Starting phenix.real_space_refine on Mon Oct 26 09:49:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jee_61414/10_2026/9jee_61414.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jee_61414/10_2026/9jee_61414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jee_61414/10_2026/9jee_61414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jee_61414/10_2026/9jee_61414.map" model { file = "/net/cci-nas-00/data/ceres_data/9jee_61414/10_2026/9jee_61414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jee_61414/10_2026/9jee_61414.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 124 5.16 5 C 13524 2.51 5 N 3296 2.21 5 O 3696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20660 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4974 Classifications: {'peptide': 612} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 14, 'TRANS': 597} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4974 Classifications: {'peptide': 612} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 14, 'TRANS': 597} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4974 Classifications: {'peptide': 612} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 14, 'TRANS': 597} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 191 Unusual residues: {'GRQ': 1, 'POV': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 191 Unusual residues: {'GRQ': 1, 'POV': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 191 Unusual residues: {'GRQ': 1, 'POV': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 7 Restraints were copied for chains: C Time building chain proxies: 7.51, per 1000 atoms: 0.36 Number of scatterers: 20660 At special positions: 0 Unit cell: (119.48, 119.48, 122.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 P 20 15.00 O 3696 8.00 N 3296 7.00 C 13524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 708.3 milliseconds 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4680 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 59.8% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 120 through 130 removed outlier: 4.267A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 146 removed outlier: 3.710A pdb=" N LEU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 removed outlier: 3.601A pdb=" N LEU A 162 " --> pdb=" O MET A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.691A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 177 " --> pdb=" O MET A 173 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 228 through 237 Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.868A pdb=" N VAL A 278 " --> pdb=" O GLN A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 315 through 329 Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.700A pdb=" N LEU A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 4.058A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 457 removed outlier: 3.617A pdb=" N SER A 444 " --> pdb=" O MET A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 490 removed outlier: 3.555A pdb=" N PHE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 485 through 490' Processing helix chain 'A' and resid 490 through 505 Processing helix chain 'A' and resid 510 through 515 removed outlier: 3.528A pdb=" N GLN A 514 " --> pdb=" O PRO A 510 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 510 through 515' Processing helix chain 'A' and resid 520 through 542 Processing helix chain 'A' and resid 551 through 559 removed outlier: 3.639A pdb=" N MET A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 568 removed outlier: 3.620A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 576 Processing helix chain 'A' and resid 577 through 586 removed outlier: 3.640A pdb=" N ILE A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 609 removed outlier: 3.542A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'A' and resid 624 through 637 Processing helix chain 'A' and resid 650 through 681 removed outlier: 3.836A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 681 " --> pdb=" O MET A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 706 removed outlier: 3.590A pdb=" N TRP A 692 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 712 Processing helix chain 'B' and resid 120 through 130 removed outlier: 4.267A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 146 removed outlier: 3.710A pdb=" N LEU B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU B 144 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 removed outlier: 3.601A pdb=" N LEU B 162 " --> pdb=" O MET B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.691A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU B 177 " --> pdb=" O MET B 173 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 197 Processing helix chain 'B' and resid 218 through 223 Processing helix chain 'B' and resid 228 through 237 Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.868A pdb=" N VAL B 278 " --> pdb=" O GLN B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 315 through 329 Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 353 through 362 Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.700A pdb=" N LEU B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 4.058A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 457 removed outlier: 3.617A pdb=" N SER B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 490 removed outlier: 3.555A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 485 through 490' Processing helix chain 'B' and resid 490 through 505 Processing helix chain 'B' and resid 510 through 515 removed outlier: 3.528A pdb=" N GLN B 514 " --> pdb=" O PRO B 510 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 510 through 515' Processing helix chain 'B' and resid 520 through 542 Processing helix chain 'B' and resid 551 through 559 removed outlier: 3.639A pdb=" N MET B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 568 removed outlier: 3.620A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 576 Processing helix chain 'B' and resid 577 through 586 removed outlier: 3.640A pdb=" N ILE B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 609 removed outlier: 3.542A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'B' and resid 624 through 637 Processing helix chain 'B' and resid 650 through 681 removed outlier: 3.836A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL B 681 " --> pdb=" O MET B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 706 removed outlier: 3.590A pdb=" N TRP B 692 " --> pdb=" O SER B 688 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 712 Processing helix chain 'C' and resid 120 through 130 removed outlier: 4.267A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 146 removed outlier: 3.710A pdb=" N LEU C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU C 144 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.601A pdb=" N LEU C 162 " --> pdb=" O MET C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.691A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU C 177 " --> pdb=" O MET C 173 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 197 Processing helix chain 'C' and resid 218 through 223 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 266 through 272 Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.868A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 Processing helix chain 'C' and resid 315 through 329 Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 353 through 362 Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.699A pdb=" N LEU C 420 " --> pdb=" O ARG C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 4.058A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 457 removed outlier: 3.618A pdb=" N SER C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 490 removed outlier: 3.555A pdb=" N PHE C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 485 through 490' Processing helix chain 'C' and resid 490 through 505 Processing helix chain 'C' and resid 510 through 515 removed outlier: 3.529A pdb=" N GLN C 514 " --> pdb=" O PRO C 510 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER C 515 " --> pdb=" O SER C 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 510 through 515' Processing helix chain 'C' and resid 520 through 542 Processing helix chain 'C' and resid 551 through 559 removed outlier: 3.639A pdb=" N MET C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 568 removed outlier: 3.620A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 576 Processing helix chain 'C' and resid 577 through 586 removed outlier: 3.640A pdb=" N ILE C 583 " --> pdb=" O ILE C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 609 removed outlier: 3.541A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'C' and resid 624 through 637 Processing helix chain 'C' and resid 650 through 681 removed outlier: 3.836A pdb=" N LEU C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL C 681 " --> pdb=" O MET C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 706 removed outlier: 3.590A pdb=" N TRP C 692 " --> pdb=" O SER C 688 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS C 705 " --> pdb=" O LEU C 701 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 712 Processing helix chain 'D' and resid 120 through 130 removed outlier: 4.267A pdb=" N PHE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 146 removed outlier: 3.710A pdb=" N LEU D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU D 144 " --> pdb=" O VAL D 140 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 removed outlier: 3.601A pdb=" N LEU D 162 " --> pdb=" O MET D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.691A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU D 177 " --> pdb=" O MET D 173 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 197 Processing helix chain 'D' and resid 218 through 223 Processing helix chain 'D' and resid 228 through 237 Processing helix chain 'D' and resid 266 through 272 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.868A pdb=" N VAL D 278 " --> pdb=" O GLN D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'D' and resid 315 through 329 Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 353 through 362 Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.700A pdb=" N LEU D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 4.058A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 457 removed outlier: 3.617A pdb=" N SER D 444 " --> pdb=" O MET D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 490 removed outlier: 3.554A pdb=" N PHE D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 485 through 490' Processing helix chain 'D' and resid 490 through 505 Processing helix chain 'D' and resid 510 through 515 removed outlier: 3.528A pdb=" N GLN D 514 " --> pdb=" O PRO D 510 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER D 515 " --> pdb=" O SER D 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 510 through 515' Processing helix chain 'D' and resid 520 through 542 Processing helix chain 'D' and resid 551 through 559 removed outlier: 3.639A pdb=" N MET D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 568 removed outlier: 3.620A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 576 Processing helix chain 'D' and resid 577 through 586 removed outlier: 3.640A pdb=" N ILE D 583 " --> pdb=" O ILE D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 609 removed outlier: 3.542A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'D' and resid 624 through 637 Processing helix chain 'D' and resid 650 through 681 removed outlier: 3.836A pdb=" N LEU D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL D 681 " --> pdb=" O MET D 677 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 706 removed outlier: 3.590A pdb=" N TRP D 692 " --> pdb=" O SER D 688 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 712 Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 382 removed outlier: 6.595A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 377 through 382 removed outlier: 6.595A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 377 through 382 removed outlier: 6.596A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 377 through 382 removed outlier: 6.595A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) 896 hydrogen bonds defined for protein. 2592 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3224 1.32 - 1.44: 5636 1.44 - 1.57: 11956 1.57 - 1.69: 40 1.69 - 1.82: 204 Bond restraints: 21060 Sorted by residual: bond pdb=" C6 GRQ D 806 " pdb=" C7 GRQ D 806 " ideal model delta sigma weight residual 1.453 1.541 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C6 GRQ C 805 " pdb=" C7 GRQ C 805 " ideal model delta sigma weight residual 1.453 1.541 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C6 GRQ A 804 " pdb=" C7 GRQ A 804 " ideal model delta sigma weight residual 1.453 1.541 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C6 GRQ B 805 " pdb=" C7 GRQ B 805 " ideal model delta sigma weight residual 1.453 1.541 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C4 GRQ B 805 " pdb=" C5 GRQ B 805 " ideal model delta sigma weight residual 1.499 1.555 -0.056 2.00e-02 2.50e+03 7.74e+00 ... (remaining 21055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 28235 3.92 - 7.84: 117 7.84 - 11.76: 12 11.76 - 15.69: 8 15.69 - 19.61: 4 Bond angle restraints: 28376 Sorted by residual: angle pdb=" C4 GRQ D 806 " pdb=" C5 GRQ D 806 " pdb=" C8 GRQ D 806 " ideal model delta sigma weight residual 115.45 95.84 19.61 3.00e+00 1.11e-01 4.27e+01 angle pdb=" C4 GRQ B 805 " pdb=" C5 GRQ B 805 " pdb=" C8 GRQ B 805 " ideal model delta sigma weight residual 115.45 95.84 19.61 3.00e+00 1.11e-01 4.27e+01 angle pdb=" C4 GRQ A 804 " pdb=" C5 GRQ A 804 " pdb=" C8 GRQ A 804 " ideal model delta sigma weight residual 115.45 95.84 19.61 3.00e+00 1.11e-01 4.27e+01 angle pdb=" C4 GRQ C 805 " pdb=" C5 GRQ C 805 " pdb=" C8 GRQ C 805 " ideal model delta sigma weight residual 115.45 95.88 19.57 3.00e+00 1.11e-01 4.26e+01 angle pdb=" C5 GRQ D 806 " pdb=" C6 GRQ D 806 " pdb=" C7 GRQ D 806 " ideal model delta sigma weight residual 125.02 111.04 13.98 3.00e+00 1.11e-01 2.17e+01 ... (remaining 28371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 10665 18.00 - 35.99: 1483 35.99 - 53.99: 456 53.99 - 71.98: 60 71.98 - 89.98: 36 Dihedral angle restraints: 12700 sinusoidal: 5492 harmonic: 7208 Sorted by residual: dihedral pdb=" CB CYS D 612 " pdb=" SG CYS D 612 " pdb=" SG CYS D 619 " pdb=" CB CYS D 619 " ideal model delta sinusoidal sigma weight residual -86.00 -39.06 -46.94 1 1.00e+01 1.00e-02 3.05e+01 dihedral pdb=" CB CYS C 612 " pdb=" SG CYS C 612 " pdb=" SG CYS C 619 " pdb=" CB CYS C 619 " ideal model delta sinusoidal sigma weight residual -86.00 -39.07 -46.93 1 1.00e+01 1.00e-02 3.04e+01 dihedral pdb=" CB CYS A 612 " pdb=" SG CYS A 612 " pdb=" SG CYS A 619 " pdb=" CB CYS A 619 " ideal model delta sinusoidal sigma weight residual -86.00 -39.09 -46.91 1 1.00e+01 1.00e-02 3.04e+01 ... (remaining 12697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2195 0.036 - 0.072: 790 0.072 - 0.108: 135 0.108 - 0.144: 32 0.144 - 0.180: 12 Chirality restraints: 3164 Sorted by residual: chirality pdb=" CG LEU A 642 " pdb=" CB LEU A 642 " pdb=" CD1 LEU A 642 " pdb=" CD2 LEU A 642 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CG LEU B 642 " pdb=" CB LEU B 642 " pdb=" CD1 LEU B 642 " pdb=" CD2 LEU B 642 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CG LEU D 642 " pdb=" CB LEU D 642 " pdb=" CD1 LEU D 642 " pdb=" CD2 LEU D 642 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.10e-01 ... (remaining 3161 not shown) Planarity restraints: 3468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 612 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO B 613 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 613 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 613 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 612 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 613 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 613 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 613 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 612 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO D 613 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 613 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 613 " -0.019 5.00e-02 4.00e+02 ... (remaining 3465 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2081 2.75 - 3.29: 20403 3.29 - 3.82: 33620 3.82 - 4.36: 40029 4.36 - 4.90: 68033 Nonbonded interactions: 164166 Sorted by model distance: nonbonded pdb=" OD2 ASP A 752 " pdb=" NZ LYS D 169 " model vdw 2.210 3.120 nonbonded pdb=" NZ LYS C 169 " pdb=" OD2 ASP D 752 " model vdw 2.211 3.120 nonbonded pdb=" NZ LYS A 169 " pdb=" OD2 ASP B 752 " model vdw 2.217 3.120 nonbonded pdb=" NZ LYS B 169 " pdb=" OD2 ASP C 752 " model vdw 2.217 3.120 nonbonded pdb=" O ASP A 512 " pdb=" OG SER A 518 " model vdw 2.292 3.040 ... (remaining 164161 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 119 through 801 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 803 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or \ name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )))) selection = (chain 'B' and (resid 119 through 801 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 803 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or \ name C31 or name C38 or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32)))) selection = (chain 'C' and (resid 119 through 801 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 803 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or \ name C31 or name C38 or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32)))) selection = (chain 'D' and (resid 119 through 755 or (resid 801 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P or name C210 or name C211)) or (resid 802 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or na \ me C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C3 or name C31 or name C32 or name C33 or name O11 or name O1 \ 2 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or nam \ e P )) or (resid 803 and (name N or name C1 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C \ 24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or nam \ e C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or \ name O31 or name O32 or name P )))) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.180 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 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 0.088 21064 Z= 0.162 Angle : 0.743 19.607 28384 Z= 0.362 Chirality : 0.039 0.180 3164 Planarity : 0.004 0.039 3468 Dihedral : 18.110 89.977 8008 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 28.51 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.15), residues: 2424 helix: -0.92 (0.13), residues: 1416 sheet: -1.36 (0.45), residues: 76 loop : -2.48 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 188 TYR 0.013 0.001 TYR C 213 PHE 0.022 0.001 PHE A 656 TRP 0.008 0.001 TRP C 380 HIS 0.003 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 (21060) covalent geometry : angle 0.74311 / 0.36 (28376) SS BOND : bond 0.00066 / 0.03 ( 4) SS BOND : angle 0.34866 / 0.16 ( 8) hydrogen bonds : bond 0.19678 / 12.93 ( 896) hydrogen bonds : angle 7.05651 / 4.92 ( 2592) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.1316 time to fit residues: 68.2881 Evaluate side-chains 297 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN A 417 HIS ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN B 417 HIS ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 ASN C 417 HIS ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN D 417 HIS ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.190643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.183192 restraints weight = 24232.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.166868 restraints weight = 33992.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.166970 restraints weight = 39530.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.166628 restraints weight = 37821.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.166794 restraints weight = 35378.813| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21064 Z= 0.134 Angle : 0.563 6.802 28384 Z= 0.288 Chirality : 0.039 0.154 3164 Planarity : 0.004 0.041 3468 Dihedral : 11.101 83.769 3220 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.46 % Allowed : 27.72 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.17), residues: 2424 helix: -0.36 (0.13), residues: 1488 sheet: -0.28 (0.57), residues: 56 loop : -2.25 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 188 TYR 0.015 0.001 TYR C 213 PHE 0.019 0.001 PHE D 310 TRP 0.009 0.001 TRP B 559 HIS 0.006 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 (21060) covalent geometry : angle 0.56269 / 0.29 (28376) SS BOND : bond 0.00063 / 0.03 ( 4) SS BOND : angle 0.03722 / 0.02 ( 8) hydrogen bonds : bond 0.03941 / 2.62 ( 896) hydrogen bonds : angle 4.38215 / 3.05 ( 2592) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 339 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 HIS cc_start: 0.7568 (m90) cc_final: 0.7362 (m90) REVERT: A 570 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7331 (tp40) REVERT: A 642 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8436 (tt) REVERT: B 523 HIS cc_start: 0.7568 (m90) cc_final: 0.7352 (m90) REVERT: B 570 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7342 (tp40) REVERT: B 642 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8436 (tt) REVERT: C 570 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7332 (tp40) REVERT: C 642 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8428 (tt) REVERT: D 523 HIS cc_start: 0.7562 (m90) cc_final: 0.7352 (m90) REVERT: D 570 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7325 (tp40) REVERT: D 642 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8441 (tt) outliers start: 75 outliers final: 20 residues processed: 408 average time/residue: 0.1409 time to fit residues: 90.0643 Evaluate side-chains 314 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 286 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 745 HIS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 745 HIS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 570 GLN Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 745 HIS Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 745 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [23, 203, 137, 159, 45, 208, 175, 7, 99, 209, 65] chunk 23 optimal weight: 0.9990 chunk 203 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 159 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 ASN A 671 ASN B 220 ASN B 671 ASN C 220 ASN C 671 ASN D 220 ASN D 671 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.188007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.180555 restraints weight = 24303.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.165512 restraints weight = 33380.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.163898 restraints weight = 33491.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.163592 restraints weight = 40901.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.163738 restraints weight = 37632.545| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21064 Z= 0.146 Angle : 0.556 6.068 28384 Z= 0.289 Chirality : 0.039 0.180 3164 Planarity : 0.004 0.047 3468 Dihedral : 11.083 84.528 3220 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 4.66 % Allowed : 25.92 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.17), residues: 2424 helix: -0.03 (0.14), residues: 1436 sheet: -1.46 (0.48), residues: 64 loop : -2.04 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 188 TYR 0.012 0.002 TYR B 213 PHE 0.010 0.001 PHE C 316 TRP 0.012 0.001 TRP B 493 HIS 0.006 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (21060) covalent geometry : angle 0.55600 / 0.29 (28376) SS BOND : bond 0.00145 / 0.07 ( 4) SS BOND : angle 0.20248 / 0.09 ( 8) hydrogen bonds : bond 0.03811 / 2.55 ( 896) hydrogen bonds : angle 4.15390 / 2.89 ( 2592) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 320 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7530 (tp40) REVERT: A 717 MET cc_start: 0.6179 (ppp) cc_final: 0.5948 (ppp) REVERT: B 570 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7552 (tp40) REVERT: B 717 MET cc_start: 0.6195 (ppp) cc_final: 0.5964 (ppp) REVERT: C 570 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7546 (tp40) REVERT: C 717 MET cc_start: 0.6219 (ppp) cc_final: 0.5993 (ppp) REVERT: D 570 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7543 (tp40) REVERT: D 717 MET cc_start: 0.6196 (ppp) cc_final: 0.5974 (ppp) outliers start: 101 outliers final: 59 residues processed: 405 average time/residue: 0.1262 time to fit residues: 82.5942 Evaluate side-chains 376 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 313 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 745 HIS Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 745 HIS Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 570 GLN Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 745 HIS Chi-restraints excluded: chain C residue 751 GLU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 716 ARG Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 745 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [117, 84, 102, 31, 33, 188, 82, 183, 139, 175, 2] chunk 117 optimal weight: 0.0270 chunk 84 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 188 optimal weight: 0.1980 chunk 82 optimal weight: 0.6980 chunk 183 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 ASN A 220 ASN A 242 ASN A 671 ASN B 182 ASN B 220 ASN B 671 ASN C 182 ASN C 220 ASN C 242 ASN C 671 ASN D 182 ASN D 220 ASN D 242 ASN D 671 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.189359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.182120 restraints weight = 24141.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.166487 restraints weight = 31895.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.166086 restraints weight = 35650.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.166145 restraints weight = 39140.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.166094 restraints weight = 37379.071| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21064 Z= 0.117 Angle : 0.526 6.380 28384 Z= 0.271 Chirality : 0.038 0.184 3164 Planarity : 0.004 0.047 3468 Dihedral : 10.769 81.578 3220 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 5.95 % Allowed : 26.29 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.17), residues: 2424 helix: 0.04 (0.14), residues: 1468 sheet: -0.92 (0.46), residues: 56 loop : -2.07 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 188 TYR 0.012 0.001 TYR C 213 PHE 0.016 0.001 PHE C 538 TRP 0.018 0.001 TRP B 493 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (21060) covalent geometry : angle 0.52650 / 0.27 (28376) SS BOND : bond 0.00134 / 0.07 ( 4) SS BOND : angle 0.22109 / 0.10 ( 8) hydrogen bonds : bond 0.03351 / 2.25 ( 896) hydrogen bonds : angle 3.93166 / 2.74 ( 2592) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 326 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 570 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7419 (tp40) REVERT: A 672 MET cc_start: 0.7538 (mmm) cc_final: 0.7301 (tpt) REVERT: B 570 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7551 (tp40) REVERT: C 570 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7680 (tp40) REVERT: D 570 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7399 (tp40) outliers start: 129 outliers final: 61 residues processed: 423 average time/residue: 0.1336 time to fit residues: 90.3294 Evaluate side-chains 379 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 314 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 745 HIS Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 745 HIS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 570 GLN Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 745 HIS Chi-restraints excluded: chain C residue 751 GLU Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 745 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [109, 138, 168, 45, 86, 203, 187, 20, 35, 123, 107] chunk 109 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 203 optimal weight: 0.8980 chunk 187 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 123 optimal weight: 0.2980 chunk 107 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 ASN A 570 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 570 GLN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN C 570 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN D 570 GLN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.189778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.182467 restraints weight = 24032.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.166296 restraints weight = 34734.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.165725 restraints weight = 38783.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.165636 restraints weight = 43570.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.165744 restraints weight = 36799.131| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21064 Z= 0.115 Angle : 0.553 9.142 28384 Z= 0.275 Chirality : 0.038 0.185 3164 Planarity : 0.004 0.047 3468 Dihedral : 10.636 80.420 3220 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 5.49 % Allowed : 26.11 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.17), residues: 2424 helix: 0.20 (0.14), residues: 1460 sheet: -0.96 (0.47), residues: 56 loop : -2.07 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 698 TYR 0.009 0.001 TYR C 213 PHE 0.013 0.001 PHE C 538 TRP 0.018 0.001 TRP C 493 HIS 0.004 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (21060) covalent geometry : angle 0.55269 / 0.28 (28376) SS BOND : bond 0.00137 / 0.07 ( 4) SS BOND : angle 0.20921 / 0.10 ( 8) hydrogen bonds : bond 0.03283 / 2.22 ( 896) hydrogen bonds : angle 3.88231 / 2.70 ( 2592) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 341 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8800 (pp) REVERT: C 672 MET cc_start: 0.7528 (mmm) cc_final: 0.7286 (tpt) REVERT: D 672 MET cc_start: 0.7581 (mmm) cc_final: 0.7324 (tpt) outliers start: 119 outliers final: 86 residues processed: 437 average time/residue: 0.1299 time to fit residues: 91.1556 Evaluate side-chains 404 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 317 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 745 HIS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 745 HIS Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 745 HIS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 716 ARG Chi-restraints excluded: chain D residue 731 CYS Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 745 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [232, 211, 21, 93, 7, 28, 102, 181, 114, 57, 37] chunk 232 optimal weight: 2.9990 chunk 211 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 181 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 37 optimal weight: 0.4980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 671 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN D 671 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.187341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.179647 restraints weight = 24097.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.164664 restraints weight = 34520.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.164509 restraints weight = 41730.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.164334 restraints weight = 41809.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.164466 restraints weight = 39794.818| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21064 Z= 0.145 Angle : 0.589 11.454 28384 Z= 0.292 Chirality : 0.040 0.210 3164 Planarity : 0.004 0.049 3468 Dihedral : 10.730 79.793 3220 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 5.72 % Allowed : 26.80 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.17), residues: 2424 helix: 0.08 (0.14), residues: 1476 sheet: -1.43 (0.46), residues: 56 loop : -2.06 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 698 TYR 0.013 0.002 TYR B 213 PHE 0.018 0.001 PHE B 538 TRP 0.017 0.001 TRP B 493 HIS 0.007 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (21060) covalent geometry : angle 0.58910 / 0.29 (28376) SS BOND : bond 0.00133 / 0.07 ( 4) SS BOND : angle 0.13460 / 0.07 ( 8) hydrogen bonds : bond 0.03409 / 2.30 ( 896) hydrogen bonds : angle 3.93792 / 2.75 ( 2592) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 338 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 672 MET cc_start: 0.7628 (mmm) cc_final: 0.7348 (tpt) REVERT: D 672 MET cc_start: 0.7625 (mmm) cc_final: 0.7348 (tpt) outliers start: 124 outliers final: 92 residues processed: 428 average time/residue: 0.1310 time to fit residues: 90.3255 Evaluate side-chains 420 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 328 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 745 HIS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 745 HIS Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 745 HIS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 716 ARG Chi-restraints excluded: chain D residue 731 CYS Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 745 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [143, 119, 181, 111, 36, 115, 159, 73, 169, 32, 19] chunk 143 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 159 optimal weight: 0.0170 chunk 73 optimal weight: 0.6980 chunk 169 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 671 ASN B 671 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.189795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.181971 restraints weight = 23962.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.167807 restraints weight = 38589.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.167720 restraints weight = 41952.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.167707 restraints weight = 38560.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.167763 restraints weight = 34711.332| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21064 Z= 0.109 Angle : 0.576 9.975 28384 Z= 0.281 Chirality : 0.039 0.192 3164 Planarity : 0.004 0.048 3468 Dihedral : 10.542 79.374 3220 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 5.90 % Allowed : 26.43 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.17), residues: 2424 helix: 0.26 (0.14), residues: 1464 sheet: -1.29 (0.47), residues: 56 loop : -2.01 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 188 TYR 0.010 0.001 TYR B 213 PHE 0.027 0.001 PHE C 310 TRP 0.017 0.001 TRP D 493 HIS 0.004 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (21060) covalent geometry : angle 0.57644 / 0.28 (28376) SS BOND : bond 0.00156 / 0.08 ( 4) SS BOND : angle 0.22308 / 0.10 ( 8) hydrogen bonds : bond 0.03086 / 2.08 ( 896) hydrogen bonds : angle 3.75862 / 2.63 ( 2592) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 328 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8744 (pp) REVERT: A 598 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8179 (tt) REVERT: B 598 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8136 (tt) REVERT: B 672 MET cc_start: 0.7592 (mmm) cc_final: 0.7294 (tpt) REVERT: C 598 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8076 (tt) REVERT: C 672 MET cc_start: 0.7578 (mmm) cc_final: 0.7312 (tpt) REVERT: D 598 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8145 (tt) outliers start: 128 outliers final: 102 residues processed: 424 average time/residue: 0.1268 time to fit residues: 86.6048 Evaluate side-chains 422 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 315 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 745 HIS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 745 HIS Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 745 HIS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 716 ARG Chi-restraints excluded: chain D residue 731 CYS Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 745 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [69, 233, 161, 227, 81, 180, 188, 58, 45, 181, 174] chunk 69 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 227 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 180 optimal weight: 6.9990 chunk 188 optimal weight: 0.3980 chunk 58 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 HIS A 671 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.188202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.180674 restraints weight = 24114.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.166594 restraints weight = 34330.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.165324 restraints weight = 41815.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.165361 restraints weight = 42058.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.165349 restraints weight = 44662.890| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21064 Z= 0.130 Angle : 0.588 9.817 28384 Z= 0.291 Chirality : 0.040 0.197 3164 Planarity : 0.004 0.049 3468 Dihedral : 10.605 79.745 3220 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 6.00 % Allowed : 26.75 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.17), residues: 2424 helix: 0.22 (0.14), residues: 1460 sheet: -1.36 (0.51), residues: 56 loop : -2.05 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 188 TYR 0.017 0.001 TYR B 213 PHE 0.016 0.001 PHE A 538 TRP 0.015 0.001 TRP B 493 HIS 0.005 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (21060) covalent geometry : angle 0.58780 / 0.29 (28376) SS BOND : bond 0.00140 / 0.07 ( 4) SS BOND : angle 0.11982 / 0.05 ( 8) hydrogen bonds : bond 0.03244 / 2.18 ( 896) hydrogen bonds : angle 3.80080 / 2.65 ( 2592) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 326 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 ASP cc_start: 0.8407 (t0) cc_final: 0.7456 (t0) REVERT: A 598 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8212 (tt) REVERT: B 598 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8166 (tt) REVERT: B 672 MET cc_start: 0.7554 (mmm) cc_final: 0.7267 (tpt) REVERT: D 293 ASP cc_start: 0.8387 (t0) cc_final: 0.7428 (t0) REVERT: D 598 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8193 (tt) outliers start: 130 outliers final: 106 residues processed: 426 average time/residue: 0.1359 time to fit residues: 91.9781 Evaluate side-chains 427 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 318 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 745 HIS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 745 HIS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 745 HIS Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 716 ARG Chi-restraints excluded: chain D residue 731 CYS Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 745 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [142, 57, 211, 237, 205, 41, 225, 104, 143, 238, 147] chunk 142 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 211 optimal weight: 3.9990 chunk 237 optimal weight: 5.9990 chunk 205 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 225 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 ASN A 220 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN B 220 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN C 220 ASN C 671 ASN D 182 ASN D 220 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.188887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.181007 restraints weight = 24066.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.166703 restraints weight = 37750.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.166945 restraints weight = 47410.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.166692 restraints weight = 42083.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.166672 restraints weight = 37183.304| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21064 Z= 0.122 Angle : 0.589 9.279 28384 Z= 0.291 Chirality : 0.039 0.203 3164 Planarity : 0.004 0.048 3468 Dihedral : 10.557 79.736 3220 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 5.58 % Allowed : 27.08 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.17), residues: 2424 helix: 0.22 (0.14), residues: 1468 sheet: -1.30 (0.51), residues: 56 loop : -2.00 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 188 TYR 0.018 0.001 TYR D 213 PHE 0.029 0.001 PHE C 310 TRP 0.015 0.001 TRP B 493 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (21060) covalent geometry : angle 0.58908 / 0.29 (28376) SS BOND : bond 0.00156 / 0.08 ( 4) SS BOND : angle 0.18018 / 0.08 ( 8) hydrogen bonds : bond 0.03165 / 2.13 ( 896) hydrogen bonds : angle 3.75830 / 2.62 ( 2592) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 314 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8170 (tt) REVERT: B 598 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8159 (tt) REVERT: B 672 MET cc_start: 0.7587 (mmm) cc_final: 0.7304 (tpt) REVERT: D 598 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8168 (tt) REVERT: D 672 MET cc_start: 0.7703 (mmm) cc_final: 0.7417 (tpt) outliers start: 121 outliers final: 109 residues processed: 400 average time/residue: 0.1222 time to fit residues: 79.2555 Evaluate side-chains 424 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 312 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 745 HIS Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 745 HIS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 745 HIS Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 716 ARG Chi-restraints excluded: chain D residue 731 CYS Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 745 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [155, 224, 231, 40, 209, 187, 104, 165, 103, 39, 75] chunk 155 optimal weight: 0.3980 chunk 224 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 HIS ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.186655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.180035 restraints weight = 24197.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.169917 restraints weight = 41919.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.167349 restraints weight = 44363.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.166532 restraints weight = 39731.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.166706 restraints weight = 33604.880| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21064 Z= 0.156 Angle : 0.618 9.477 28384 Z= 0.307 Chirality : 0.041 0.215 3164 Planarity : 0.004 0.049 3468 Dihedral : 10.724 80.541 3220 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 5.17 % Allowed : 27.35 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.17), residues: 2424 helix: 0.06 (0.13), residues: 1484 sheet: -1.44 (0.52), residues: 56 loop : -2.01 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 188 TYR 0.020 0.002 TYR B 213 PHE 0.027 0.001 PHE C 310 TRP 0.015 0.001 TRP C 493 HIS 0.007 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (21060) covalent geometry : angle 0.61776 / 0.31 (28376) SS BOND : bond 0.00144 / 0.07 ( 4) SS BOND : angle 0.11515 / 0.06 ( 8) hydrogen bonds : bond 0.03413 / 2.29 ( 896) hydrogen bonds : angle 3.90136 / 2.72 ( 2592) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 325 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.4959 (mmm) cc_final: 0.4680 (mmm) REVERT: A 598 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8195 (tt) REVERT: B 574 MET cc_start: 0.4971 (mmm) cc_final: 0.4638 (mmm) REVERT: B 598 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8203 (tt) REVERT: C 694 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8323 (mt) REVERT: D 574 MET cc_start: 0.5008 (mmm) cc_final: 0.4681 (mmm) REVERT: D 598 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8197 (tt) REVERT: D 672 MET cc_start: 0.7698 (mmm) cc_final: 0.7426 (tpt) outliers start: 112 outliers final: 106 residues processed: 407 average time/residue: 0.1322 time to fit residues: 86.5463 Evaluate side-chains 430 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 320 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 745 HIS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 745 HIS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 745 HIS Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 716 ARG Chi-restraints excluded: chain D residue 731 CYS Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 745 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [26, 124, 84, 186, 138, 220, 107, 174, 60, 113, 160] chunk 26 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 186 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.185503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.178940 restraints weight = 24413.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.168536 restraints weight = 45649.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.166669 restraints weight = 50745.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.166008 restraints weight = 39722.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.165906 restraints weight = 35891.549| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21064 Z= 0.174 Angle : 0.640 10.295 28384 Z= 0.317 Chirality : 0.042 0.258 3164 Planarity : 0.004 0.050 3468 Dihedral : 10.884 80.706 3220 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 5.44 % Allowed : 26.89 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.17), residues: 2424 helix: -0.05 (0.13), residues: 1492 sheet: -1.47 (0.52), residues: 56 loop : -2.03 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 188 TYR 0.023 0.002 TYR B 213 PHE 0.026 0.002 PHE C 310 TRP 0.016 0.001 TRP B 493 HIS 0.007 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 (21060) covalent geometry : angle 0.63978 / 0.32 (28376) SS BOND : bond 0.00164 / 0.08 ( 4) SS BOND : angle 0.18675 / 0.09 ( 8) hydrogen bonds : bond 0.03568 / 2.39 ( 896) hydrogen bonds : angle 3.98950 / 2.79 ( 2592) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3209.33 seconds wall clock time: 56 minutes 29.83 seconds (3389.83 seconds total)