Starting phenix.real_space_refine on Sun May 18 15:22:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jd6_36177/05_2025/8jd6_36177.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jd6_36177/05_2025/8jd6_36177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jd6_36177/05_2025/8jd6_36177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jd6_36177/05_2025/8jd6_36177.map" model { file = "/net/cci-nas-00/data/ceres_data/8jd6_36177/05_2025/8jd6_36177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jd6_36177/05_2025/8jd6_36177.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.899 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 114 5.16 5 Cl 1 4.86 5 C 10941 2.51 5 N 2938 2.21 5 O 3196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17192 Number of models: 1 Model: "" Number of chains: 8 Chain: "S" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5700 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 36, 'TRANS': 724} Chain breaks: 4 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 260 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 196 Chain: "R" Number of atoms: 5779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 5779 Classifications: {'peptide': 774} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 38, 'TRANS': 735} Chain breaks: 4 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 407 Unresolved non-hydrogen dihedrals: 279 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 3, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 195 Chain: "D" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1730 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 114 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2188 Classifications: {'peptide': 301} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 4, 'TRANS': 296} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 90 Chain: "A" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1643 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 97 Chain: "S" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'BK0': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "R" 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: 10.47, per 1000 atoms: 0.61 Number of scatterers: 17192 At special positions: 0 Unit cell: (98.23, 128.535, 231.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 114 16.00 P 2 15.00 O 3196 8.00 N 2938 7.00 C 10941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 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 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 D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 159 " - pdb=" SG CYS D 229 " 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: 4.50 Conformation dependent library (CDL) restraints added in 2.2 seconds 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4294 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 28 sheets defined 38.4% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'S' and resid 74 through 92 Processing helix chain 'S' and resid 111 through 124 Processing helix chain 'S' and resid 158 through 172 removed outlier: 3.660A pdb=" N MET S 164 " --> pdb=" O SER S 160 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE S 168 " --> pdb=" O MET S 164 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU S 171 " --> pdb=" O ASN S 167 " (cutoff:3.500A) removed outlier: 3.873A 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: 3.901A pdb=" N GLN S 205 " --> pdb=" O SER S 201 " (cutoff:3.500A) Processing helix chain 'S' and resid 228 through 245 removed outlier: 3.532A pdb=" N GLU S 232 " --> pdb=" O GLY S 228 " (cutoff:3.500A) Processing helix chain 'S' and resid 264 through 274 removed outlier: 3.591A pdb=" N ILE S 269 " --> pdb=" O PHE S 265 " (cutoff:3.500A) Processing helix chain 'S' and resid 286 through 300 removed outlier: 3.611A pdb=" N ARG S 292 " --> pdb=" O ASP S 288 " (cutoff:3.500A) Processing helix chain 'S' and resid 311 through 315 Processing helix chain 'S' and resid 341 through 349 Processing helix chain 'S' and resid 361 through 370 Processing helix chain 'S' and resid 405 through 427 Processing helix chain 'S' and resid 435 through 439 Processing helix chain 'S' and resid 442 through 452 Processing helix chain 'S' and resid 502 through 506 removed outlier: 3.505A pdb=" N ARG S 505 " --> pdb=" O ARG S 502 " (cutoff:3.500A) Processing helix chain 'S' and resid 588 through 612 Processing helix chain 'S' and resid 623 through 644 removed outlier: 4.431A pdb=" N ILE S 644 " --> pdb=" O THR S 640 " (cutoff:3.500A) Processing helix chain 'S' and resid 648 through 683 removed outlier: 3.588A pdb=" N SER S 666 " --> pdb=" O GLY S 662 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR S 667 " --> pdb=" O MET S 663 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU S 670 " --> pdb=" O SER S 666 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN S 683 " --> pdb=" O ARG S 679 " (cutoff:3.500A) Processing helix chain 'S' and resid 695 through 719 removed outlier: 4.078A pdb=" N VAL S 719 " --> pdb=" O CYS S 715 " (cutoff:3.500A) Processing helix chain 'S' and resid 749 through 775 removed outlier: 3.602A pdb=" N LEU S 753 " --> pdb=" O SER S 749 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU S 756 " --> pdb=" O SER S 752 " (cutoff:3.500A) Processing helix chain 'S' and resid 784 through 808 removed outlier: 3.637A pdb=" N ILE S 802 " --> pdb=" O TRP S 798 " (cutoff:3.500A) Proline residue: S 803 - end of helix Processing helix chain 'S' and resid 817 through 838 removed outlier: 3.750A pdb=" N LEU S 822 " --> pdb=" O GLN S 818 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR S 823 " --> pdb=" O THR S 819 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER S 833 " --> pdb=" O SER S 829 " (cutoff:3.500A) Processing helix chain 'S' and resid 838 through 848 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: 3.633A pdb=" N ASN R 167 " --> pdb=" O ILE R 163 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE R 168 " --> pdb=" O MET R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 188 Processing helix chain 'R' and resid 201 through 216 removed outlier: 3.501A pdb=" N GLN R 205 " --> pdb=" O SER R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 230 through 244 Processing helix chain 'R' and resid 263 through 275 removed outlier: 3.790A pdb=" N THR R 275 " --> pdb=" O ARG R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 301 Processing helix chain 'R' and resid 341 through 350 removed outlier: 3.521A pdb=" N SER R 350 " --> pdb=" O ARG R 346 " (cutoff:3.500A) Processing helix chain 'R' and resid 359 through 367 removed outlier: 3.996A pdb=" N ALA R 363 " --> pdb=" O ASN R 359 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU R 364 " --> pdb=" O ILE R 360 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 428 Processing helix chain 'R' and resid 435 through 439 Processing helix chain 'R' and resid 442 through 452 removed outlier: 3.663A pdb=" N LEU R 446 " --> pdb=" O ASP R 442 " (cutoff:3.500A) Processing helix chain 'R' and resid 502 through 506 removed outlier: 3.570A pdb=" N ARG R 505 " --> pdb=" O ARG R 502 " (cutoff:3.500A) Processing helix chain 'R' and resid 588 through 612 removed outlier: 3.626A pdb=" N GLY R 598 " --> pdb=" O LEU R 594 " (cutoff:3.500A) Processing helix chain 'R' and resid 615 through 621 Processing helix chain 'R' and resid 623 through 645 removed outlier: 4.088A pdb=" N TYR R 627 " --> pdb=" O ARG R 623 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL R 628 " --> pdb=" O GLU R 624 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU R 629 " --> pdb=" O LEU R 625 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR R 640 " --> pdb=" O CYS R 636 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE R 641 " --> pdb=" O TYR R 637 " (cutoff:3.500A) Processing helix chain 'R' and resid 648 through 685 removed outlier: 3.893A pdb=" N SER R 664 " --> pdb=" O GLY R 660 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER R 666 " --> pdb=" O GLY R 662 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TYR R 667 " --> pdb=" O MET R 663 " (cutoff:3.500A) Processing helix chain 'R' and resid 695 through 721 removed outlier: 3.714A pdb=" N GLN R 710 " --> pdb=" O LEU R 706 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY R 713 " --> pdb=" O LEU R 709 " (cutoff:3.500A) Processing helix chain 'R' and resid 749 through 774 Processing helix chain 'R' and resid 784 through 808 Proline residue: R 803 - end of helix removed outlier: 3.780A pdb=" N THR R 808 " --> pdb=" O ILE R 804 " (cutoff:3.500A) Processing helix chain 'R' and resid 813 through 848 removed outlier: 3.533A pdb=" N THR R 819 " --> pdb=" O LEU R 815 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR R 820 " --> pdb=" O TYR R 816 " (cutoff:3.500A) Proline residue: R 840 - end of helix removed outlier: 3.582A pdb=" N HIS R 848 " --> pdb=" O ILE R 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 56 removed outlier: 3.796A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.550A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 36 removed outlier: 4.235A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 33 Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.583A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 50' Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.607A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 212' Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 241 through 254 removed outlier: 3.786A pdb=" N SER A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.022A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 308 removed outlier: 3.542A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 350 removed outlier: 3.547A pdb=" N ASP A 337 " --> pdb=" O GLN A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing sheet with id=AA1, first strand: chain 'S' and resid 105 through 107 removed outlier: 7.524A pdb=" N THR S 50 " --> pdb=" O GLY S 152 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N ILE S 154 " --> pdb=" O THR S 50 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLY S 52 " --> pdb=" O ILE S 154 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ILE S 177 " --> pdb=" O VAL S 151 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL S 153 " --> pdb=" O ILE S 177 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S' and resid 249 through 256 removed outlier: 6.728A pdb=" N VAL S 221 " --> pdb=" O ILE S 250 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLN S 252 " --> pdb=" O VAL S 221 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TYR S 220 " --> pdb=" O ALA S 280 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE S 282 " --> pdb=" O TYR S 220 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER S 222 " --> pdb=" O ILE S 282 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL S 281 " --> pdb=" O MET S 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 455 through 456 removed outlier: 4.079A pdb=" N PHE S 455 " --> pdb=" O VAL S 463 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 530 through 532 Processing sheet with id=AA5, first strand: chain 'S' and resid 550 through 551 Processing sheet with id=AA6, first strand: chain 'S' and resid 578 through 579 Processing sheet with id=AA7, first strand: chain 'R' and resid 43 through 45 removed outlier: 3.717A pdb=" N ALA R 103 " --> pdb=" O ILE R 45 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE R 49 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ARG R 104 " --> pdb=" O ILE R 49 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU R 51 " --> pdb=" O ARG R 104 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU R 106 " --> pdb=" O LEU R 51 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLY R 53 " --> pdb=" O LEU R 106 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY R 152 " --> pdb=" O THR R 50 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL R 153 " --> pdb=" O ILE R 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 58 through 60 removed outlier: 4.896A pdb=" N GLU R 69 " --> pdb=" O GLY R 59 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 249 through 256 removed outlier: 7.770A pdb=" N VAL R 221 " --> pdb=" O ALA R 251 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N SER R 253 " --> pdb=" O VAL R 221 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR R 223 " --> pdb=" O SER R 253 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LYS R 255 " --> pdb=" O THR R 223 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA R 225 " --> pdb=" O LYS R 255 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA R 280 " --> pdb=" O TYR R 220 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA R 331 " --> pdb=" O TYR R 480 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N GLN R 479 " --> pdb=" O VAL R 491 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VAL R 491 " --> pdb=" O GLN R 479 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLN R 481 " --> pdb=" O TYR R 489 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N TYR R 489 " --> pdb=" O GLN R 481 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 454 through 455 Processing sheet with id=AB2, first strand: chain 'R' and resid 530 through 532 Processing sheet with id=AB3, first strand: chain 'R' and resid 549 through 550 Processing sheet with id=AB4, first strand: chain 'R' and resid 565 through 566 removed outlier: 4.101A pdb=" N ARG R 565 " --> pdb=" O ARG R 574 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG R 574 " --> pdb=" O ARG R 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.603A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 50 through 51 removed outlier: 3.689A pdb=" N HIS D 35 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL D 97 " --> pdb=" O HIS D 35 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 45 through 46 Processing sheet with id=AB8, first strand: chain 'D' and resid 159 through 160 removed outlier: 3.920A pdb=" N PHE D 212 " --> pdb=" O CYS D 159 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 185 through 187 Processing sheet with id=AC1, first strand: chain 'D' and resid 189 through 190 removed outlier: 3.618A pdb=" N ASN D 194 " --> pdb=" O TYR D 190 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 51 removed outlier: 4.049A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY B 319 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 60 through 63 removed outlier: 4.496A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.606A pdb=" N CYS B 114 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 146 through 148 removed outlier: 3.884A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 156 through 157 removed outlier: 6.477A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 187 through 191 removed outlier: 4.614A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.372A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.590A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 186 through 190 removed outlier: 3.769A pdb=" N THR A 187 " --> pdb=" O MET A 198 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS A 322 " --> pdb=" O LEU A 266 " (cutoff:3.500A) 740 hydrogen bonds defined for protein. 2088 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: 6.13 Time building geometry restraints manager: 5.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2790 1.31 - 1.44: 4833 1.44 - 1.57: 9775 1.57 - 1.69: 8 1.69 - 1.82: 158 Bond restraints: 17564 Sorted by residual: bond pdb=" C07 BK0 S1001 " pdb=" N09 BK0 S1001 " ideal model delta sigma weight residual 1.358 1.454 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" N ASP D 74 " pdb=" CA ASP D 74 " ideal model delta sigma weight residual 1.461 1.488 -0.027 9.20e-03 1.18e+04 8.56e+00 bond pdb=" N ILE S 694 " pdb=" CA ILE S 694 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.51e+00 bond pdb=" N THR D 78 " pdb=" CA THR D 78 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.09e-02 8.42e+03 8.42e+00 bond pdb=" C10 BK0 S1001 " pdb=" N09 BK0 S1001 " ideal model delta sigma weight residual 1.397 1.455 -0.058 2.00e-02 2.50e+03 8.40e+00 ... (remaining 17559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 23415 1.73 - 3.47: 440 3.47 - 5.20: 58 5.20 - 6.94: 11 6.94 - 8.67: 4 Bond angle restraints: 23928 Sorted by residual: angle pdb=" C LEU A 234 " pdb=" CA LEU A 234 " pdb=" CB LEU A 234 " ideal model delta sigma weight residual 116.54 110.72 5.82 1.15e+00 7.56e-01 2.56e+01 angle pdb=" N ILE R 694 " pdb=" CA ILE R 694 " pdb=" C ILE R 694 " ideal model delta sigma weight residual 112.80 108.15 4.65 1.15e+00 7.56e-01 1.64e+01 angle pdb=" N PRO S 696 " pdb=" CA PRO S 696 " pdb=" C PRO S 696 " ideal model delta sigma weight residual 113.53 107.93 5.60 1.39e+00 5.18e-01 1.63e+01 angle pdb=" N LYS D 76 " pdb=" CA LYS D 76 " pdb=" C LYS D 76 " ideal model delta sigma weight residual 113.28 109.05 4.23 1.22e+00 6.72e-01 1.20e+01 angle pdb=" CA LEU D 79 " pdb=" C LEU D 79 " pdb=" O LEU D 79 " ideal model delta sigma weight residual 121.45 118.10 3.35 1.07e+00 8.73e-01 9.80e+00 ... (remaining 23923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9172 17.98 - 35.95: 940 35.95 - 53.93: 215 53.93 - 71.90: 29 71.90 - 89.88: 7 Dihedral angle restraints: 10363 sinusoidal: 3694 harmonic: 6669 Sorted by residual: dihedral pdb=" CB CYS S 249 " pdb=" SG CYS S 249 " pdb=" SG CYS S 538 " pdb=" CB CYS S 538 " ideal model delta sinusoidal sigma weight residual -86.00 -173.95 87.95 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS R 524 " pdb=" SG CYS R 524 " pdb=" SG CYS R 542 " pdb=" CB CYS R 542 " ideal model delta sinusoidal sigma weight residual 93.00 159.39 -66.39 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CB CYS S 372 " pdb=" SG CYS S 372 " pdb=" SG CYS S 388 " pdb=" CB CYS S 388 " ideal model delta sinusoidal sigma weight residual 93.00 41.79 51.21 1 1.00e+01 1.00e-02 3.59e+01 ... (remaining 10360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2058 0.042 - 0.083: 509 0.083 - 0.125: 182 0.125 - 0.166: 13 0.166 - 0.208: 8 Chirality restraints: 2770 Sorted by residual: chirality pdb=" CB ILE D 58 " pdb=" CA ILE D 58 " pdb=" CG1 ILE D 58 " pdb=" CG2 ILE D 58 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE R 677 " pdb=" N ILE R 677 " pdb=" C ILE R 677 " pdb=" CB ILE R 677 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.49e-01 chirality pdb=" CA ILE R 694 " pdb=" N ILE R 694 " pdb=" C ILE R 694 " pdb=" CB ILE R 694 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.86e-01 ... (remaining 2767 not shown) Planarity restraints: 3062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 679 " -0.193 9.50e-02 1.11e+02 8.66e-02 4.60e+00 pdb=" NE ARG R 679 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG R 679 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG R 679 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG R 679 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 231 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" CG ASP A 231 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASP A 231 " -0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP A 231 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET R 839 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO R 840 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO R 840 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 840 " 0.021 5.00e-02 4.00e+02 ... (remaining 3059 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2110 2.75 - 3.29: 17304 3.29 - 3.83: 29396 3.83 - 4.36: 32875 4.36 - 4.90: 57263 Nonbonded interactions: 138948 Sorted by model distance: nonbonded pdb=" OG SER D 193 " pdb=" O GLY D 205 " model vdw 2.218 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THR R 734 " pdb=" O ALA R 740 " model vdw 2.268 3.040 nonbonded pdb=" OG SER D 106 " pdb=" OD2 ASP D 109 " model vdw 2.278 3.040 nonbonded pdb=" O GLN R 118 " pdb=" OG1 THR R 121 " model vdw 2.281 3.040 ... (remaining 138943 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 93 or (resid 94 and (name N or name CA or name \ C or name O or name CB )) or resid 95 through 126 or resid 148 through 172 or (r \ esid 173 and (name N or name CA or name C or name O or name CB )) or resid 174 t \ hrough 266 or (resid 267 and (name N or name CA or name C or name O or name CB ) \ ) or resid 268 through 276 or (resid 277 through 280 and (name N or name CA or n \ ame C or name O or name CB )) or resid 281 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 3 \ 00 or (resid 301 and (name N or name CA or name C or name O or name CB )) or res \ id 302 through 321 or (resid 322 through 326 and (name N or name CA or name C or \ name O or name CB )) or resid 327 through 373 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 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 (resid 488 and (name \ N or name CA or name C or name O or name CB )) or resid 489 through 503 or (resi \ d 504 and (name N or name CA or name C or name O or name CB )) or resid 505 thro \ ugh 550 or (resid 551 through 556 and (name N or name CA or name C or name O or \ name CB )) or resid 557 through 582 or (resid 583 and (name N or name CA or name \ C or name O or name CB )) or resid 584 through 618 or (resid 619 through 620 an \ d (name N or name CA or name C or name O or name CB )) or resid 621 through 648 \ or (resid 649 and (name N or name CA or name C or name O or name CB )) or resid \ 650 through 654 or (resid 655 and (name N or name CA or name C or name O or name \ CB )) or resid 656 through 681 or (resid 682 and (name N or name CA or name C o \ r name O or name CB )) or resid 683 or (resid 692 through 694 and (name N or nam \ e CA or name C or name O or name CB )) or resid 695 through 699 or (resid 700 th \ rough 701 and (name N or name CA or name C or name O or name CB )) or resid 702 \ through 706 or (resid 707 and (name N or name CA or name C or name O or name CB \ )) or resid 708 through 711 or (resid 712 and (name N or name CA or name C or na \ me O or name CB )) or resid 713 through 723 or (resid 724 and (name N or name CA \ or name C or name O or name CB )) or resid 725 through 732 or (resid 733 and (n \ ame N or name CA or name C or name O or name CB )) or resid 734 or (resid 735 an \ d (name N or name CA or name C or name O or name CB )) or resid 736 through 743 \ or (resid 744 through 745 and (name N or name CA or name C or name O or name CB \ )) or resid 746 or (resid 747 through 749 and (name N or name CA or name C or na \ me O or name CB )) or resid 750 or (resid 751 through 752 and (name N or name CA \ or name C or name O or name CB )) or resid 753 or (resid 754 and (name N or nam \ e CA or name C or name O or name CB )) or resid 755 through 768 or (resid 769 an \ d (name N or name CA or name C or name O or name CB )) or resid 770 through 772 \ or (resid 773 and (name N or name CA or name C or name O or name CB )) or resid \ 774 through 847 or (resid 848 and (name N or name CA or name C or name O or name \ CB )) or resid 1001)) selection = (chain 'S' and (resid 41 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 70 or (resid 71 through 72 and (na \ me N or name CA or name C or name O or name CB )) or resid 73 through 278 or (re \ sid 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 o \ r name CB )) or resid 292 through 322 or (resid 323 through 326 and (name N or n \ ame CA or name C or name O or name CB )) or resid 327 through 341 or (resid 342 \ and (name N or name CA or name C or name O or name CB )) or resid 343 through 35 \ 3 or (resid 354 and (name N or name CA or name C or name O or name CB )) or resi \ d 355 through 373 or (resid 386 through 387 and (name N or name CA or name C or \ name O or name CB )) or resid 388 through 400 or (resid 401 and (name N or name \ CA or name C or name O or name CB )) or resid 402 through 483 or resid 487 throu \ gh 521 or (resid 522 and (name N or name CA or name C or name O or name CB )) or \ resid 523 through 529 or (resid 530 and (name N or name CA or name C or name O \ or name CB )) or resid 531 or (resid 532 through 534 and (name N or name CA or n \ ame 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 name O or name CB )) or resid 544 throu \ gh 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 name CA or name C or name O or name CB ) \ ) or resid 549 or (resid 550 through 556 and (name N or name CA or name C or nam \ e 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 563 or (resid 564 and (na \ me N or name CA or name C or name O or name CB )) or resid 565 through 567 or (r \ esid 568 and (name N or name CA or name C or name O or name CB )) or resid 569 o \ r (resid 570 through 571 and (name N or name CA or name C or name O or name CB ) \ ) or resid 572 through 578 or (resid 579 through 583 and (name N or name CA or n \ ame C or name O or name CB )) or resid 584 through 591 or (resid 592 and (name N \ or name CA or name C or name O or name CB )) or resid 593 through 607 or (resid \ 608 and (name N or name CA or name C or name O or name CB )) or resid 609 throu \ gh 613 or (resid 614 and (name N or name CA or name C or name O or name CB )) or \ resid 615 through 653 or (resid 654 through 655 and (name N or name CA or name \ C or name O or name CB )) or resid 656 through 715 or (resid 716 and (name N or \ name CA or name C or name O or name CB )) or resid 717 through 718 or (resid 719 \ and (name N or name CA or name C or name O or name CB )) or resid 720 through 7 \ 25 or (resid 726 and (name N or name CA or name C or name O or name CB )) or res \ id 727 or (resid 728 through 729 and (name N or name CA or name C or name O or n \ ame CB )) or resid 730 or (resid 731 and (name N or name CA or name C or name O \ or name CB )) or resid 732 through 737 or (resid 738 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 7 \ 51 or (resid 752 and (name N or name CA or name C or name O or name CB )) or res \ id 753 through 760 or (resid 761 through 762 and (name N or name CA or name C or \ name O or name CB )) or resid 763 through 848 or resid 1002)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 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: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 40.780 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.080 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 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 0.096 17582 Z= 0.181 Angle : 0.565 8.674 23964 Z= 0.329 Chirality : 0.042 0.208 2770 Planarity : 0.004 0.087 3062 Dihedral : 15.115 89.879 6015 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.93 % Favored : 94.03 % Rotamer: Outliers : 0.35 % Allowed : 18.40 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.18), residues: 2278 helix: 1.44 (0.19), residues: 801 sheet: -0.78 (0.30), residues: 358 loop : -1.91 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 211 HIS 0.009 0.000 HIS D 167 PHE 0.017 0.001 PHE S 806 TYR 0.019 0.001 TYR D 59 ARG 0.009 0.000 ARG S 270 Details of bonding type rmsd hydrogen bonds : bond 0.18330 ( 740) hydrogen bonds : angle 6.41452 ( 2088) SS BOND : bond 0.00120 ( 18) SS BOND : angle 0.45661 ( 36) covalent geometry : bond 0.00292 (17564) covalent geometry : angle 0.56542 (23928) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 223 time to evaluate : 1.989 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 226 average time/residue: 0.2597 time to fit residues: 92.5449 Evaluate side-chains 207 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 204 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain B residue 93 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 193 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 179 optimal weight: 0.0040 chunk 69 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.205673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.180457 restraints weight = 22308.240| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.69 r_work: 0.3858 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17582 Z= 0.183 Angle : 0.608 8.800 23964 Z= 0.321 Chirality : 0.044 0.169 2770 Planarity : 0.004 0.054 3062 Dihedral : 4.897 72.006 2498 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.24 % Favored : 92.71 % Rotamer: Outliers : 3.69 % Allowed : 16.32 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.18), residues: 2278 helix: 1.25 (0.18), residues: 804 sheet: -1.15 (0.29), residues: 359 loop : -1.82 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 111 HIS 0.007 0.001 HIS D 167 PHE 0.025 0.002 PHE D 239 TYR 0.021 0.002 TYR D 103 ARG 0.008 0.001 ARG R 270 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 740) hydrogen bonds : angle 4.75544 ( 2088) SS BOND : bond 0.00237 ( 18) SS BOND : angle 0.64125 ( 36) covalent geometry : bond 0.00427 (17564) covalent geometry : angle 0.60818 (23928) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 248 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 603 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7120 (mm) REVERT: R 112 ASP cc_start: 0.6597 (m-30) cc_final: 0.6262 (m-30) REVERT: D 117 LEU cc_start: 0.3467 (tp) cc_final: 0.3235 (tp) REVERT: B 225 HIS cc_start: 0.3221 (OUTLIER) cc_final: 0.2539 (t-170) outliers start: 64 outliers final: 34 residues processed: 295 average time/residue: 0.2766 time to fit residues: 128.1871 Evaluate side-chains 247 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 254 VAL Chi-restraints excluded: chain S residue 414 TYR Chi-restraints excluded: chain S residue 564 MET Chi-restraints excluded: chain S residue 568 GLU Chi-restraints excluded: chain S residue 603 LEU Chi-restraints excluded: chain S residue 644 ILE Chi-restraints excluded: chain S residue 718 PHE Chi-restraints excluded: chain S residue 736 ASP Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain R residue 618 VAL Chi-restraints excluded: chain R residue 626 SER Chi-restraints excluded: chain R residue 644 ILE Chi-restraints excluded: chain R residue 712 LEU Chi-restraints excluded: chain R residue 714 ILE Chi-restraints excluded: chain R residue 780 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 311 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 99 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 189 optimal weight: 0.0170 chunk 176 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 38 optimal weight: 0.0670 chunk 95 optimal weight: 0.4980 chunk 227 optimal weight: 0.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 98 ASN S 305 HIS D 167 HIS D 183 GLN B 311 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.208198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.184059 restraints weight = 22390.027| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 2.51 r_work: 0.3898 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17582 Z= 0.116 Angle : 0.531 9.164 23964 Z= 0.277 Chirality : 0.042 0.228 2770 Planarity : 0.004 0.046 3062 Dihedral : 4.764 77.423 2496 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.60 % Allowed : 19.67 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.18), residues: 2278 helix: 1.49 (0.18), residues: 809 sheet: -1.14 (0.29), residues: 360 loop : -1.81 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.003 0.000 HIS B 54 PHE 0.024 0.001 PHE D 239 TYR 0.021 0.001 TYR D 190 ARG 0.006 0.000 ARG D 218 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 740) hydrogen bonds : angle 4.53907 ( 2088) SS BOND : bond 0.00134 ( 18) SS BOND : angle 1.06919 ( 36) covalent geometry : bond 0.00263 (17564) covalent geometry : angle 0.52969 (23928) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 224 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 603 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7094 (mm) REVERT: R 112 ASP cc_start: 0.6441 (m-30) cc_final: 0.6180 (m-30) REVERT: R 843 TYR cc_start: 0.7404 (t80) cc_final: 0.6964 (t80) REVERT: D 117 LEU cc_start: 0.3547 (tp) cc_final: 0.3275 (tp) REVERT: B 146 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6949 (tt) REVERT: B 225 HIS cc_start: 0.3371 (OUTLIER) cc_final: 0.2662 (t-170) outliers start: 45 outliers final: 24 residues processed: 256 average time/residue: 0.2794 time to fit residues: 110.2727 Evaluate side-chains 232 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 254 VAL Chi-restraints excluded: chain S residue 414 TYR Chi-restraints excluded: chain S residue 603 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 122 PHE Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain R residue 618 VAL Chi-restraints excluded: chain R residue 626 SER Chi-restraints excluded: chain R residue 644 ILE Chi-restraints excluded: chain R residue 746 CYS Chi-restraints excluded: chain R residue 834 LEU Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 311 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 179 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 193 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 115 optimal weight: 0.0980 chunk 2 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 818 GLN R 402 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.199535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.176021 restraints weight = 21631.869| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.18 r_work: 0.3803 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17582 Z= 0.237 Angle : 0.670 10.873 23964 Z= 0.351 Chirality : 0.046 0.202 2770 Planarity : 0.004 0.053 3062 Dihedral : 5.370 75.837 2496 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.61 % Allowed : 18.97 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.18), residues: 2278 helix: 1.08 (0.18), residues: 815 sheet: -1.52 (0.28), residues: 351 loop : -1.92 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.008 0.001 HIS B 54 PHE 0.028 0.002 PHE R 681 TYR 0.027 0.002 TYR D 103 ARG 0.041 0.001 ARG R 270 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 740) hydrogen bonds : angle 4.89470 ( 2088) SS BOND : bond 0.00524 ( 18) SS BOND : angle 1.11169 ( 36) covalent geometry : bond 0.00556 (17564) covalent geometry : angle 0.66937 (23928) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 230 time to evaluate : 1.845 Fit side-chains revert: symmetry clash REVERT: S 216 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7549 (mp) REVERT: S 400 TYR cc_start: 0.5720 (OUTLIER) cc_final: 0.4188 (p90) REVERT: S 603 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7493 (mm) REVERT: R 112 ASP cc_start: 0.6339 (m-30) cc_final: 0.5841 (m-30) REVERT: R 843 TYR cc_start: 0.7791 (t80) cc_final: 0.7410 (t80) REVERT: B 119 ASN cc_start: 0.8318 (m-40) cc_final: 0.7933 (m-40) REVERT: B 225 HIS cc_start: 0.4089 (OUTLIER) cc_final: 0.3740 (t-170) REVERT: B 278 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.5608 (m-80) outliers start: 80 outliers final: 46 residues processed: 292 average time/residue: 0.2624 time to fit residues: 119.3245 Evaluate side-chains 252 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 201 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 254 VAL Chi-restraints excluded: chain S residue 256 ILE Chi-restraints excluded: chain S residue 340 SER Chi-restraints excluded: chain S residue 400 TYR Chi-restraints excluded: chain S residue 414 TYR Chi-restraints excluded: chain S residue 564 MET Chi-restraints excluded: chain S residue 568 GLU Chi-restraints excluded: chain S residue 603 LEU Chi-restraints excluded: chain S residue 644 ILE Chi-restraints excluded: chain S residue 736 ASP Chi-restraints excluded: chain S residue 847 PHE Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain R residue 618 VAL Chi-restraints excluded: chain R residue 626 SER Chi-restraints excluded: chain R residue 644 ILE Chi-restraints excluded: chain R residue 712 LEU Chi-restraints excluded: chain R residue 714 ILE Chi-restraints excluded: chain R residue 780 THR Chi-restraints excluded: chain R residue 791 MET Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 231 GLN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 327 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 82 optimal weight: 1.9990 chunk 192 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 221 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 216 optimal weight: 0.5980 chunk 152 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 189 ASN ** R 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN A 294 ASN A 346 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.201285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.177888 restraints weight = 21893.301| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 2.28 r_work: 0.3834 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17582 Z= 0.152 Angle : 0.587 10.057 23964 Z= 0.306 Chirality : 0.044 0.255 2770 Planarity : 0.004 0.052 3062 Dihedral : 5.211 82.101 2496 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.21 % Allowed : 20.93 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.18), residues: 2278 helix: 1.17 (0.18), residues: 824 sheet: -1.67 (0.28), residues: 353 loop : -1.90 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 63 HIS 0.004 0.001 HIS A 322 PHE 0.019 0.002 PHE A 336 TYR 0.023 0.001 TYR D 190 ARG 0.009 0.000 ARG R 270 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 740) hydrogen bonds : angle 4.67414 ( 2088) SS BOND : bond 0.00197 ( 18) SS BOND : angle 1.20664 ( 36) covalent geometry : bond 0.00356 (17564) covalent geometry : angle 0.58568 (23928) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 224 time to evaluate : 1.875 Fit side-chains revert: symmetry clash REVERT: S 216 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7528 (mp) REVERT: S 603 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7494 (mm) REVERT: R 45 ILE cc_start: 0.5858 (OUTLIER) cc_final: 0.5618 (pt) REVERT: R 112 ASP cc_start: 0.6280 (m-30) cc_final: 0.5823 (m-30) REVERT: R 270 ARG cc_start: 0.7855 (ptt-90) cc_final: 0.7588 (ptt-90) REVERT: D 183 GLN cc_start: 0.7650 (tt0) cc_final: 0.7422 (tt0) REVERT: B 119 ASN cc_start: 0.8171 (m-40) cc_final: 0.7910 (m-40) REVERT: B 225 HIS cc_start: 0.4456 (OUTLIER) cc_final: 0.4075 (t-170) REVERT: B 278 PHE cc_start: 0.6864 (OUTLIER) cc_final: 0.5530 (m-80) REVERT: A 186 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: A 252 SER cc_start: 0.8343 (p) cc_final: 0.8106 (m) outliers start: 73 outliers final: 46 residues processed: 283 average time/residue: 0.2484 time to fit residues: 111.9798 Evaluate side-chains 253 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 201 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 254 VAL Chi-restraints excluded: chain S residue 269 ILE Chi-restraints excluded: chain S residue 340 SER Chi-restraints excluded: chain S residue 464 THR Chi-restraints excluded: chain S residue 564 MET Chi-restraints excluded: chain S residue 603 LEU Chi-restraints excluded: chain S residue 718 PHE Chi-restraints excluded: chain S residue 847 PHE Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain R residue 618 VAL Chi-restraints excluded: chain R residue 626 SER Chi-restraints excluded: chain R residue 639 THR Chi-restraints excluded: chain R residue 644 ILE Chi-restraints excluded: chain R residue 712 LEU Chi-restraints excluded: chain R residue 714 ILE Chi-restraints excluded: chain R residue 834 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 231 GLN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 327 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 92 optimal weight: 4.9990 chunk 50 optimal weight: 0.0040 chunk 61 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 145 optimal weight: 0.1980 chunk 195 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 189 ASN ** R 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.200969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.176630 restraints weight = 21892.541| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 2.31 r_work: 0.3815 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17582 Z= 0.144 Angle : 0.574 10.140 23964 Z= 0.298 Chirality : 0.043 0.246 2770 Planarity : 0.004 0.055 3062 Dihedral : 5.152 84.408 2496 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.16 % Favored : 92.80 % Rotamer: Outliers : 4.67 % Allowed : 21.05 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.18), residues: 2278 helix: 1.20 (0.18), residues: 829 sheet: -1.61 (0.27), residues: 367 loop : -1.90 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 63 HIS 0.004 0.001 HIS A 322 PHE 0.021 0.002 PHE S 806 TYR 0.024 0.001 TYR D 190 ARG 0.013 0.000 ARG R 270 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 740) hydrogen bonds : angle 4.59943 ( 2088) SS BOND : bond 0.00257 ( 18) SS BOND : angle 0.98217 ( 36) covalent geometry : bond 0.00338 (17564) covalent geometry : angle 0.57340 (23928) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 222 time to evaluate : 1.904 Fit side-chains REVERT: S 216 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7519 (mp) REVERT: S 400 TYR cc_start: 0.5823 (OUTLIER) cc_final: 0.4404 (p90) REVERT: R 45 ILE cc_start: 0.5885 (OUTLIER) cc_final: 0.5490 (pt) REVERT: R 112 ASP cc_start: 0.6258 (m-30) cc_final: 0.5733 (m-30) REVERT: R 270 ARG cc_start: 0.8048 (ptt-90) cc_final: 0.7374 (ptp90) REVERT: R 836 MET cc_start: 0.7844 (ppp) cc_final: 0.7493 (ptp) REVERT: R 843 TYR cc_start: 0.7774 (t80) cc_final: 0.7376 (t80) REVERT: B 119 ASN cc_start: 0.8010 (m-40) cc_final: 0.7794 (m-40) REVERT: B 225 HIS cc_start: 0.4635 (OUTLIER) cc_final: 0.4253 (t-170) REVERT: B 278 PHE cc_start: 0.6854 (OUTLIER) cc_final: 0.5599 (m-80) REVERT: A 186 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7462 (tm-30) REVERT: A 252 SER cc_start: 0.8311 (p) cc_final: 0.8045 (m) outliers start: 81 outliers final: 57 residues processed: 283 average time/residue: 0.2717 time to fit residues: 121.7107 Evaluate side-chains 266 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 203 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 254 VAL Chi-restraints excluded: chain S residue 269 ILE Chi-restraints excluded: chain S residue 340 SER Chi-restraints excluded: chain S residue 400 TYR Chi-restraints excluded: chain S residue 414 TYR Chi-restraints excluded: chain S residue 464 THR Chi-restraints excluded: chain S residue 564 MET Chi-restraints excluded: chain S residue 644 ILE Chi-restraints excluded: chain S residue 718 PHE Chi-restraints excluded: chain S residue 808 THR Chi-restraints excluded: chain S residue 822 LEU Chi-restraints excluded: chain S residue 842 VAL Chi-restraints excluded: chain S residue 847 PHE Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain R residue 573 CYS Chi-restraints excluded: chain R residue 618 VAL Chi-restraints excluded: chain R residue 626 SER Chi-restraints excluded: chain R residue 639 THR Chi-restraints excluded: chain R residue 644 ILE Chi-restraints excluded: chain R residue 712 LEU Chi-restraints excluded: chain R residue 714 ILE Chi-restraints excluded: chain R residue 754 ILE Chi-restraints excluded: chain R residue 791 MET Chi-restraints excluded: chain R residue 820 THR Chi-restraints excluded: chain R residue 834 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 231 GLN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 327 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 210 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 181 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 176 GLN S 189 ASN ** R 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 306 GLN A 346 ASN A 347 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.196408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.171646 restraints weight = 21813.003| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 2.30 r_work: 0.3757 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 17582 Z= 0.196 Angle : 0.626 11.174 23964 Z= 0.327 Chirality : 0.045 0.261 2770 Planarity : 0.004 0.052 3062 Dihedral : 5.278 78.649 2496 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.59 % Favored : 92.36 % Rotamer: Outliers : 4.38 % Allowed : 21.68 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.18), residues: 2278 helix: 1.03 (0.18), residues: 828 sheet: -1.66 (0.27), residues: 376 loop : -2.00 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 63 HIS 0.004 0.001 HIS A 322 PHE 0.023 0.002 PHE S 806 TYR 0.024 0.002 TYR D 190 ARG 0.007 0.000 ARG D 218 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 740) hydrogen bonds : angle 4.79740 ( 2088) SS BOND : bond 0.00188 ( 18) SS BOND : angle 1.07472 ( 36) covalent geometry : bond 0.00463 (17564) covalent geometry : angle 0.62554 (23928) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 218 time to evaluate : 1.821 Fit side-chains REVERT: S 164 MET cc_start: 0.7571 (ttm) cc_final: 0.7210 (ttm) REVERT: S 216 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7481 (mp) REVERT: S 266 ASP cc_start: 0.7002 (p0) cc_final: 0.6106 (p0) REVERT: S 270 ARG cc_start: 0.7679 (ptp90) cc_final: 0.7127 (mtm-85) REVERT: S 400 TYR cc_start: 0.5845 (OUTLIER) cc_final: 0.4161 (p90) REVERT: S 603 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7218 (mm) REVERT: R 112 ASP cc_start: 0.6249 (m-30) cc_final: 0.5778 (m-30) REVERT: R 270 ARG cc_start: 0.8087 (ptt-90) cc_final: 0.7536 (ptp90) REVERT: R 594 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7830 (tp) REVERT: R 663 MET cc_start: 0.6133 (tpt) cc_final: 0.5431 (tpt) REVERT: B 118 ASP cc_start: 0.8143 (t0) cc_final: 0.7938 (t0) REVERT: B 119 ASN cc_start: 0.8175 (m-40) cc_final: 0.7955 (m-40) REVERT: B 278 PHE cc_start: 0.6898 (OUTLIER) cc_final: 0.5654 (m-80) outliers start: 76 outliers final: 62 residues processed: 281 average time/residue: 0.2655 time to fit residues: 116.2249 Evaluate side-chains 271 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 204 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 72 LYS Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 189 ASN Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 254 VAL Chi-restraints excluded: chain S residue 269 ILE Chi-restraints excluded: chain S residue 340 SER Chi-restraints excluded: chain S residue 400 TYR Chi-restraints excluded: chain S residue 414 TYR Chi-restraints excluded: chain S residue 464 THR Chi-restraints excluded: chain S residue 564 MET Chi-restraints excluded: chain S residue 603 LEU Chi-restraints excluded: chain S residue 644 ILE Chi-restraints excluded: chain S residue 718 PHE Chi-restraints excluded: chain S residue 821 THR Chi-restraints excluded: chain S residue 822 LEU Chi-restraints excluded: chain S residue 842 VAL Chi-restraints excluded: chain S residue 847 PHE Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain R residue 573 CYS Chi-restraints excluded: chain R residue 594 LEU Chi-restraints excluded: chain R residue 618 VAL Chi-restraints excluded: chain R residue 626 SER Chi-restraints excluded: chain R residue 639 THR Chi-restraints excluded: chain R residue 644 ILE Chi-restraints excluded: chain R residue 712 LEU Chi-restraints excluded: chain R residue 714 ILE Chi-restraints excluded: chain R residue 754 ILE Chi-restraints excluded: chain R residue 791 MET Chi-restraints excluded: chain R residue 820 THR Chi-restraints excluded: chain R residue 834 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 231 GLN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 311 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 37 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 81 optimal weight: 0.0040 chunk 169 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN A 294 ASN A 346 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.199074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.173628 restraints weight = 21795.891| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.25 r_work: 0.3801 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17582 Z= 0.143 Angle : 0.588 10.129 23964 Z= 0.305 Chirality : 0.043 0.266 2770 Planarity : 0.004 0.052 3062 Dihedral : 5.190 83.969 2496 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.51 % Favored : 92.45 % Rotamer: Outliers : 4.44 % Allowed : 21.80 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.18), residues: 2278 helix: 1.16 (0.18), residues: 830 sheet: -1.61 (0.27), residues: 369 loop : -1.98 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.004 0.001 HIS A 322 PHE 0.020 0.002 PHE S 806 TYR 0.024 0.002 TYR A 302 ARG 0.008 0.000 ARG D 218 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 740) hydrogen bonds : angle 4.66166 ( 2088) SS BOND : bond 0.00131 ( 18) SS BOND : angle 0.87276 ( 36) covalent geometry : bond 0.00335 (17564) covalent geometry : angle 0.58776 (23928) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 210 time to evaluate : 1.801 Fit side-chains revert: symmetry clash REVERT: S 216 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7421 (mp) REVERT: S 266 ASP cc_start: 0.6909 (p0) cc_final: 0.5987 (p0) REVERT: S 270 ARG cc_start: 0.7571 (ptp90) cc_final: 0.7133 (mtm-85) REVERT: S 400 TYR cc_start: 0.5742 (OUTLIER) cc_final: 0.3996 (p90) REVERT: S 603 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7144 (mm) REVERT: S 612 TYR cc_start: 0.6841 (m-80) cc_final: 0.6466 (m-10) REVERT: S 847 PHE cc_start: 0.5405 (OUTLIER) cc_final: 0.4880 (m-10) REVERT: R 112 ASP cc_start: 0.6125 (m-30) cc_final: 0.5718 (m-30) REVERT: R 594 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7768 (tp) REVERT: R 843 TYR cc_start: 0.7735 (t80) cc_final: 0.7303 (t80) REVERT: R 846 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7677 (pp) REVERT: D 38 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7569 (ptt-90) REVERT: B 118 ASP cc_start: 0.8245 (t0) cc_final: 0.8006 (t0) REVERT: B 119 ASN cc_start: 0.8216 (m-40) cc_final: 0.7997 (m-40) REVERT: B 278 PHE cc_start: 0.6829 (OUTLIER) cc_final: 0.5536 (m-80) REVERT: A 186 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7517 (tm-30) outliers start: 77 outliers final: 60 residues processed: 266 average time/residue: 0.2680 time to fit residues: 112.1177 Evaluate side-chains 266 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 197 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 72 LYS Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 254 VAL Chi-restraints excluded: chain S residue 269 ILE Chi-restraints excluded: chain S residue 340 SER Chi-restraints excluded: chain S residue 400 TYR Chi-restraints excluded: chain S residue 414 TYR Chi-restraints excluded: chain S residue 464 THR Chi-restraints excluded: chain S residue 564 MET Chi-restraints excluded: chain S residue 568 GLU Chi-restraints excluded: chain S residue 603 LEU Chi-restraints excluded: chain S residue 718 PHE Chi-restraints excluded: chain S residue 842 VAL Chi-restraints excluded: chain S residue 847 PHE Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 163 ILE Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 333 THR Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain R residue 573 CYS Chi-restraints excluded: chain R residue 594 LEU Chi-restraints excluded: chain R residue 618 VAL Chi-restraints excluded: chain R residue 626 SER Chi-restraints excluded: chain R residue 639 THR Chi-restraints excluded: chain R residue 644 ILE Chi-restraints excluded: chain R residue 712 LEU Chi-restraints excluded: chain R residue 714 ILE Chi-restraints excluded: chain R residue 754 ILE Chi-restraints excluded: chain R residue 791 MET Chi-restraints excluded: chain R residue 834 LEU Chi-restraints excluded: chain R residue 846 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 231 GLN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 327 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 226 optimal weight: 0.9990 chunk 228 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 35 optimal weight: 20.0000 chunk 224 optimal weight: 0.6980 chunk 181 optimal weight: 0.5980 chunk 180 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 174 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 189 ASN B 230 ASN B 340 ASN A 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.198340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.174170 restraints weight = 21858.538| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.30 r_work: 0.3786 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17582 Z= 0.154 Angle : 0.595 10.613 23964 Z= 0.309 Chirality : 0.044 0.254 2770 Planarity : 0.004 0.052 3062 Dihedral : 5.179 84.169 2496 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.81 % Favored : 92.14 % Rotamer: Outliers : 4.27 % Allowed : 21.91 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.18), residues: 2278 helix: 1.17 (0.18), residues: 829 sheet: -1.61 (0.27), residues: 377 loop : -1.99 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 798 HIS 0.005 0.001 HIS A 322 PHE 0.021 0.002 PHE S 806 TYR 0.024 0.002 TYR D 190 ARG 0.007 0.000 ARG D 218 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 740) hydrogen bonds : angle 4.66707 ( 2088) SS BOND : bond 0.00141 ( 18) SS BOND : angle 0.88843 ( 36) covalent geometry : bond 0.00364 (17564) covalent geometry : angle 0.59490 (23928) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 210 time to evaluate : 1.927 Fit side-chains revert: symmetry clash REVERT: S 216 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7370 (mp) REVERT: S 266 ASP cc_start: 0.6952 (p0) cc_final: 0.6057 (p0) REVERT: S 270 ARG cc_start: 0.7456 (ptp90) cc_final: 0.7084 (mtm-85) REVERT: S 387 LYS cc_start: 0.6360 (tppt) cc_final: 0.5609 (tptt) REVERT: S 400 TYR cc_start: 0.5877 (OUTLIER) cc_final: 0.4171 (p90) REVERT: S 603 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7054 (mm) REVERT: S 847 PHE cc_start: 0.5385 (OUTLIER) cc_final: 0.4916 (m-10) REVERT: R 112 ASP cc_start: 0.6157 (m-30) cc_final: 0.5764 (m-30) REVERT: R 594 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7802 (tp) REVERT: R 663 MET cc_start: 0.6030 (tpt) cc_final: 0.5426 (tpt) REVERT: R 704 PHE cc_start: 0.7334 (m-10) cc_final: 0.6723 (m-80) REVERT: R 843 TYR cc_start: 0.7773 (t80) cc_final: 0.7356 (t80) REVERT: R 846 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7629 (pp) REVERT: D 20 LEU cc_start: 0.4738 (tp) cc_final: 0.4478 (tp) REVERT: D 38 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7576 (ptt-90) REVERT: D 180 ARG cc_start: 0.7019 (mtm110) cc_final: 0.6297 (mtm110) REVERT: D 183 GLN cc_start: 0.7457 (pp30) cc_final: 0.6785 (pt0) REVERT: B 118 ASP cc_start: 0.8213 (t0) cc_final: 0.7961 (t0) REVERT: B 119 ASN cc_start: 0.8165 (m-40) cc_final: 0.7954 (m-40) REVERT: B 278 PHE cc_start: 0.6846 (OUTLIER) cc_final: 0.5542 (m-80) REVERT: A 186 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7505 (tm-30) outliers start: 74 outliers final: 62 residues processed: 267 average time/residue: 0.2692 time to fit residues: 112.2244 Evaluate side-chains 277 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 206 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 72 LYS Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 189 ASN Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 254 VAL Chi-restraints excluded: chain S residue 269 ILE Chi-restraints excluded: chain S residue 340 SER Chi-restraints excluded: chain S residue 400 TYR Chi-restraints excluded: chain S residue 414 TYR Chi-restraints excluded: chain S residue 464 THR Chi-restraints excluded: chain S residue 564 MET Chi-restraints excluded: chain S residue 568 GLU Chi-restraints excluded: chain S residue 603 LEU Chi-restraints excluded: chain S residue 718 PHE Chi-restraints excluded: chain S residue 746 CYS Chi-restraints excluded: chain S residue 842 VAL Chi-restraints excluded: chain S residue 847 PHE Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 163 ILE Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 333 THR Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain R residue 573 CYS Chi-restraints excluded: chain R residue 594 LEU Chi-restraints excluded: chain R residue 618 VAL Chi-restraints excluded: chain R residue 626 SER Chi-restraints excluded: chain R residue 639 THR Chi-restraints excluded: chain R residue 644 ILE Chi-restraints excluded: chain R residue 712 LEU Chi-restraints excluded: chain R residue 714 ILE Chi-restraints excluded: chain R residue 754 ILE Chi-restraints excluded: chain R residue 791 MET Chi-restraints excluded: chain R residue 846 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 231 GLN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 327 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 166 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 75 optimal weight: 0.5980 chunk 177 optimal weight: 3.9990 chunk 114 optimal weight: 0.0270 chunk 47 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 189 ASN R 114 HIS B 230 ASN A 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.198398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.173814 restraints weight = 21738.770| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.25 r_work: 0.3798 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17582 Z= 0.152 Angle : 0.595 10.219 23964 Z= 0.309 Chirality : 0.043 0.249 2770 Planarity : 0.004 0.052 3062 Dihedral : 5.171 84.719 2496 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.99 % Favored : 91.97 % Rotamer: Outliers : 4.56 % Allowed : 21.80 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.18), residues: 2278 helix: 1.18 (0.18), residues: 828 sheet: -1.53 (0.27), residues: 371 loop : -2.00 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 798 HIS 0.005 0.001 HIS A 322 PHE 0.021 0.002 PHE S 806 TYR 0.025 0.002 TYR A 302 ARG 0.008 0.000 ARG D 218 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 740) hydrogen bonds : angle 4.65727 ( 2088) SS BOND : bond 0.00135 ( 18) SS BOND : angle 0.89392 ( 36) covalent geometry : bond 0.00358 (17564) covalent geometry : angle 0.59471 (23928) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 212 time to evaluate : 1.849 Fit side-chains revert: symmetry clash REVERT: S 216 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7370 (mp) REVERT: S 266 ASP cc_start: 0.6901 (p0) cc_final: 0.5996 (p0) REVERT: S 270 ARG cc_start: 0.7421 (ptp90) cc_final: 0.7090 (mtm-85) REVERT: S 387 LYS cc_start: 0.6354 (tppt) cc_final: 0.5648 (tptt) REVERT: S 400 TYR cc_start: 0.5916 (OUTLIER) cc_final: 0.4227 (p90) REVERT: S 603 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7015 (mm) REVERT: S 847 PHE cc_start: 0.5405 (OUTLIER) cc_final: 0.4925 (m-10) REVERT: R 112 ASP cc_start: 0.6182 (m-30) cc_final: 0.5844 (m-30) REVERT: R 594 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7800 (tp) REVERT: R 663 MET cc_start: 0.5992 (tpt) cc_final: 0.5399 (tpt) REVERT: R 704 PHE cc_start: 0.7315 (m-10) cc_final: 0.6748 (m-80) REVERT: R 843 TYR cc_start: 0.7758 (t80) cc_final: 0.7337 (t80) REVERT: R 846 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7643 (pp) REVERT: D 38 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7565 (ptt-90) REVERT: D 160 ARG cc_start: 0.6681 (ptm-80) cc_final: 0.6088 (ttp-110) REVERT: D 183 GLN cc_start: 0.7441 (pp30) cc_final: 0.7234 (pp30) REVERT: B 118 ASP cc_start: 0.8219 (t0) cc_final: 0.7960 (t0) REVERT: B 119 ASN cc_start: 0.8141 (m-40) cc_final: 0.7933 (m-40) REVERT: B 278 PHE cc_start: 0.6806 (OUTLIER) cc_final: 0.5522 (m-80) REVERT: A 186 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7488 (tm-30) outliers start: 79 outliers final: 67 residues processed: 272 average time/residue: 0.2678 time to fit residues: 113.9139 Evaluate side-chains 281 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 205 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 72 LYS Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 189 ASN Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 254 VAL Chi-restraints excluded: chain S residue 269 ILE Chi-restraints excluded: chain S residue 340 SER Chi-restraints excluded: chain S residue 400 TYR Chi-restraints excluded: chain S residue 414 TYR Chi-restraints excluded: chain S residue 464 THR Chi-restraints excluded: chain S residue 564 MET Chi-restraints excluded: chain S residue 568 GLU Chi-restraints excluded: chain S residue 603 LEU Chi-restraints excluded: chain S residue 644 ILE Chi-restraints excluded: chain S residue 718 PHE Chi-restraints excluded: chain S residue 746 CYS Chi-restraints excluded: chain S residue 822 LEU Chi-restraints excluded: chain S residue 842 VAL Chi-restraints excluded: chain S residue 847 PHE Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 163 ILE Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 333 THR Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain R residue 573 CYS Chi-restraints excluded: chain R residue 594 LEU Chi-restraints excluded: chain R residue 618 VAL Chi-restraints excluded: chain R residue 626 SER Chi-restraints excluded: chain R residue 639 THR Chi-restraints excluded: chain R residue 644 ILE Chi-restraints excluded: chain R residue 712 LEU Chi-restraints excluded: chain R residue 714 ILE Chi-restraints excluded: chain R residue 754 ILE Chi-restraints excluded: chain R residue 780 THR Chi-restraints excluded: chain R residue 791 MET Chi-restraints excluded: chain R residue 846 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 231 GLN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 327 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 180 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 202 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 340 ASN A 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.196980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.171944 restraints weight = 21792.819| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.34 r_work: 0.3766 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17582 Z= 0.169 Angle : 0.615 10.510 23964 Z= 0.318 Chirality : 0.044 0.243 2770 Planarity : 0.004 0.052 3062 Dihedral : 5.215 83.335 2496 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.86 % Favored : 92.10 % Rotamer: Outliers : 4.50 % Allowed : 22.26 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.18), residues: 2278 helix: 1.15 (0.18), residues: 826 sheet: -1.56 (0.27), residues: 373 loop : -2.00 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 587 HIS 0.005 0.001 HIS A 322 PHE 0.022 0.002 PHE R 847 TYR 0.024 0.002 TYR D 190 ARG 0.008 0.000 ARG D 218 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 740) hydrogen bonds : angle 4.69366 ( 2088) SS BOND : bond 0.00148 ( 18) SS BOND : angle 0.91408 ( 36) covalent geometry : bond 0.00398 (17564) covalent geometry : angle 0.61425 (23928) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7834.70 seconds wall clock time: 136 minutes 56.19 seconds (8216.19 seconds total)