9990 chunk 208 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 149 optimal weight: 20.0000 chunk 203 optimal weight: 0.7980 overall best weight: 1.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.150876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.123448 restraints weight = 42249.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.117445 restraints weight = 46122.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.116624 restraints weight = 35583.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.115380 restraints weight = 34851.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.115641 restraints weight = 30798.009| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17599 Z= 0.163 Angle : 0.722 15.644 24281 Z= 0.348 Chirality : 0.048 0.521 3037 Planarity : 0.005 0.077 3125 Dihedral : 7.932 70.791 3053 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.46 % Favored : 92.50 % Rotamer: Outliers : 5.86 % Allowed : 27.69 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.17), residues: 2561 helix: 1.42 (0.18), residues: 882 sheet: -1.30 (0.25), residues: 429 loop : -1.93 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 467 TYR 0.015 0.001 TYR D 476 PHE 0.021 0.001 PHE A 533 TRP 0.023 0.001 TRP B 793 HIS 0.006 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00385 (17570) covalent geometry : angle 0.69562 (24210) SS BOND : bond 0.00432 ( 13) SS BOND : angle 2.30026 ( 26) hydrogen bonds : bond 0.03639 ( 719) hydrogen bonds : angle 4.75815 ( 2073) Misc. bond : bond 0.00003 ( 1) link_BETA1-4 : bond 0.00923 ( 6) link_BETA1-4 : angle 2.80198 ( 18) link_NAG-ASN : bond 0.00643 ( 9) link_NAG-ASN : angle 4.99106 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 147 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.6310 (ttt90) cc_final: 0.5878 (ttt90) REVERT: A 315 TRP cc_start: 0.6876 (t60) cc_final: 0.6422 (t60) REVERT: A 528 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6863 (tt0) REVERT: A 686 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7627 (pm20) REVERT: A 688 SER cc_start: 0.7236 (OUTLIER) cc_final: 0.6521 (t) REVERT: A 780 HIS cc_start: 0.8230 (OUTLIER) cc_final: 0.7933 (m-70) REVERT: B 415 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.7064 (mt) REVERT: B 494 MET cc_start: 0.6976 (mmt) cc_final: 0.6732 (mmt) REVERT: B 699 MET cc_start: 0.8606 (mpp) cc_final: 0.8252 (mpp) REVERT: B 723 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6434 (pp) REVERT: C 109 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7681 (m-10) REVERT: C 139 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.6834 (mtt90) REVERT: C 166 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8216 (tt) REVERT: C 354 MET cc_start: 0.7945 (mmm) cc_final: 0.7299 (mpp) REVERT: C 478 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8030 (mp) REVERT: C 512 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8044 (ttp) REVERT: C 746 LEU cc_start: 0.8588 (tp) cc_final: 0.8354 (tt) REVERT: C 785 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6587 (mmm) outliers start: 80 outliers final: 64 residues processed: 216 average time/residue: 0.1029 time to fit residues: 35.6343 Evaluate side-chains 219 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 143 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 686 GLN Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 356 PRO Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 512 MET Chi-restraints excluded: chain C residue 526 TYR Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 731 TRP Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 785 MET Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 754 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 175 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 167 optimal weight: 20.0000 chunk 247 optimal weight: 10.0000 chunk 93 optimal weight: 0.0470 chunk 170 optimal weight: 9.9990 chunk 140 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 overall best weight: 2.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.150358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3778 r_free = 0.3778 target = 0.114274 restraints weight = 42167.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.110731 restraints weight = 34049.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.111000 restraints weight = 32900.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.111475 restraints weight = 32167.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.111628 restraints weight = 29410.500| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17599 Z= 0.181 Angle : 0.725 15.252 24281 Z= 0.351 Chirality : 0.048 0.513 3037 Planarity : 0.005 0.077 3125 Dihedral : 7.763 70.489 3053 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.93 % Favored : 92.03 % Rotamer: Outliers : 5.79 % Allowed : 27.55 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.17), residues: 2561 helix: 1.44 (0.18), residues: 882 sheet: -1.24 (0.26), residues: 415 loop : -1.96 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 771 TYR 0.016 0.001 TYR D 476 PHE 0.022 0.002 PHE A 533 TRP 0.023 0.001 TRP B 793 HIS 0.007 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00430 (17570) covalent geometry : angle 0.69866 (24210) SS BOND : bond 0.00428 ( 13) SS BOND : angle 2.23042 ( 26) hydrogen bonds : bond 0.03787 ( 719) hydrogen bonds : angle 4.78902 ( 2073) Misc. bond : bond 0.00005 ( 1) link_BETA1-4 : bond 0.00935 ( 6) link_BETA1-4 : angle 2.82040 ( 18) link_NAG-ASN : bond 0.00654 ( 9) link_NAG-ASN : angle 5.00605 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 143 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.6671 (ttt90) cc_final: 0.6190 (ttt90) REVERT: A 315 TRP cc_start: 0.6992 (t60) cc_final: 0.6551 (t60) REVERT: A 528 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6913 (tt0) REVERT: A 688 SER cc_start: 0.7038 (OUTLIER) cc_final: 0.6254 (t) REVERT: A 780 HIS cc_start: 0.8285 (OUTLIER) cc_final: 0.8026 (m-70) REVERT: B 494 MET cc_start: 0.7167 (mmt) cc_final: 0.6863 (mmt) REVERT: B 501 LYS cc_start: 0.9034 (mmtt) cc_final: 0.8763 (mtpp) REVERT: B 699 MET cc_start: 0.8732 (mpp) cc_final: 0.8330 (mpp) REVERT: B 723 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.6707 (pp) REVERT: B 736 MET cc_start: 0.7876 (tpp) cc_final: 0.7570 (ttm) REVERT: B 787 GLN cc_start: 0.7864 (tp-100) cc_final: 0.7331 (tp-100) REVERT: C 109 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.7999 (m-10) REVERT: C 139 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.6924 (mtt90) REVERT: C 166 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8236 (tt) REVERT: C 354 MET cc_start: 0.7936 (mmm) cc_final: 0.7231 (mpp) REVERT: C 478 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8125 (mp) REVERT: C 512 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8034 (ttp) REVERT: C 785 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.6616 (mmm) REVERT: D 467 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7866 (tmm-80) outliers start: 79 outliers final: 65 residues processed: 210 average time/residue: 0.1032 time to fit residues: 35.1404 Evaluate side-chains 213 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 138 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 356 PRO Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 512 MET Chi-restraints excluded: chain C residue 526 TYR Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 731 TRP Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 785 MET Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 754 PHE Chi-restraints excluded: chain D residue 791 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 177 optimal weight: 0.9980 chunk 74 optimal weight: 30.0000 chunk 246 optimal weight: 2.9990 chunk 17 optimal weight: 30.0000 chunk 121 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 237 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 195 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.151872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.125552 restraints weight = 42055.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.117965 restraints weight = 47514.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.116886 restraints weight = 38654.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.114920 restraints weight = 34926.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.115237 restraints weight = 34077.477| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17599 Z= 0.122 Angle : 0.684 14.754 24281 Z= 0.328 Chirality : 0.047 0.516 3037 Planarity : 0.005 0.075 3125 Dihedral : 7.438 69.694 3053 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.79 % Favored : 93.17 % Rotamer: Outliers : 4.91 % Allowed : 28.28 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.17), residues: 2561 helix: 1.51 (0.18), residues: 883 sheet: -1.31 (0.25), residues: 426 loop : -1.85 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 771 TYR 0.015 0.001 TYR A 392 PHE 0.014 0.001 PHE A 533 TRP 0.022 0.001 TRP B 793 HIS 0.007 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00287 (17570) covalent geometry : angle 0.65805 (24210) SS BOND : bond 0.00367 ( 13) SS BOND : angle 2.14485 ( 26) hydrogen bonds : bond 0.03220 ( 719) hydrogen bonds : angle 4.62228 ( 2073) Misc. bond : bond 0.00015 ( 1) link_BETA1-4 : bond 0.00980 ( 6) link_BETA1-4 : angle 2.84815 ( 18) link_NAG-ASN : bond 0.00603 ( 9) link_NAG-ASN : angle 4.77654 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2813.15 seconds wall clock time: 49 minutes 10.91 seconds (2950.91 seconds total)