Starting phenix.real_space_refine on Wed Mar 4 22:24:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e9h_31032/03_2026/7e9h_31032.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e9h_31032/03_2026/7e9h_31032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e9h_31032/03_2026/7e9h_31032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e9h_31032/03_2026/7e9h_31032.map" model { file = "/net/cci-nas-00/data/ceres_data/7e9h_31032/03_2026/7e9h_31032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e9h_31032/03_2026/7e9h_31032.cif" } resolution = 4.0 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= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 108 5.16 5 C 10657 2.51 5 N 2905 2.21 5 O 3175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16847 Number of models: 1 Model: "" Number of chains: 8 Chain: "R" Number of atoms: 5580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 5580 Classifications: {'peptide': 766} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 37, 'TRANS': 728} Chain breaks: 4 Unresolved non-hydrogen bonds: 468 Unresolved non-hydrogen angles: 587 Unresolved non-hydrogen dihedrals: 400 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 14, 'PHE:plan': 6, 'GLN:plan1': 6, 'TRP:plan': 2, 'TYR:plan': 7, 'ASP:plan': 8, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 271 Chain: "S" Number of atoms: 5547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5547 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 36, 'TRANS': 724} Chain breaks: 4 Unresolved non-hydrogen bonds: 476 Unresolved non-hydrogen angles: 592 Unresolved non-hydrogen dihedrals: 397 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 10, 'ARG:plan': 14, 'ASN:plan1': 3, 'GLN:plan1': 5, 'TYR:plan': 2, 'TRP:plan': 1, 'PHE:plan': 10, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 278 Chain: "A" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1627 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 12, 'ARG:plan': 5, 'ASP:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 108 Chain: "B" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2208 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 300} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 4, 'ARG:plan': 12, 'HIS:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 113 Chain: "C" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 121 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1742 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "S" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 4.05, per 1000 atoms: 0.24 Number of scatterers: 16847 At special positions: 0 Unit cell: (225.72, 146.3, 151.525, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 P 2 15.00 O 3175 8.00 N 2905 7.00 C 10657 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS R 67 " - pdb=" SG CYS R 109 " distance=2.03 Simple disulfide: pdb=" SG CYS R 249 " - pdb=" SG CYS R 538 " distance=2.03 Simple disulfide: pdb=" SG CYS R 428 " - pdb=" SG CYS R 435 " distance=2.03 Simple disulfide: pdb=" SG CYS R 520 " - pdb=" SG CYS R 539 " distance=2.03 Simple disulfide: pdb=" SG CYS R 524 " - pdb=" SG CYS R 542 " distance=2.03 Simple disulfide: pdb=" SG CYS R 545 " - pdb=" SG CYS R 557 " distance=2.03 Simple disulfide: pdb=" SG CYS R 560 " - pdb=" SG CYS R 573 " distance=2.03 Simple disulfide: pdb=" SG CYS R 652 " - pdb=" SG CYS R 746 " distance=2.03 Simple disulfide: pdb=" SG CYS S 249 " - pdb=" SG CYS S 538 " distance=2.03 Simple disulfide: pdb=" SG CYS S 372 " - pdb=" SG CYS S 388 " distance=2.03 Simple disulfide: pdb=" SG CYS S 428 " - pdb=" SG CYS S 435 " distance=2.03 Simple disulfide: pdb=" SG CYS S 520 " - pdb=" SG CYS S 539 " distance=2.03 Simple disulfide: pdb=" SG CYS S 524 " - pdb=" SG CYS S 542 " distance=2.03 Simple disulfide: pdb=" SG CYS S 545 " - pdb=" SG CYS S 557 " distance=2.03 Simple disulfide: pdb=" SG CYS S 560 " - pdb=" SG CYS S 573 " distance=2.03 Simple disulfide: pdb=" SG CYS S 652 " - pdb=" SG CYS S 746 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " 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=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 940.1 milliseconds 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4288 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 28 sheets defined 37.6% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'R' and resid 74 through 92 Processing helix chain 'R' and resid 111 through 127 Processing helix chain 'R' and resid 158 through 170 removed outlier: 3.679A pdb=" N MET R 164 " --> pdb=" O SER R 160 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN R 167 " --> pdb=" O ILE R 163 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE R 168 " --> pdb=" O MET R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 188 removed outlier: 3.654A pdb=" N ASP R 188 " --> pdb=" O ASP R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 216 removed outlier: 3.543A pdb=" N GLN R 205 " --> pdb=" O SER R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 230 through 246 removed outlier: 3.788A pdb=" N ASP R 245 " --> pdb=" O LYS R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 275 removed outlier: 3.539A pdb=" N LYS R 267 " --> pdb=" O GLY R 263 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR R 275 " --> pdb=" O ARG R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 300 Processing helix chain 'R' and resid 341 through 350 removed outlier: 3.783A pdb=" N ASP R 345 " --> pdb=" O VAL R 341 " (cutoff:3.500A) Processing helix chain 'R' and resid 359 through 370 removed outlier: 4.075A pdb=" N ALA R 363 " --> pdb=" O ASN R 359 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU R 364 " --> pdb=" O ILE R 360 " (cutoff:3.500A) Processing helix chain 'R' and resid 403 through 428 removed outlier: 4.226A pdb=" N GLN R 407 " --> pdb=" O GLU R 403 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE R 408 " --> pdb=" O GLY R 404 " (cutoff:3.500A) Processing helix chain 'R' and resid 435 through 439 Processing helix chain 'R' and resid 442 through 452 removed outlier: 3.665A pdb=" N ARG R 451 " --> pdb=" O LEU R 447 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN R 452 " --> pdb=" O LYS R 448 " (cutoff:3.500A) Processing helix chain 'R' and resid 458 through 460 No H-bonds generated for 'chain 'R' and resid 458 through 460' Processing helix chain 'R' and resid 588 through 612 removed outlier: 3.549A pdb=" N LEU R 592 " --> pdb=" O ALA R 588 " (cutoff:3.500A) Processing helix chain 'R' and resid 615 through 621 removed outlier: 3.586A pdb=" N LYS R 619 " --> pdb=" O THR R 615 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER R 621 " --> pdb=" O ILE R 617 " (cutoff:3.500A) Processing helix chain 'R' and resid 622 through 644 removed outlier: 4.555A pdb=" N THR R 640 " --> pdb=" O CYS R 636 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE R 641 " --> pdb=" O TYR R 637 " (cutoff:3.500A) Processing helix chain 'R' and resid 648 through 687 removed outlier: 4.259A pdb=" N PHE R 681 " --> pdb=" O ILE R 677 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU R 682 " --> pdb=" O TYR R 678 " (cutoff:3.500A) Processing helix chain 'R' and resid 695 through 721 Processing helix chain 'R' and resid 748 through 775 removed outlier: 3.654A pdb=" N SER R 752 " --> pdb=" O ILE R 748 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR R 768 " --> pdb=" O MET R 764 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG R 775 " --> pdb=" O ALA R 771 " (cutoff:3.500A) Processing helix chain 'R' and resid 784 through 811 Proline residue: R 803 - end of helix Processing helix chain 'R' and resid 814 through 848 removed outlier: 3.794A pdb=" N GLN R 818 " --> pdb=" O LYS R 814 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR R 819 " --> pdb=" O LEU R 815 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR R 820 " --> pdb=" O TYR R 816 " (cutoff:3.500A) Proline residue: R 840 - end of helix Processing helix chain 'S' and resid 76 through 92 Processing helix chain 'S' and resid 111 through 123 Processing helix chain 'S' and resid 158 through 172 removed outlier: 3.501A pdb=" N PHE S 172 " --> pdb=" O ILE S 168 " (cutoff:3.500A) Processing helix chain 'S' and resid 183 through 187 Processing helix chain 'S' and resid 201 through 216 removed outlier: 3.800A pdb=" N GLN S 205 " --> pdb=" O SER S 201 " (cutoff:3.500A) Processing helix chain 'S' and resid 227 through 245 removed outlier: 4.401A pdb=" N GLY S 231 " --> pdb=" O GLU S 227 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU S 232 " --> pdb=" O GLY S 228 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP S 245 " --> pdb=" O LYS S 241 " (cutoff:3.500A) Processing helix chain 'S' and resid 265 through 274 removed outlier: 3.667A pdb=" N ILE S 269 " --> pdb=" O PHE S 265 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU S 272 " --> pdb=" O ILE S 268 " (cutoff:3.500A) Processing helix chain 'S' and resid 286 through 299 Processing helix chain 'S' and resid 311 through 315 removed outlier: 3.598A pdb=" N TRP S 314 " --> pdb=" O SER S 311 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY S 315 " --> pdb=" O ASP S 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 311 through 315' Processing helix chain 'S' and resid 320 through 327 Processing helix chain 'S' and resid 341 through 349 Processing helix chain 'S' and resid 360 through 370 removed outlier: 4.556A pdb=" N GLU S 364 " --> pdb=" O ILE S 360 " (cutoff:3.500A) Processing helix chain 'S' and resid 405 through 428 Processing helix chain 'S' and resid 435 through 439 removed outlier: 3.590A pdb=" N ASP S 439 " --> pdb=" O PRO S 436 " (cutoff:3.500A) Processing helix chain 'S' and resid 442 through 451 removed outlier: 3.720A pdb=" N TYR S 449 " --> pdb=" O GLN S 445 " (cutoff:3.500A) Processing helix chain 'S' and resid 585 through 587 No H-bonds generated for 'chain 'S' and resid 585 through 587' Processing helix chain 'S' and resid 588 through 612 removed outlier: 3.817A pdb=" N LEU S 592 " --> pdb=" O ALA S 588 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL S 597 " --> pdb=" O PHE S 593 " (cutoff:3.500A) Processing helix chain 'S' and resid 615 through 619 removed outlier: 4.221A pdb=" N VAL S 618 " --> pdb=" O THR S 615 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS S 619 " --> pdb=" O PRO S 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 615 through 619' Processing helix chain 'S' and resid 623 through 644 removed outlier: 4.398A pdb=" N THR S 640 " --> pdb=" O CYS S 636 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE S 641 " --> pdb=" O TYR S 637 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE S 644 " --> pdb=" O THR S 640 " (cutoff:3.500A) Processing helix chain 'S' and resid 648 through 682 removed outlier: 3.554A pdb=" N CYS S 652 " --> pdb=" O ASP S 648 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE S 680 " --> pdb=" O ARG S 676 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE S 681 " --> pdb=" O ILE S 677 " (cutoff:3.500A) Processing helix chain 'S' and resid 696 through 720 Processing helix chain 'S' and resid 749 through 774 Processing helix chain 'S' and resid 783 through 800 removed outlier: 3.890A pdb=" N ILE S 787 " --> pdb=" O GLU S 783 " (cutoff:3.500A) Processing helix chain 'S' and resid 800 through 808 removed outlier: 4.126A pdb=" N ILE S 804 " --> pdb=" O ALA S 800 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE S 805 " --> pdb=" O PHE S 801 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR S 808 " --> pdb=" O ILE S 804 " (cutoff:3.500A) Processing helix chain 'S' and resid 813 through 836 removed outlier: 3.524A pdb=" N ILE S 817 " --> pdb=" O ASP S 813 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER S 833 " --> pdb=" O SER S 829 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU S 834 " --> pdb=" O ALA S 830 " (cutoff:3.500A) Processing helix chain 'S' and resid 838 through 848 removed outlier: 3.920A pdb=" N HIS S 848 " --> pdb=" O ILE S 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 31 removed outlier: 3.730A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.524A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 306 removed outlier: 3.688A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N CYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.926A pdb=" N ASP A 337 " --> pdb=" O GLN A 333 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 4.236A pdb=" N PHE D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 43 through 45 removed outlier: 6.797A pdb=" N LEU R 51 " --> pdb=" O ARG R 104 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU R 106 " --> pdb=" O LEU R 51 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY R 53 " --> pdb=" O LEU R 106 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N THR R 50 " --> pdb=" O GLY R 152 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ILE R 154 " --> pdb=" O THR R 50 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY R 52 " --> pdb=" O ILE R 154 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N ILE R 177 " --> pdb=" O VAL R 151 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL R 153 " --> pdb=" O ILE R 177 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 58 through 60 removed outlier: 4.506A pdb=" N GLY R 59 " --> pdb=" O GLY R 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 249 through 256 removed outlier: 7.048A pdb=" N THR R 223 " --> pdb=" O ALA R 251 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER R 253 " --> pdb=" O THR R 223 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA R 225 " --> pdb=" O SER R 253 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS R 255 " --> pdb=" O ALA R 225 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE R 282 " --> pdb=" O TYR R 220 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER R 222 " --> pdb=" O ILE R 282 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE R 334 " --> pdb=" O GLY R 310 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TYR R 475 " --> pdb=" O SER R 494 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N SER R 494 " --> pdb=" O TYR R 475 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE R 477 " --> pdb=" O ILE R 492 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 455 through 456 removed outlier: 3.893A pdb=" N PHE R 455 " --> pdb=" O VAL R 463 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 530 through 532 removed outlier: 3.838A pdb=" N HIS R 541 " --> pdb=" O THR R 532 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 564 through 566 Processing sheet with id=AA7, first strand: chain 'S' and resid 43 through 45 removed outlier: 6.226A pdb=" N ILE S 49 " --> pdb=" O GLY S 102 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ARG S 104 " --> pdb=" O ILE S 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 43 through 45 removed outlier: 3.930A pdb=" N LEU S 106 " --> pdb=" O GLY S 53 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE S 55 " --> pdb=" O LEU S 106 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY S 52 " --> pdb=" O ILE S 154 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL S 153 " --> pdb=" O ILE S 177 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 249 through 255 removed outlier: 7.997A pdb=" N VAL S 221 " --> pdb=" O ALA S 251 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N SER S 253 " --> pdb=" O VAL S 221 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N THR S 223 " --> pdb=" O SER S 253 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LYS S 255 " --> pdb=" O THR S 223 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA S 225 " --> pdb=" O LYS S 255 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA S 280 " --> pdb=" O TYR S 220 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL S 281 " --> pdb=" O MET S 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 331 through 336 removed outlier: 4.314A pdb=" N GLN S 481 " --> pdb=" O GLU S 488 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU S 488 " --> pdb=" O GLN S 481 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 530 through 533 Processing sheet with id=AB3, first strand: chain 'S' and resid 564 through 565 Processing sheet with id=AB4, first strand: chain 'A' and resid 185 through 188 removed outlier: 6.369A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 225 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 268 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.684A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 61 through 63 removed outlier: 3.902A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.648A pdb=" N CYS B 114 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.786A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.548A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.357A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY B 244 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.733A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.967A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.208A pdb=" N THR D 118 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL D 12 " --> pdb=" O THR D 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.625A pdb=" N TYR D 59 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR D 50 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE D 51 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N MET D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 45 through 46 Processing sheet with id=AC7, first strand: chain 'D' and resid 69 through 70 removed outlier: 3.881A pdb=" N THR D 69 " --> pdb=" O GLN D 82 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 146 through 147 removed outlier: 3.530A pdb=" N VAL D 147 " --> pdb=" O LYS D 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 155 through 159 removed outlier: 3.880A pdb=" N SER D 204 " --> pdb=" O THR D 215 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 194 through 195 removed outlier: 3.627A pdb=" N ASN D 194 " --> pdb=" O TYR D 190 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR D 190 " --> pdb=" O ASN D 194 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU D 187 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE D 189 " --> pdb=" O TRP D 176 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL D 226 " --> pdb=" O GLN D 179 " (cutoff:3.500A) 719 hydrogen bonds defined for protein. 2070 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: 3.25 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5563 1.34 - 1.46: 4102 1.46 - 1.58: 7382 1.58 - 1.70: 2 1.70 - 1.82: 145 Bond restraints: 17194 Sorted by residual: bond pdb=" O2P SEP S1001 " pdb=" P SEP S1001 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" O1P SEP S1001 " pdb=" P SEP S1001 " ideal model delta sigma weight residual 1.610 1.510 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" O1P SEP R1001 " pdb=" P SEP R1001 " ideal model delta sigma weight residual 1.610 1.510 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" O2P SEP R1001 " pdb=" P SEP R1001 " ideal model delta sigma weight residual 1.610 1.510 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" O3P SEP R1001 " pdb=" P SEP R1001 " ideal model delta sigma weight residual 1.610 1.510 0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 17189 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 23164 1.68 - 3.36: 224 3.36 - 5.03: 43 5.03 - 6.71: 14 6.71 - 8.39: 4 Bond angle restraints: 23449 Sorted by residual: angle pdb=" N VAL D 224 " pdb=" CA VAL D 224 " pdb=" C VAL D 224 " ideal model delta sigma weight residual 113.20 108.84 4.36 9.60e-01 1.09e+00 2.06e+01 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.42 109.61 3.81 1.17e+00 7.31e-01 1.06e+01 angle pdb=" C CYS R 524 " pdb=" N GLN R 525 " pdb=" CA GLN R 525 " ideal model delta sigma weight residual 119.78 123.29 -3.51 1.24e+00 6.50e-01 8.03e+00 angle pdb=" CB SEP R1001 " pdb=" OG SEP R1001 " pdb=" P SEP R1001 " ideal model delta sigma weight residual 110.00 118.39 -8.39 3.00e+00 1.11e-01 7.82e+00 angle pdb=" CB SEP S1001 " pdb=" OG SEP S1001 " pdb=" P SEP S1001 " ideal model delta sigma weight residual 110.00 118.31 -8.31 3.00e+00 1.11e-01 7.67e+00 ... (remaining 23444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 9529 17.91 - 35.82: 535 35.82 - 53.73: 79 53.73 - 71.64: 11 71.64 - 89.55: 14 Dihedral angle restraints: 10168 sinusoidal: 3512 harmonic: 6656 Sorted by residual: dihedral pdb=" CB CYS R 249 " pdb=" SG CYS R 249 " pdb=" SG CYS R 538 " pdb=" CB CYS R 538 " ideal model delta sinusoidal sigma weight residual 93.00 161.56 -68.56 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS S 520 " pdb=" SG CYS S 520 " pdb=" SG CYS S 539 " pdb=" CB CYS S 539 " ideal model delta sinusoidal sigma weight residual -86.00 -24.23 -61.77 1 1.00e+01 1.00e-02 5.06e+01 dihedral pdb=" CB CYS S 560 " pdb=" SG CYS S 560 " pdb=" SG CYS S 573 " pdb=" CB CYS S 573 " ideal model delta sinusoidal sigma weight residual 93.00 37.74 55.26 1 1.00e+01 1.00e-02 4.13e+01 ... (remaining 10165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1665 0.029 - 0.058: 740 0.058 - 0.087: 192 0.087 - 0.116: 123 0.116 - 0.145: 16 Chirality restraints: 2736 Sorted by residual: chirality pdb=" CB ILE S 282 " pdb=" CA ILE S 282 " pdb=" CG1 ILE S 282 " pdb=" CG2 ILE S 282 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA ILE S 256 " pdb=" N ILE S 256 " pdb=" C ILE S 256 " pdb=" CB ILE S 256 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CB ILE A 264 " pdb=" CA ILE A 264 " pdb=" CG1 ILE A 264 " pdb=" CG2 ILE A 264 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 2733 not shown) Planarity restraints: 3021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG R 104 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" C ARG R 104 " -0.034 2.00e-02 2.50e+03 pdb=" O ARG R 104 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE R 105 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 777 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO R 778 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO R 778 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 778 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 471 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO R 472 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO R 472 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 472 " -0.018 5.00e-02 4.00e+02 ... (remaining 3018 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1402 2.74 - 3.28: 17209 3.28 - 3.82: 28228 3.82 - 4.36: 31003 4.36 - 4.90: 53911 Nonbonded interactions: 131753 Sorted by model distance: nonbonded pdb=" O ASP R 648 " pdb=" N THR R 651 " model vdw 2.202 3.120 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.214 3.040 nonbonded pdb=" OG1 THR S 223 " pdb=" OG SER S 253 " model vdw 2.215 3.040 nonbonded pdb=" O CYS R 636 " pdb=" OG1 THR R 639 " model vdw 2.221 3.040 nonbonded pdb=" N GLY R 330 " pdb=" O TYR R 480 " model vdw 2.231 3.120 ... (remaining 131748 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 'R' and (resid 41 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 93 or (resid 94 and (name N or nam \ e CA or name C or name O or name CB )) or resid 95 through 126 or resid 148 or ( \ resid 149 and (name N or name CA or name C or name O or name CB )) or resid 150 \ through 172 or (resid 173 and (name N or name CA or name C or name O or name CB \ )) or resid 174 through 258 or (resid 259 and (name N or name CA or name C or na \ me O or name CB )) or resid 260 through 294 or (resid 295 through 297 and (name \ N or name CA or name C or name O or name CB )) or resid 298 through 300 or (resi \ d 301 and (name N or name CA or name C or name O or name CB )) or resid 302 thro \ ugh 321 or (resid 322 and (name N or name CA or name C or name O or name CB )) o \ r resid 323 or (resid 324 through 326 and (name N or name CA or name C or name O \ or name CB )) or resid 327 through 356 or (resid 357 and (name N or name CA or \ name C or name O or name CB )) or resid 358 through 372 or (resid 373 and (name \ N or name CA or name C or name O or name CB )) or resid 386 through 425 or (resi \ d 426 and (name N or name CA or name C or name O or name CB )) or resid 427 thro \ ugh 441 or (resid 442 and (name N or name CA or name C or name O or name CB )) o \ r resid 443 through 447 or (resid 448 and (name N or name CA or name C or name O \ or name CB )) or resid 449 through 466 or (resid 467 and (name N or name CA or \ name C or name O or name CB )) or resid 468 through 473 or (resid 474 and (name \ N or name CA or name C or name O or name CB )) or resid 475 through 487 or (resi \ d 488 and (name N or name CA or name C or name O or name CB )) or resid 489 or ( \ resid 490 and (name N or name CA or name C or name O or name CB )) or resid 491 \ through 503 or resid 515 through 516 or (resid 517 and (name N or name CA or nam \ e C or name O or name CB )) or resid 518 through 588 or (resid 589 through 590 a \ nd (name N or name CA or name C or name O or name CB )) or resid 591 through 618 \ or (resid 619 through 620 and (name N or name CA or name C or name O or name CB \ )) or resid 621 through 623 or (resid 624 through 625 and (name N or name CA or \ name C or name O or name CB )) or resid 626 through 633 or (resid 634 through 6 \ 35 and (name N or name CA or name C or name O or name CB )) or resid 636 or (res \ id 637 through 638 and (name N or name CA or name C or name O or name CB )) or r \ esid 639 through 640 or (resid 641 and (name N or name CA or name C or name O or \ name CB )) or resid 642 through 645 or (resid 646 and (name N or name CA or nam \ e C or name O or name CB )) or resid 647 through 648 or (resid 649 and (name N o \ r name CA or name C or name O or name CB )) or resid 650 through 655 or (resid 6 \ 56 through 658 and (name N or name CA or name C or name O or name CB )) or resid \ 659 through 681 or (resid 682 through 683 and (name N or name CA or name C or n \ ame O or name CB )) or resid 692 or (resid 693 through 694 and (name N or name C \ A or name C or name O or name CB )) or resid 695 through 703 or (resid 704 and ( \ name N or name CA or name C or name O or name CB )) or resid 705 through 706 or \ (resid 707 and (name N or name CA or name C or name O or name CB )) or resid 708 \ or (resid 709 and (name N or name CA or name C or name O or name CB )) or resid \ 710 or (resid 711 through 712 and (name N or name CA or name C or name O or nam \ e CB )) or resid 713 or (resid 714 and (name N or name CA or name C or name O or \ name CB )) or resid 715 through 726 or (resid 727 through 733 and (name N or na \ me CA or name C or name O or name CB )) or resid 734 or (resid 735 through 736 a \ nd (name N or name CA or name C or name O or name CB )) or resid 737 through 753 \ or (resid 754 and (name N or name CA or name C or name O or name CB )) or resid \ 755 or (resid 756 through 757 and (name N or name CA or name C or name O or nam \ e CB )) or resid 758 through 768 or (resid 769 through 773 and (name N or name C \ A or name C or name O or name CB )) or resid 774 or (resid 775 and (name N or na \ me CA or name C or name O or name CB )) or resid 776 through 780 or (resid 781 t \ hrough 785 and (name N or name CA or name C or name O or name CB )) or resid 786 \ through 817 or (resid 818 and (name N or name CA or name C or name O or name CB \ )) or resid 819 through 835 or (resid 836 and (name N or name CA or name C or n \ ame O or name CB )) or resid 837 through 1001)) selection = (chain 'S' and (resid 41 through 71 or (resid 72 and (name N or name CA or name \ C or name O or name CB )) or resid 73 through 278 or (resid 279 through 280 and \ (name N or name CA or name C or name O or name CB )) or resid 281 through 290 or \ (resid 291 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 2 through 369 or (resid 370 and (name N or name CA or name C or name O or name C \ B )) or resid 371 through 373 or (resid 386 through 387 and (name N or name CA o \ r name C or name O or name CB )) or resid 388 through 400 or (resid 401 and (nam \ e N or name CA or name C or name O or name CB )) or resid 402 through 483 or res \ id 487 through 503 or resid 515 through 521 or (resid 522 and (name N or name CA \ or name C or name O or name CB )) or resid 523 through 528 or (resid 529 and (n \ ame N or name CA or name C or name O or name CB )) or resid 530 or (resid 531 th \ rough 534 and (name N or name CA or name C or name O or name CB )) or resid 535 \ through 539 or (resid 540 and (name N or name CA or name C or name O or name CB \ )) or resid 541 through 542 or (resid 543 and (name N or name CA or name C or na \ me O or name CB )) or resid 544 through 545 or (resid 546 and (name N or name CA \ or name C or name O or name CB )) or resid 547 or (resid 548 and (name N or nam \ e CA or name C or name O or name CB )) or resid 549 or (resid 550 through 556 an \ d (name N or name CA or name C or name O or name CB )) or resid 557 through 558 \ or (resid 559 and (name N or name CA or name C or name O or name CB )) or resid \ 560 through 561 or (resid 562 through 563 and (name N or name CA or name C or na \ me O or name CB )) or resid 564 through 567 or (resid 568 and (name N or name CA \ or name C or name O or name CB )) or resid 569 or (resid 570 through 571 and (n \ ame N or name CA or name C or name O or name CB )) or resid 572 through 577 or ( \ resid 578 through 583 and (name N or name CA or name C or name O or name CB )) o \ r resid 584 through 591 or (resid 592 through 593 and (name N or name CA or name \ C or name O or name CB )) or resid 594 through 596 or (resid 597 and (name N or \ name CA or name C or name O or name CB )) or resid 598 through 607 or (resid 60 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 609 through \ 611 or (resid 612 and (name N or name CA or name C or name O or name CB )) or re \ sid 613 through 643 or (resid 644 through 646 and (name N or name CA or name C o \ r name O or name CB )) or resid 647 through 656 or (resid 657 through 658 and (n \ ame N or name CA or name C or name O or name CB )) or resid 659 through 680 or ( \ resid 681 through 683 and (name N or name CA or name C or name O or name CB )) o \ r resid 692 through 715 or (resid 716 and (name N or name CA or name C or name O \ or name CB )) or resid 717 through 725 or (resid 726 through 733 and (name N or \ name CA or name C or name O or name CB )) or resid 734 through 737 or (resid 73 \ 8 through 741 and (name N or name CA or name C or name O or name CB )) or resid \ 742 through 748 or (resid 749 and (name N or name CA or name C or name O or name \ CB )) or resid 750 through 751 or (resid 752 through 754 and (name N or name CA \ or name C or name O or name CB )) or resid 755 through 769 or (resid 770 throug \ h 773 and (name N or name CA or name C or name O or name CB )) or resid 774 thro \ ugh 782 or (resid 783 through 785 and (name N or name CA or name C or name O or \ name CB )) or resid 786 through 790 or (resid 791 and (name N or name CA or name \ C or name O or name CB )) or resid 792 through 813 or (resid 814 and (name N or \ name CA or name C or name O or name CB )) or resid 815 through 837 or (resid 83 \ 8 through 839 and (name N or name CA or name C or name O or name CB )) or resid \ 840 or (resid 841 and (name N or name CA or name C or name O or name CB )) or re \ sid 842 through 1001)) } 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: 5.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.810 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6022 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 : 0.003 0.101 17211 Z= 0.138 Angle : 0.486 8.388 23483 Z= 0.262 Chirality : 0.039 0.145 2736 Planarity : 0.003 0.033 3021 Dihedral : 11.361 89.552 5829 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.06 % Allowed : 2.41 % Favored : 97.53 % 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 are not related in a simple way. whole: -2.83 (0.15), residues: 2275 helix: -0.47 (0.16), residues: 812 sheet: -2.17 (0.24), residues: 349 loop : -2.94 (0.15), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 243 TYR 0.008 0.001 TYR S 843 PHE 0.012 0.001 PHE S 847 TRP 0.005 0.001 TRP R 366 HIS 0.002 0.000 HIS S 418 Details of bonding type rmsd covalent geometry : bond 0.00265 (17194) covalent geometry : angle 0.48406 (23449) SS BOND : bond 0.00226 ( 17) SS BOND : angle 1.13004 ( 34) hydrogen bonds : bond 0.13910 ( 715) hydrogen bonds : angle 5.63500 ( 2070) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 393 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 114 HIS cc_start: 0.6386 (t70) cc_final: 0.5936 (t70) REVERT: S 269 ILE cc_start: 0.7886 (tp) cc_final: 0.7613 (tp) REVERT: S 591 PRO cc_start: 0.8512 (Cg_exo) cc_final: 0.8203 (Cg_endo) REVERT: S 791 MET cc_start: 0.7400 (mmp) cc_final: 0.7064 (mmp) REVERT: B 337 LYS cc_start: 0.8052 (ptpt) cc_final: 0.7535 (ptpt) REVERT: D 230 MET cc_start: 0.5228 (ppp) cc_final: 0.4642 (ttp) REVERT: D 237 LEU cc_start: 0.7127 (mt) cc_final: 0.6684 (mt) outliers start: 1 outliers final: 1 residues processed: 393 average time/residue: 0.1522 time to fit residues: 85.0293 Evaluate side-chains 276 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 275 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 679 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 77 HIS R 118 GLN R 356 ASN R 500 HIS R 549 GLN ** R 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 818 GLN S 77 HIS ** S 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 219 ASN S 355 ASN ** S 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 445 GLN S 500 HIS S 675 ASN S 683 GLN A 244 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 230 ASN B 295 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN D 194 ASN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.112777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.090801 restraints weight = 61586.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.091908 restraints weight = 40540.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.092015 restraints weight = 28219.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.092249 restraints weight = 26195.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.092378 restraints weight = 25700.653| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.103 17211 Z= 0.371 Angle : 0.792 14.742 23483 Z= 0.410 Chirality : 0.051 0.320 2736 Planarity : 0.005 0.053 3021 Dihedral : 5.009 56.956 2482 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.59 % Allowed : 15.91 % Favored : 81.49 % 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 are not related in a simple way. whole: -2.24 (0.16), residues: 2275 helix: -0.04 (0.18), residues: 815 sheet: -1.96 (0.25), residues: 353 loop : -2.49 (0.16), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 197 TYR 0.028 0.003 TYR R 220 PHE 0.031 0.003 PHE R 465 TRP 0.030 0.003 TRP R 308 HIS 0.012 0.003 HIS S 114 Details of bonding type rmsd covalent geometry : bond 0.00869 (17194) covalent geometry : angle 0.79047 (23449) SS BOND : bond 0.00885 ( 17) SS BOND : angle 1.67840 ( 34) hydrogen bonds : bond 0.04661 ( 715) hydrogen bonds : angle 4.78529 ( 2070) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 292 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 438 MET cc_start: 0.7433 (ttp) cc_final: 0.7159 (ttm) REVERT: R 801 PHE cc_start: 0.8140 (t80) cc_final: 0.7929 (t80) REVERT: S 112 ASP cc_start: 0.6676 (m-30) cc_final: 0.6438 (m-30) REVERT: S 289 ASP cc_start: 0.6965 (m-30) cc_final: 0.6613 (m-30) REVERT: S 591 PRO cc_start: 0.8226 (Cg_exo) cc_final: 0.7973 (Cg_endo) REVERT: A 186 GLU cc_start: 0.7877 (tp30) cc_final: 0.7387 (tp30) REVERT: A 247 MET cc_start: 0.8371 (mmp) cc_final: 0.7756 (ptp) REVERT: B 51 LEU cc_start: 0.8378 (mt) cc_final: 0.8029 (mt) REVERT: B 82 TRP cc_start: 0.7082 (m100) cc_final: 0.6843 (m100) REVERT: B 293 ASN cc_start: 0.8461 (p0) cc_final: 0.8216 (p0) REVERT: B 337 LYS cc_start: 0.8560 (ptpt) cc_final: 0.8068 (ptmt) REVERT: D 171 ASN cc_start: 0.7433 (p0) cc_final: 0.6756 (p0) outliers start: 43 outliers final: 32 residues processed: 312 average time/residue: 0.1435 time to fit residues: 65.7590 Evaluate side-chains 276 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 244 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain R residue 368 ASP Chi-restraints excluded: chain R residue 406 VAL Chi-restraints excluded: chain R residue 519 ILE Chi-restraints excluded: chain R residue 659 LEU Chi-restraints excluded: chain R residue 679 ARG Chi-restraints excluded: chain R residue 816 TYR Chi-restraints excluded: chain R residue 822 LEU Chi-restraints excluded: chain R residue 826 VAL Chi-restraints excluded: chain R residue 837 LEU Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 341 VAL Chi-restraints excluded: chain S residue 352 THR Chi-restraints excluded: chain S residue 389 THR Chi-restraints excluded: chain S residue 416 MET Chi-restraints excluded: chain S residue 423 MET Chi-restraints excluded: chain S residue 602 THR Chi-restraints excluded: chain S residue 659 LEU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 51 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 41 optimal weight: 0.0870 chunk 84 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 148 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 178 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 GLN R 699 GLN R 818 GLN ** S 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 541 HIS S 613 ASN S 699 GLN B 75 GLN B 119 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.115785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.095118 restraints weight = 61419.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.095521 restraints weight = 41805.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.095804 restraints weight = 30091.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.096136 restraints weight = 29903.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.096312 restraints weight = 25387.303| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17211 Z= 0.135 Angle : 0.589 15.380 23483 Z= 0.291 Chirality : 0.042 0.150 2736 Planarity : 0.004 0.048 3021 Dihedral : 4.375 61.168 2482 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.47 % Allowed : 19.71 % Favored : 77.82 % 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 are not related in a simple way. whole: -1.65 (0.17), residues: 2275 helix: 0.62 (0.18), residues: 811 sheet: -1.67 (0.25), residues: 356 loop : -2.27 (0.16), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 251 TYR 0.017 0.001 TYR D 103 PHE 0.023 0.001 PHE R 805 TRP 0.020 0.002 TRP B 99 HIS 0.006 0.001 HIS R 418 Details of bonding type rmsd covalent geometry : bond 0.00311 (17194) covalent geometry : angle 0.58851 (23449) SS BOND : bond 0.00271 ( 17) SS BOND : angle 0.91822 ( 34) hydrogen bonds : bond 0.03605 ( 715) hydrogen bonds : angle 4.25467 ( 2070) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 271 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 438 MET cc_start: 0.7185 (ttp) cc_final: 0.6860 (ttm) REVERT: R 686 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7515 (mtm110) REVERT: R 827 SER cc_start: 0.8822 (t) cc_final: 0.8598 (t) REVERT: S 71 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7677 (ptpp) REVERT: S 112 ASP cc_start: 0.6617 (m-30) cc_final: 0.6113 (m-30) REVERT: S 289 ASP cc_start: 0.6976 (m-30) cc_final: 0.6697 (m-30) REVERT: S 309 MET cc_start: 0.7969 (tpt) cc_final: 0.7092 (tpt) REVERT: S 323 HIS cc_start: 0.6730 (m90) cc_final: 0.6367 (m-70) REVERT: S 564 MET cc_start: 0.4794 (mmm) cc_final: 0.4587 (mmm) REVERT: S 591 PRO cc_start: 0.8197 (Cg_exo) cc_final: 0.7985 (Cg_endo) REVERT: A 210 LYS cc_start: 0.8083 (mmmt) cc_final: 0.7661 (mmmm) REVERT: A 247 MET cc_start: 0.8197 (mmp) cc_final: 0.7619 (ptp) REVERT: A 267 PHE cc_start: 0.7114 (OUTLIER) cc_final: 0.6893 (t80) REVERT: B 51 LEU cc_start: 0.7961 (mt) cc_final: 0.7405 (mt) REVERT: B 337 LYS cc_start: 0.8490 (ptpt) cc_final: 0.8055 (ptmt) REVERT: B 339 TRP cc_start: 0.8121 (m100) cc_final: 0.7491 (m100) REVERT: D 140 MET cc_start: 0.3466 (tpp) cc_final: 0.2830 (tpp) outliers start: 41 outliers final: 24 residues processed: 290 average time/residue: 0.1313 time to fit residues: 56.5635 Evaluate side-chains 270 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain R residue 368 ASP Chi-restraints excluded: chain R residue 394 ILE Chi-restraints excluded: chain R residue 406 VAL Chi-restraints excluded: chain R residue 594 LEU Chi-restraints excluded: chain R residue 628 VAL Chi-restraints excluded: chain R residue 679 ARG Chi-restraints excluded: chain R residue 796 ILE Chi-restraints excluded: chain R residue 816 TYR Chi-restraints excluded: chain R residue 822 LEU Chi-restraints excluded: chain R residue 837 LEU Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 659 LEU Chi-restraints excluded: chain S residue 847 PHE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 175 optimal weight: 9.9990 chunk 138 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 199 optimal weight: 8.9990 chunk 225 optimal weight: 0.0770 chunk 45 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 169 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 overall best weight: 1.4542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 GLN R 356 ASN R 418 HIS R 818 GLN ** S 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN B 44 GLN B 75 GLN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.115887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.094524 restraints weight = 60218.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.095129 restraints weight = 47447.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.095146 restraints weight = 37495.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.095619 restraints weight = 35511.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.095653 restraints weight = 29586.654| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17211 Z= 0.214 Angle : 0.639 13.467 23483 Z= 0.321 Chirality : 0.044 0.228 2736 Planarity : 0.004 0.045 3021 Dihedral : 4.662 57.401 2482 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.38 % Allowed : 22.06 % Favored : 74.56 % 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 are not related in a simple way. whole: -1.49 (0.17), residues: 2275 helix: 0.70 (0.18), residues: 809 sheet: -1.69 (0.26), residues: 376 loop : -2.08 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 243 TYR 0.019 0.002 TYR R 220 PHE 0.021 0.002 PHE S 365 TRP 0.024 0.002 TRP D 176 HIS 0.007 0.001 HIS S 507 Details of bonding type rmsd covalent geometry : bond 0.00503 (17194) covalent geometry : angle 0.63770 (23449) SS BOND : bond 0.00373 ( 17) SS BOND : angle 1.30145 ( 34) hydrogen bonds : bond 0.03900 ( 715) hydrogen bonds : angle 4.31172 ( 2070) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 266 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 255 LYS cc_start: 0.8011 (tppt) cc_final: 0.7680 (tppt) REVERT: R 306 PHE cc_start: 0.5390 (OUTLIER) cc_final: 0.4724 (p90) REVERT: R 438 MET cc_start: 0.7530 (ttp) cc_final: 0.7088 (ttm) REVERT: S 71 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7607 (ptpp) REVERT: S 112 ASP cc_start: 0.6165 (m-30) cc_final: 0.5918 (m-30) REVERT: S 309 MET cc_start: 0.8102 (tpt) cc_final: 0.7457 (tpt) REVERT: S 414 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.6661 (m-80) REVERT: S 564 MET cc_start: 0.5576 (mmm) cc_final: 0.4631 (mpp) REVERT: S 591 PRO cc_start: 0.8384 (Cg_exo) cc_final: 0.8177 (Cg_endo) REVERT: A 199 PHE cc_start: 0.7020 (m-80) cc_final: 0.6709 (m-80) REVERT: A 210 LYS cc_start: 0.8285 (mmmt) cc_final: 0.8053 (mmmm) REVERT: B 337 LYS cc_start: 0.8678 (ptpt) cc_final: 0.8144 (ptmt) REVERT: B 339 TRP cc_start: 0.8194 (m100) cc_final: 0.7609 (m100) outliers start: 56 outliers final: 43 residues processed: 298 average time/residue: 0.1329 time to fit residues: 59.0418 Evaluate side-chains 285 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 239 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain R residue 254 VAL Chi-restraints excluded: chain R residue 256 ILE Chi-restraints excluded: chain R residue 277 ASN Chi-restraints excluded: chain R residue 306 PHE Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain R residue 368 ASP Chi-restraints excluded: chain R residue 406 VAL Chi-restraints excluded: chain R residue 594 LEU Chi-restraints excluded: chain R residue 626 SER Chi-restraints excluded: chain R residue 628 VAL Chi-restraints excluded: chain R residue 659 LEU Chi-restraints excluded: chain R residue 679 ARG Chi-restraints excluded: chain R residue 787 ILE Chi-restraints excluded: chain R residue 796 ILE Chi-restraints excluded: chain R residue 804 ILE Chi-restraints excluded: chain R residue 816 TYR Chi-restraints excluded: chain R residue 822 LEU Chi-restraints excluded: chain R residue 826 VAL Chi-restraints excluded: chain R residue 837 LEU Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 282 ILE Chi-restraints excluded: chain S residue 413 VAL Chi-restraints excluded: chain S residue 414 TYR Chi-restraints excluded: chain S residue 423 MET Chi-restraints excluded: chain S residue 659 LEU Chi-restraints excluded: chain S residue 847 PHE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 47 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 109 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 200 optimal weight: 0.0070 chunk 110 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 190 optimal weight: 8.9990 chunk 204 optimal weight: 0.8980 chunk 216 optimal weight: 10.0000 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 GLN R 818 GLN ** S 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.110553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.095068 restraints weight = 63206.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.095117 restraints weight = 72155.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.095987 restraints weight = 56744.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.095842 restraints weight = 42716.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.095921 restraints weight = 42016.682| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17211 Z= 0.129 Angle : 0.586 14.174 23483 Z= 0.288 Chirality : 0.041 0.153 2736 Planarity : 0.004 0.042 3021 Dihedral : 4.413 58.292 2482 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.83 % Allowed : 24.17 % Favored : 73.00 % 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 are not related in a simple way. whole: -1.20 (0.17), residues: 2275 helix: 0.99 (0.18), residues: 814 sheet: -1.46 (0.26), residues: 370 loop : -1.99 (0.17), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 529 TYR 0.014 0.001 TYR D 102 PHE 0.026 0.001 PHE R 805 TRP 0.025 0.001 TRP B 82 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00297 (17194) covalent geometry : angle 0.58508 (23449) SS BOND : bond 0.00310 ( 17) SS BOND : angle 1.10141 ( 34) hydrogen bonds : bond 0.03502 ( 715) hydrogen bonds : angle 4.10905 ( 2070) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 264 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 149 ARG cc_start: 0.6648 (mtt90) cc_final: 0.6212 (mtt90) REVERT: R 255 LYS cc_start: 0.7919 (tppt) cc_final: 0.7695 (tppt) REVERT: R 438 MET cc_start: 0.7450 (ttp) cc_final: 0.6985 (ttm) REVERT: R 467 GLU cc_start: 0.7363 (mp0) cc_final: 0.7145 (mp0) REVERT: R 685 LYS cc_start: 0.7944 (tptp) cc_final: 0.7485 (tmmt) REVERT: S 71 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7582 (ptpp) REVERT: S 112 ASP cc_start: 0.6175 (m-30) cc_final: 0.5922 (m-30) REVERT: S 414 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.6674 (m-80) REVERT: S 564 MET cc_start: 0.5039 (mmm) cc_final: 0.4354 (mpp) REVERT: A 186 GLU cc_start: 0.7215 (tp30) cc_final: 0.6246 (tp30) REVERT: A 267 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.6811 (t80) REVERT: B 45 MET cc_start: 0.8401 (tpp) cc_final: 0.7557 (mmm) REVERT: B 188 MET cc_start: 0.8252 (pmm) cc_final: 0.7953 (pmm) REVERT: B 337 LYS cc_start: 0.8537 (ptpt) cc_final: 0.8207 (ptmt) REVERT: B 339 TRP cc_start: 0.7822 (m100) cc_final: 0.7017 (m100) REVERT: D 83 MET cc_start: 0.2723 (mmt) cc_final: 0.2289 (mmt) outliers start: 47 outliers final: 33 residues processed: 291 average time/residue: 0.1239 time to fit residues: 54.1849 Evaluate side-chains 277 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 241 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 256 ILE Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain R residue 368 ASP Chi-restraints excluded: chain R residue 394 ILE Chi-restraints excluded: chain R residue 406 VAL Chi-restraints excluded: chain R residue 519 ILE Chi-restraints excluded: chain R residue 524 CYS Chi-restraints excluded: chain R residue 594 LEU Chi-restraints excluded: chain R residue 628 VAL Chi-restraints excluded: chain R residue 679 ARG Chi-restraints excluded: chain R residue 796 ILE Chi-restraints excluded: chain R residue 822 LEU Chi-restraints excluded: chain R residue 837 LEU Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 282 ILE Chi-restraints excluded: chain S residue 414 TYR Chi-restraints excluded: chain S residue 428 CYS Chi-restraints excluded: chain S residue 659 LEU Chi-restraints excluded: chain S residue 847 PHE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 108 optimal weight: 0.0570 chunk 192 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 GLN R 818 GLN ** S 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 323 HIS ** S 402 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 = 0.3990 r_free = 0.3990 target = 0.114948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.094187 restraints weight = 60020.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.094516 restraints weight = 51037.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.094796 restraints weight = 39945.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.095024 restraints weight = 36827.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.095170 restraints weight = 33817.848| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 17211 Z= 0.253 Angle : 0.684 14.036 23483 Z= 0.344 Chirality : 0.045 0.210 2736 Planarity : 0.004 0.047 3021 Dihedral : 4.854 54.842 2482 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.58 % Allowed : 23.21 % Favored : 72.21 % 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 are not related in a simple way. whole: -1.31 (0.17), residues: 2275 helix: 0.78 (0.18), residues: 818 sheet: -1.54 (0.26), residues: 374 loop : -1.95 (0.17), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 270 TYR 0.026 0.002 TYR R 816 PHE 0.033 0.002 PHE R 362 TRP 0.023 0.002 TRP B 99 HIS 0.008 0.002 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00598 (17194) covalent geometry : angle 0.68110 (23449) SS BOND : bond 0.00648 ( 17) SS BOND : angle 1.70785 ( 34) hydrogen bonds : bond 0.04140 ( 715) hydrogen bonds : angle 4.39433 ( 2070) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 265 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 306 PHE cc_start: 0.5522 (OUTLIER) cc_final: 0.4757 (p90) REVERT: R 438 MET cc_start: 0.7525 (ttp) cc_final: 0.7051 (ttm) REVERT: R 685 LYS cc_start: 0.8133 (tptp) cc_final: 0.7924 (tmtt) REVERT: S 71 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7574 (ptpp) REVERT: S 112 ASP cc_start: 0.6387 (m-30) cc_final: 0.6087 (m-30) REVERT: S 306 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.5933 (p90) REVERT: S 414 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.6619 (m-80) REVERT: S 564 MET cc_start: 0.5746 (mmm) cc_final: 0.4881 (mpp) REVERT: S 791 MET cc_start: 0.8063 (mmp) cc_final: 0.7819 (mmp) REVERT: A 186 GLU cc_start: 0.7246 (tp30) cc_final: 0.6071 (tp30) REVERT: B 45 MET cc_start: 0.8696 (tpp) cc_final: 0.8453 (tpp) REVERT: B 80 ILE cc_start: 0.8256 (tp) cc_final: 0.8011 (tt) REVERT: B 337 LYS cc_start: 0.8638 (ptpt) cc_final: 0.7974 (ptpt) REVERT: B 339 TRP cc_start: 0.8131 (m100) cc_final: 0.7051 (m100) REVERT: D 83 MET cc_start: 0.2845 (mmt) cc_final: 0.2489 (mmt) REVERT: D 160 ARG cc_start: 0.6941 (mmm160) cc_final: 0.6708 (mmm160) outliers start: 76 outliers final: 59 residues processed: 317 average time/residue: 0.1237 time to fit residues: 59.5872 Evaluate side-chains 310 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 247 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain R residue 253 SER Chi-restraints excluded: chain R residue 256 ILE Chi-restraints excluded: chain R residue 277 ASN Chi-restraints excluded: chain R residue 306 PHE Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain R residue 368 ASP Chi-restraints excluded: chain R residue 394 ILE Chi-restraints excluded: chain R residue 406 VAL Chi-restraints excluded: chain R residue 519 ILE Chi-restraints excluded: chain R residue 524 CYS Chi-restraints excluded: chain R residue 594 LEU Chi-restraints excluded: chain R residue 626 SER Chi-restraints excluded: chain R residue 628 VAL Chi-restraints excluded: chain R residue 659 LEU Chi-restraints excluded: chain R residue 679 ARG Chi-restraints excluded: chain R residue 796 ILE Chi-restraints excluded: chain R residue 804 ILE Chi-restraints excluded: chain R residue 820 THR Chi-restraints excluded: chain R residue 822 LEU Chi-restraints excluded: chain R residue 826 VAL Chi-restraints excluded: chain R residue 837 LEU Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 165 VAL Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 282 ILE Chi-restraints excluded: chain S residue 306 PHE Chi-restraints excluded: chain S residue 341 VAL Chi-restraints excluded: chain S residue 352 THR Chi-restraints excluded: chain S residue 392 GLU Chi-restraints excluded: chain S residue 414 TYR Chi-restraints excluded: chain S residue 416 MET Chi-restraints excluded: chain S residue 423 MET Chi-restraints excluded: chain S residue 659 LEU Chi-restraints excluded: chain S residue 847 PHE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 10 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 chunk 127 optimal weight: 0.6980 chunk 2 optimal weight: 0.0980 chunk 121 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 0.0980 chunk 141 optimal weight: 6.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 GLN R 818 GLN S 323 HIS B 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.117368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.097831 restraints weight = 61461.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.097961 restraints weight = 50714.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.098681 restraints weight = 37137.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.098857 restraints weight = 31291.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.099200 restraints weight = 27424.220| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17211 Z= 0.125 Angle : 0.605 14.356 23483 Z= 0.296 Chirality : 0.042 0.172 2736 Planarity : 0.004 0.057 3021 Dihedral : 4.523 56.126 2482 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.98 % Allowed : 24.53 % Favored : 71.49 % 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 are not related in a simple way. whole: -1.11 (0.17), residues: 2275 helix: 1.01 (0.18), residues: 819 sheet: -1.47 (0.26), residues: 386 loop : -1.87 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 270 TYR 0.016 0.001 TYR S 562 PHE 0.024 0.001 PHE R 805 TRP 0.025 0.002 TRP B 82 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00288 (17194) covalent geometry : angle 0.60302 (23449) SS BOND : bond 0.00349 ( 17) SS BOND : angle 1.27378 ( 34) hydrogen bonds : bond 0.03503 ( 715) hydrogen bonds : angle 4.16908 ( 2070) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 266 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 104 ARG cc_start: 0.7122 (ttp-170) cc_final: 0.6844 (ttp-170) REVERT: R 306 PHE cc_start: 0.5482 (OUTLIER) cc_final: 0.4771 (p90) REVERT: R 438 MET cc_start: 0.7467 (ttp) cc_final: 0.6985 (ttm) REVERT: S 71 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7463 (ptpp) REVERT: S 112 ASP cc_start: 0.6286 (m-30) cc_final: 0.5962 (m-30) REVERT: S 306 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.5974 (p90) REVERT: S 414 TYR cc_start: 0.7435 (OUTLIER) cc_final: 0.6648 (m-80) REVERT: A 186 GLU cc_start: 0.7270 (tp30) cc_final: 0.6084 (tp30) REVERT: A 210 LYS cc_start: 0.7916 (mttp) cc_final: 0.7400 (mmmm) REVERT: B 45 MET cc_start: 0.8475 (tpp) cc_final: 0.7666 (mmm) REVERT: B 80 ILE cc_start: 0.8227 (tp) cc_final: 0.7974 (tt) REVERT: B 82 TRP cc_start: 0.6715 (OUTLIER) cc_final: 0.6264 (m-10) REVERT: B 337 LYS cc_start: 0.8595 (ptpt) cc_final: 0.8053 (ptmt) REVERT: B 339 TRP cc_start: 0.7927 (m100) cc_final: 0.6932 (m100) REVERT: D 83 MET cc_start: 0.2918 (mmt) cc_final: 0.2676 (mmt) outliers start: 66 outliers final: 45 residues processed: 310 average time/residue: 0.1233 time to fit residues: 57.8337 Evaluate side-chains 302 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 252 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 253 SER Chi-restraints excluded: chain R residue 254 VAL Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 306 PHE Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain R residue 368 ASP Chi-restraints excluded: chain R residue 406 VAL Chi-restraints excluded: chain R residue 519 ILE Chi-restraints excluded: chain R residue 524 CYS Chi-restraints excluded: chain R residue 594 LEU Chi-restraints excluded: chain R residue 628 VAL Chi-restraints excluded: chain R residue 679 ARG Chi-restraints excluded: chain R residue 787 ILE Chi-restraints excluded: chain R residue 796 ILE Chi-restraints excluded: chain R residue 822 LEU Chi-restraints excluded: chain R residue 837 LEU Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 282 ILE Chi-restraints excluded: chain S residue 306 PHE Chi-restraints excluded: chain S residue 341 VAL Chi-restraints excluded: chain S residue 413 VAL Chi-restraints excluded: chain S residue 414 TYR Chi-restraints excluded: chain S residue 659 LEU Chi-restraints excluded: chain S residue 847 PHE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 37 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 208 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 130 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 chunk 69 optimal weight: 0.0170 chunk 23 optimal weight: 0.5980 chunk 226 optimal weight: 5.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 818 GLN ** S 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.117049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.097164 restraints weight = 62295.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.097078 restraints weight = 50006.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.097794 restraints weight = 38232.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.097799 restraints weight = 34409.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.098086 restraints weight = 30852.600| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17211 Z= 0.158 Angle : 0.637 14.096 23483 Z= 0.311 Chirality : 0.043 0.166 2736 Planarity : 0.004 0.068 3021 Dihedral : 4.523 55.191 2482 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.56 % Allowed : 25.44 % Favored : 71.01 % 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 are not related in a simple way. whole: -1.08 (0.17), residues: 2275 helix: 1.04 (0.18), residues: 821 sheet: -1.48 (0.26), residues: 372 loop : -1.85 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 38 TYR 0.016 0.001 TYR S 562 PHE 0.024 0.001 PHE R 805 TRP 0.028 0.002 TRP B 82 HIS 0.003 0.001 HIS S 305 Details of bonding type rmsd covalent geometry : bond 0.00371 (17194) covalent geometry : angle 0.63576 (23449) SS BOND : bond 0.00273 ( 17) SS BOND : angle 1.25324 ( 34) hydrogen bonds : bond 0.03590 ( 715) hydrogen bonds : angle 4.16622 ( 2070) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 260 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 104 ARG cc_start: 0.7164 (ttp-170) cc_final: 0.6826 (ttp-170) REVERT: R 306 PHE cc_start: 0.5324 (OUTLIER) cc_final: 0.4618 (p90) REVERT: R 438 MET cc_start: 0.7533 (ttp) cc_final: 0.7042 (ttm) REVERT: R 816 TYR cc_start: 0.7475 (t80) cc_final: 0.7259 (t80) REVERT: S 71 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7528 (ptpp) REVERT: S 112 ASP cc_start: 0.6288 (m-30) cc_final: 0.5956 (m-30) REVERT: S 306 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.5943 (p90) REVERT: S 414 TYR cc_start: 0.7432 (OUTLIER) cc_final: 0.6659 (m-80) REVERT: S 791 MET cc_start: 0.7873 (mmp) cc_final: 0.7627 (mmp) REVERT: A 186 GLU cc_start: 0.7260 (tp30) cc_final: 0.6068 (tp30) REVERT: A 210 LYS cc_start: 0.7992 (mttp) cc_final: 0.7430 (mmmm) REVERT: B 80 ILE cc_start: 0.8309 (tp) cc_final: 0.8043 (tt) REVERT: B 82 TRP cc_start: 0.6956 (OUTLIER) cc_final: 0.6705 (m-10) REVERT: B 337 LYS cc_start: 0.8606 (ptpt) cc_final: 0.7883 (ptpt) REVERT: B 339 TRP cc_start: 0.7975 (m100) cc_final: 0.7157 (m100) REVERT: D 67 ARG cc_start: 0.4294 (ptm160) cc_final: 0.3955 (ptm160) REVERT: D 83 MET cc_start: 0.3080 (mmt) cc_final: 0.2856 (mmt) REVERT: D 140 MET cc_start: 0.3739 (tpp) cc_final: 0.3446 (tpp) outliers start: 59 outliers final: 49 residues processed: 301 average time/residue: 0.1278 time to fit residues: 58.3225 Evaluate side-chains 309 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 255 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 253 SER Chi-restraints excluded: chain R residue 254 VAL Chi-restraints excluded: chain R residue 256 ILE Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 306 PHE Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain R residue 368 ASP Chi-restraints excluded: chain R residue 394 ILE Chi-restraints excluded: chain R residue 406 VAL Chi-restraints excluded: chain R residue 519 ILE Chi-restraints excluded: chain R residue 524 CYS Chi-restraints excluded: chain R residue 594 LEU Chi-restraints excluded: chain R residue 628 VAL Chi-restraints excluded: chain R residue 679 ARG Chi-restraints excluded: chain R residue 787 ILE Chi-restraints excluded: chain R residue 796 ILE Chi-restraints excluded: chain R residue 822 LEU Chi-restraints excluded: chain R residue 826 VAL Chi-restraints excluded: chain R residue 837 LEU Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 282 ILE Chi-restraints excluded: chain S residue 306 PHE Chi-restraints excluded: chain S residue 341 VAL Chi-restraints excluded: chain S residue 392 GLU Chi-restraints excluded: chain S residue 413 VAL Chi-restraints excluded: chain S residue 414 TYR Chi-restraints excluded: chain S residue 659 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 167 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 200 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 195 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 139 optimal weight: 30.0000 chunk 181 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 818 GLN D 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.115580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.095505 restraints weight = 59526.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.095804 restraints weight = 46536.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.095844 restraints weight = 35811.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.096144 restraints weight = 34563.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.096180 restraints weight = 30689.633| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17211 Z= 0.145 Angle : 0.630 14.100 23483 Z= 0.306 Chirality : 0.043 0.168 2736 Planarity : 0.004 0.056 3021 Dihedral : 4.486 55.543 2482 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.80 % Allowed : 24.89 % Favored : 71.31 % 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 are not related in a simple way. whole: -0.99 (0.17), residues: 2275 helix: 1.11 (0.18), residues: 821 sheet: -1.45 (0.26), residues: 369 loop : -1.80 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 243 TYR 0.015 0.001 TYR S 562 PHE 0.032 0.001 PHE R 362 TRP 0.026 0.002 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00340 (17194) covalent geometry : angle 0.62864 (23449) SS BOND : bond 0.00274 ( 17) SS BOND : angle 1.12768 ( 34) hydrogen bonds : bond 0.03501 ( 715) hydrogen bonds : angle 4.15603 ( 2070) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 261 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 104 ARG cc_start: 0.7118 (ttp-170) cc_final: 0.6814 (ttp-170) REVERT: R 306 PHE cc_start: 0.5329 (OUTLIER) cc_final: 0.4617 (p90) REVERT: R 438 MET cc_start: 0.7453 (ttp) cc_final: 0.6945 (ttm) REVERT: R 816 TYR cc_start: 0.7473 (t80) cc_final: 0.7262 (t80) REVERT: S 71 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7472 (ptpp) REVERT: S 112 ASP cc_start: 0.6243 (m-30) cc_final: 0.5911 (m-30) REVERT: S 306 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.5959 (p90) REVERT: S 414 TYR cc_start: 0.7362 (OUTLIER) cc_final: 0.6591 (m-80) REVERT: S 534 LYS cc_start: 0.6500 (pttt) cc_final: 0.6187 (tttp) REVERT: S 791 MET cc_start: 0.8056 (mmp) cc_final: 0.7830 (mmp) REVERT: A 186 GLU cc_start: 0.7209 (tp30) cc_final: 0.6011 (tp30) REVERT: A 210 LYS cc_start: 0.8070 (mttp) cc_final: 0.7549 (mmmm) REVERT: B 45 MET cc_start: 0.8268 (tpp) cc_final: 0.7708 (mmm) REVERT: B 80 ILE cc_start: 0.8275 (tp) cc_final: 0.8010 (tt) REVERT: B 82 TRP cc_start: 0.6850 (OUTLIER) cc_final: 0.6647 (m-10) REVERT: B 278 PHE cc_start: 0.8147 (m-80) cc_final: 0.7933 (m-10) REVERT: B 337 LYS cc_start: 0.8552 (ptpt) cc_final: 0.7836 (ptpt) REVERT: D 67 ARG cc_start: 0.4260 (ptm160) cc_final: 0.3883 (ptm160) REVERT: D 140 MET cc_start: 0.3868 (tpp) cc_final: 0.3615 (tpp) outliers start: 63 outliers final: 52 residues processed: 307 average time/residue: 0.1281 time to fit residues: 59.1874 Evaluate side-chains 310 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 253 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 254 VAL Chi-restraints excluded: chain R residue 256 ILE Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 306 PHE Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain R residue 368 ASP Chi-restraints excluded: chain R residue 394 ILE Chi-restraints excluded: chain R residue 406 VAL Chi-restraints excluded: chain R residue 519 ILE Chi-restraints excluded: chain R residue 524 CYS Chi-restraints excluded: chain R residue 594 LEU Chi-restraints excluded: chain R residue 626 SER Chi-restraints excluded: chain R residue 628 VAL Chi-restraints excluded: chain R residue 679 ARG Chi-restraints excluded: chain R residue 787 ILE Chi-restraints excluded: chain R residue 796 ILE Chi-restraints excluded: chain R residue 822 LEU Chi-restraints excluded: chain R residue 837 LEU Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 113 THR Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 282 ILE Chi-restraints excluded: chain S residue 306 PHE Chi-restraints excluded: chain S residue 341 VAL Chi-restraints excluded: chain S residue 392 GLU Chi-restraints excluded: chain S residue 413 VAL Chi-restraints excluded: chain S residue 414 TYR Chi-restraints excluded: chain S residue 659 LEU Chi-restraints excluded: chain S residue 847 PHE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 199 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 0.0670 chunk 110 optimal weight: 0.5980 chunk 224 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 chunk 127 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 818 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.114555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.094758 restraints weight = 59753.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.094576 restraints weight = 53576.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.095055 restraints weight = 39504.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.095200 restraints weight = 36390.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.095392 restraints weight = 33210.797| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17211 Z= 0.151 Angle : 0.645 14.076 23483 Z= 0.315 Chirality : 0.043 0.269 2736 Planarity : 0.004 0.053 3021 Dihedral : 4.504 55.461 2482 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.68 % Allowed : 25.32 % Favored : 71.01 % 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 are not related in a simple way. whole: -0.95 (0.18), residues: 2275 helix: 1.12 (0.18), residues: 820 sheet: -1.46 (0.26), residues: 365 loop : -1.73 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 243 TYR 0.017 0.001 TYR S 562 PHE 0.031 0.001 PHE R 805 TRP 0.026 0.002 TRP B 82 HIS 0.003 0.001 HIS S 305 Details of bonding type rmsd covalent geometry : bond 0.00355 (17194) covalent geometry : angle 0.64378 (23449) SS BOND : bond 0.00272 ( 17) SS BOND : angle 1.16370 ( 34) hydrogen bonds : bond 0.03544 ( 715) hydrogen bonds : angle 4.16413 ( 2070) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 261 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 104 ARG cc_start: 0.7002 (ttp-170) cc_final: 0.6704 (ttp-170) REVERT: R 306 PHE cc_start: 0.5386 (OUTLIER) cc_final: 0.4687 (p90) REVERT: R 438 MET cc_start: 0.7469 (ttp) cc_final: 0.6960 (ttm) REVERT: R 816 TYR cc_start: 0.7491 (t80) cc_final: 0.7288 (t80) REVERT: S 71 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7504 (ptpp) REVERT: S 112 ASP cc_start: 0.6250 (m-30) cc_final: 0.5930 (m-30) REVERT: S 114 HIS cc_start: 0.7133 (OUTLIER) cc_final: 0.6834 (m-70) REVERT: S 306 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.5980 (p90) REVERT: S 414 TYR cc_start: 0.7382 (OUTLIER) cc_final: 0.6618 (m-80) REVERT: S 472 PRO cc_start: 0.6080 (Cg_endo) cc_final: 0.5746 (Cg_exo) REVERT: S 534 LYS cc_start: 0.6562 (pttt) cc_final: 0.6213 (tttp) REVERT: S 791 MET cc_start: 0.8036 (mmp) cc_final: 0.7810 (mmp) REVERT: A 186 GLU cc_start: 0.7167 (tp30) cc_final: 0.5907 (tp30) REVERT: A 210 LYS cc_start: 0.8022 (mttp) cc_final: 0.7469 (mmmm) REVERT: A 256 ASN cc_start: 0.7215 (OUTLIER) cc_final: 0.7000 (p0) REVERT: B 45 MET cc_start: 0.8268 (tpp) cc_final: 0.7639 (mmm) REVERT: B 80 ILE cc_start: 0.8300 (tp) cc_final: 0.8021 (tt) REVERT: B 278 PHE cc_start: 0.8223 (m-80) cc_final: 0.8004 (m-10) REVERT: B 337 LYS cc_start: 0.8530 (ptpt) cc_final: 0.7806 (ptpt) outliers start: 61 outliers final: 49 residues processed: 306 average time/residue: 0.1261 time to fit residues: 58.7555 Evaluate side-chains 313 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 258 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 254 VAL Chi-restraints excluded: chain R residue 256 ILE Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 306 PHE Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain R residue 368 ASP Chi-restraints excluded: chain R residue 394 ILE Chi-restraints excluded: chain R residue 406 VAL Chi-restraints excluded: chain R residue 519 ILE Chi-restraints excluded: chain R residue 524 CYS Chi-restraints excluded: chain R residue 594 LEU Chi-restraints excluded: chain R residue 626 SER Chi-restraints excluded: chain R residue 628 VAL Chi-restraints excluded: chain R residue 679 ARG Chi-restraints excluded: chain R residue 787 ILE Chi-restraints excluded: chain R residue 796 ILE Chi-restraints excluded: chain R residue 822 LEU Chi-restraints excluded: chain R residue 826 VAL Chi-restraints excluded: chain R residue 837 LEU Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 113 THR Chi-restraints excluded: chain S residue 114 HIS Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 282 ILE Chi-restraints excluded: chain S residue 306 PHE Chi-restraints excluded: chain S residue 341 VAL Chi-restraints excluded: chain S residue 352 THR Chi-restraints excluded: chain S residue 392 GLU Chi-restraints excluded: chain S residue 413 VAL Chi-restraints excluded: chain S residue 414 TYR Chi-restraints excluded: chain S residue 659 LEU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 0.0070 chunk 192 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 23 optimal weight: 0.4980 chunk 112 optimal weight: 7.9990 chunk 185 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 223 optimal weight: 0.0980 overall best weight: 0.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 818 GLN S 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.114953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.095278 restraints weight = 59263.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.095668 restraints weight = 44449.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.095799 restraints weight = 33888.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.095915 restraints weight = 30128.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.096055 restraints weight = 30670.775| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17211 Z= 0.127 Angle : 0.637 14.058 23483 Z= 0.308 Chirality : 0.042 0.233 2736 Planarity : 0.004 0.050 3021 Dihedral : 4.417 56.552 2482 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.01 % Allowed : 26.10 % Favored : 70.89 % 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 are not related in a simple way. whole: -0.85 (0.18), residues: 2275 helix: 1.17 (0.18), residues: 827 sheet: -1.42 (0.26), residues: 377 loop : -1.65 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 243 TYR 0.017 0.001 TYR S 562 PHE 0.034 0.001 PHE S 789 TRP 0.030 0.002 TRP B 82 HIS 0.004 0.001 HIS S 305 Details of bonding type rmsd covalent geometry : bond 0.00295 (17194) covalent geometry : angle 0.63616 (23449) SS BOND : bond 0.00236 ( 17) SS BOND : angle 1.03706 ( 34) hydrogen bonds : bond 0.03393 ( 715) hydrogen bonds : angle 4.11811 ( 2070) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3592.19 seconds wall clock time: 62 minutes 26.25 seconds (3746.25 seconds total)