Starting phenix.real_space_refine on Tue Aug 26 17:47:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k96_36976/08_2025/8k96_36976.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k96_36976/08_2025/8k96_36976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k96_36976/08_2025/8k96_36976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k96_36976/08_2025/8k96_36976.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k96_36976/08_2025/8k96_36976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k96_36976/08_2025/8k96_36976.map" } resolution = 2.89 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= 0.001 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 196 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 7 5.49 5 S 49 5.16 5 B 7 2.79 5 C 24808 2.51 5 N 7028 2.21 5 O 7364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39263 Number of models: 1 Model: "" Number of chains: 14 Chain: "B" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "A" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "G" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "F" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "E" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "D" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "C" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'BO2': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'BO2': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'BO2': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'BO2': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'BO2': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'BO2': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'BO2': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.04, per 1000 atoms: 0.23 Number of scatterers: 39263 At special positions: 0 Unit cell: (151.7, 152.52, 167.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 49 16.00 P 7 15.00 O 7364 8.00 N 7028 7.00 C 24808 6.00 B 7 5.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9240 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 76 sheets defined 54.7% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 58 through 69 removed outlier: 3.530A pdb=" N THR B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 119 removed outlier: 4.082A pdb=" N VAL B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ASN B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 152 Processing helix chain 'B' and resid 173 through 221 removed outlier: 4.066A pdb=" N ASN B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 224 through 242 Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'B' and resid 273 through 279 Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 363 through 368 removed outlier: 3.641A pdb=" N PHE B 367 " --> pdb=" O THR B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 380 removed outlier: 3.778A pdb=" N SER B 377 " --> pdb=" O ASP B 373 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU B 378 " --> pdb=" O PRO B 374 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 408 Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 436 through 452 Processing helix chain 'B' and resid 456 through 471 removed outlier: 3.944A pdb=" N SER B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 539 through 557 removed outlier: 3.647A pdb=" N LYS B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 545 " --> pdb=" O ILE B 541 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 546 " --> pdb=" O PHE B 542 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 547 " --> pdb=" O HIS B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 597 Processing helix chain 'B' and resid 621 through 637 Processing helix chain 'B' and resid 649 through 654 removed outlier: 3.976A pdb=" N ALA B 652 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 666 Processing helix chain 'B' and resid 676 through 686 Processing helix chain 'B' and resid 694 through 719 Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 32 through 46 Processing helix chain 'A' and resid 58 through 69 removed outlier: 3.532A pdb=" N THR A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 119 removed outlier: 4.062A pdb=" N VAL A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASN A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 152 Processing helix chain 'A' and resid 173 through 221 removed outlier: 4.073A pdb=" N ASN A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 224 through 242 Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 273 through 279 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 363 through 368 removed outlier: 3.647A pdb=" N PHE A 367 " --> pdb=" O THR A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 removed outlier: 3.760A pdb=" N SER A 377 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU A 378 " --> pdb=" O PRO A 374 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 408 Processing helix chain 'A' and resid 412 through 427 Processing helix chain 'A' and resid 436 through 452 Processing helix chain 'A' and resid 456 through 471 removed outlier: 3.921A pdb=" N SER A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 539 through 557 removed outlier: 3.548A pdb=" N LYS A 544 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 545 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 547 " --> pdb=" O HIS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 597 Processing helix chain 'A' and resid 621 through 637 Processing helix chain 'A' and resid 649 through 654 removed outlier: 3.839A pdb=" N ALA A 652 " --> pdb=" O ALA A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 676 through 686 removed outlier: 3.552A pdb=" N ALA A 680 " --> pdb=" O THR A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 719 Processing helix chain 'G' and resid 4 through 9 Processing helix chain 'G' and resid 32 through 46 Processing helix chain 'G' and resid 58 through 69 removed outlier: 3.529A pdb=" N THR G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 119 removed outlier: 4.081A pdb=" N VAL G 112 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ASN G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG G 114 " --> pdb=" O LEU G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 152 Processing helix chain 'G' and resid 173 through 221 removed outlier: 4.074A pdb=" N ASN G 212 " --> pdb=" O HIS G 208 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG G 213 " --> pdb=" O TYR G 209 " (cutoff:3.500A) Proline residue: G 216 - end of helix Processing helix chain 'G' and resid 224 through 242 Processing helix chain 'G' and resid 246 through 250 Processing helix chain 'G' and resid 273 through 279 Processing helix chain 'G' and resid 293 through 297 Processing helix chain 'G' and resid 300 through 305 Processing helix chain 'G' and resid 314 through 320 Processing helix chain 'G' and resid 322 through 333 Processing helix chain 'G' and resid 363 through 368 removed outlier: 3.645A pdb=" N PHE G 367 " --> pdb=" O THR G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 373 through 380 removed outlier: 3.777A pdb=" N SER G 377 " --> pdb=" O ASP G 373 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU G 378 " --> pdb=" O PRO G 374 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU G 379 " --> pdb=" O ALA G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 393 through 408 Processing helix chain 'G' and resid 412 through 427 Processing helix chain 'G' and resid 436 through 452 Processing helix chain 'G' and resid 456 through 471 removed outlier: 3.914A pdb=" N SER G 471 " --> pdb=" O ARG G 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 484 Processing helix chain 'G' and resid 539 through 557 removed outlier: 3.553A pdb=" N ALA G 545 " --> pdb=" O ILE G 541 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU G 547 " --> pdb=" O HIS G 543 " (cutoff:3.500A) Processing helix chain 'G' and resid 584 through 597 Processing helix chain 'G' and resid 621 through 637 Processing helix chain 'G' and resid 649 through 654 removed outlier: 3.997A pdb=" N ALA G 652 " --> pdb=" O ALA G 649 " (cutoff:3.500A) Processing helix chain 'G' and resid 657 through 666 Processing helix chain 'G' and resid 676 through 686 removed outlier: 3.521A pdb=" N ALA G 680 " --> pdb=" O THR G 676 " (cutoff:3.500A) Processing helix chain 'G' and resid 694 through 719 Processing helix chain 'F' and resid 4 through 9 Processing helix chain 'F' and resid 32 through 46 Processing helix chain 'F' and resid 58 through 69 removed outlier: 3.530A pdb=" N THR F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 119 removed outlier: 4.063A pdb=" N VAL F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASN F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG F 114 " --> pdb=" O LEU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 152 Processing helix chain 'F' and resid 173 through 221 removed outlier: 4.067A pdb=" N ASN F 212 " --> pdb=" O HIS F 208 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG F 213 " --> pdb=" O TYR F 209 " (cutoff:3.500A) Proline residue: F 216 - end of helix Processing helix chain 'F' and resid 224 through 242 Processing helix chain 'F' and resid 246 through 250 Processing helix chain 'F' and resid 273 through 279 Processing helix chain 'F' and resid 293 through 297 Processing helix chain 'F' and resid 300 through 305 Processing helix chain 'F' and resid 314 through 320 Processing helix chain 'F' and resid 322 through 333 Processing helix chain 'F' and resid 363 through 368 removed outlier: 3.636A pdb=" N PHE F 367 " --> pdb=" O THR F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 380 removed outlier: 3.842A pdb=" N SER F 377 " --> pdb=" O ASP F 373 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU F 378 " --> pdb=" O PRO F 374 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 408 Processing helix chain 'F' and resid 412 through 427 Processing helix chain 'F' and resid 436 through 452 Processing helix chain 'F' and resid 456 through 471 removed outlier: 3.930A pdb=" N SER F 471 " --> pdb=" O ARG F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 539 through 557 removed outlier: 3.631A pdb=" N LEU F 547 " --> pdb=" O HIS F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 597 Processing helix chain 'F' and resid 621 through 637 Processing helix chain 'F' and resid 649 through 654 removed outlier: 3.885A pdb=" N ALA F 652 " --> pdb=" O ALA F 649 " (cutoff:3.500A) Processing helix chain 'F' and resid 657 through 666 Processing helix chain 'F' and resid 676 through 686 removed outlier: 3.520A pdb=" N ALA F 680 " --> pdb=" O THR F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 694 through 719 Processing helix chain 'E' and resid 4 through 9 Processing helix chain 'E' and resid 32 through 46 Processing helix chain 'E' and resid 58 through 69 removed outlier: 3.531A pdb=" N THR E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 119 removed outlier: 4.064A pdb=" N VAL E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 152 Processing helix chain 'E' and resid 173 through 221 removed outlier: 4.075A pdb=" N ASN E 212 " --> pdb=" O HIS E 208 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG E 213 " --> pdb=" O TYR E 209 " (cutoff:3.500A) Proline residue: E 216 - end of helix Processing helix chain 'E' and resid 224 through 242 Processing helix chain 'E' and resid 246 through 250 Processing helix chain 'E' and resid 273 through 279 Processing helix chain 'E' and resid 293 through 297 Processing helix chain 'E' and resid 300 through 305 Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 322 through 333 Processing helix chain 'E' and resid 363 through 368 removed outlier: 3.636A pdb=" N PHE E 367 " --> pdb=" O THR E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 380 removed outlier: 3.820A pdb=" N SER E 377 " --> pdb=" O ASP E 373 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU E 378 " --> pdb=" O PRO E 374 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU E 379 " --> pdb=" O ALA E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 408 Processing helix chain 'E' and resid 412 through 427 Processing helix chain 'E' and resid 436 through 452 Processing helix chain 'E' and resid 456 through 471 removed outlier: 3.925A pdb=" N SER E 471 " --> pdb=" O ARG E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 539 through 557 removed outlier: 3.682A pdb=" N LYS E 544 " --> pdb=" O GLN E 540 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA E 545 " --> pdb=" O ILE E 541 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL E 546 " --> pdb=" O PHE E 542 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU E 547 " --> pdb=" O HIS E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 597 Processing helix chain 'E' and resid 621 through 637 Processing helix chain 'E' and resid 649 through 654 removed outlier: 3.869A pdb=" N ALA E 652 " --> pdb=" O ALA E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 666 Processing helix chain 'E' and resid 676 through 686 removed outlier: 3.544A pdb=" N ALA E 680 " --> pdb=" O THR E 676 " (cutoff:3.500A) Processing helix chain 'E' and resid 694 through 719 Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 32 through 46 Processing helix chain 'D' and resid 58 through 69 removed outlier: 3.534A pdb=" N THR D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 119 removed outlier: 4.076A pdb=" N VAL D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ASN D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 152 Processing helix chain 'D' and resid 173 through 221 removed outlier: 4.073A pdb=" N ASN D 212 " --> pdb=" O HIS D 208 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG D 213 " --> pdb=" O TYR D 209 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 224 through 242 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 273 through 279 Processing helix chain 'D' and resid 293 through 297 Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 314 through 320 Processing helix chain 'D' and resid 322 through 333 Processing helix chain 'D' and resid 363 through 368 removed outlier: 3.640A pdb=" N PHE D 367 " --> pdb=" O THR D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 380 removed outlier: 3.750A pdb=" N SER D 377 " --> pdb=" O ASP D 373 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU D 378 " --> pdb=" O PRO D 374 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 408 Processing helix chain 'D' and resid 412 through 427 Processing helix chain 'D' and resid 436 through 452 Processing helix chain 'D' and resid 456 through 471 removed outlier: 3.935A pdb=" N SER D 471 " --> pdb=" O ARG D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 539 through 557 removed outlier: 3.514A pdb=" N LEU D 547 " --> pdb=" O HIS D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 597 Processing helix chain 'D' and resid 621 through 637 Processing helix chain 'D' and resid 649 through 654 removed outlier: 3.833A pdb=" N ALA D 652 " --> pdb=" O ALA D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 666 Processing helix chain 'D' and resid 676 through 686 removed outlier: 3.564A pdb=" N ALA D 680 " --> pdb=" O THR D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 694 through 719 Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 58 through 69 removed outlier: 3.531A pdb=" N THR C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 119 removed outlier: 4.439A pdb=" N HIS C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASN C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 152 Processing helix chain 'C' and resid 173 through 221 removed outlier: 4.059A pdb=" N ASN C 212 " --> pdb=" O HIS C 208 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG C 213 " --> pdb=" O TYR C 209 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 224 through 242 Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 273 through 279 Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 322 through 333 Processing helix chain 'C' and resid 363 through 368 removed outlier: 3.644A pdb=" N PHE C 367 " --> pdb=" O THR C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 380 removed outlier: 3.745A pdb=" N SER C 377 " --> pdb=" O ASP C 373 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU C 378 " --> pdb=" O PRO C 374 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 408 Processing helix chain 'C' and resid 412 through 427 Processing helix chain 'C' and resid 436 through 452 Processing helix chain 'C' and resid 456 through 471 removed outlier: 3.920A pdb=" N SER C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 484 Processing helix chain 'C' and resid 539 through 557 removed outlier: 3.522A pdb=" N LYS C 544 " --> pdb=" O GLN C 540 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 547 " --> pdb=" O HIS C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 597 Processing helix chain 'C' and resid 621 through 637 Processing helix chain 'C' and resid 649 through 654 removed outlier: 3.902A pdb=" N ALA C 652 " --> pdb=" O ALA C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 666 Processing helix chain 'C' and resid 676 through 686 removed outlier: 3.559A pdb=" N ALA C 680 " --> pdb=" O THR C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 719 Processing sheet with id=AA1, first strand: chain 'B' and resid 266 through 269 removed outlier: 6.589A pdb=" N VAL B 267 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ASP B 313 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLU B 269 " --> pdb=" O ASP B 313 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU B 310 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL B 361 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU B 312 " --> pdb=" O VAL B 361 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 77 through 82 Processing sheet with id=AA3, first strand: chain 'B' and resid 156 through 159 Processing sheet with id=AA4, first strand: chain 'B' and resid 284 through 286 Processing sheet with id=AA5, first strand: chain 'B' and resid 334 through 335 Processing sheet with id=AA6, first strand: chain 'B' and resid 389 through 391 Processing sheet with id=AA7, first strand: chain 'B' and resid 410 through 411 removed outlier: 7.289A pdb=" N GLN B 410 " --> pdb=" O LEU B 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 494 through 496 Processing sheet with id=AA9, first strand: chain 'B' and resid 498 through 504 removed outlier: 6.700A pdb=" N ILE B 529 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N PHE B 571 " --> pdb=" O ILE B 529 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 604 through 606 removed outlier: 6.526A pdb=" N ALA B 605 " --> pdb=" O ILE B 645 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 266 through 269 removed outlier: 6.418A pdb=" N VAL A 267 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASP A 313 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N GLU A 269 " --> pdb=" O ASP A 313 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU A 310 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL A 361 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU A 312 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 77 through 82 Processing sheet with id=AB4, first strand: chain 'A' and resid 156 through 159 Processing sheet with id=AB5, first strand: chain 'A' and resid 284 through 286 Processing sheet with id=AB6, first strand: chain 'A' and resid 334 through 335 Processing sheet with id=AB7, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AB8, first strand: chain 'A' and resid 410 through 411 removed outlier: 7.283A pdb=" N GLN A 410 " --> pdb=" O LEU A 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 494 through 496 Processing sheet with id=AC1, first strand: chain 'A' and resid 498 through 504 removed outlier: 6.737A pdb=" N ILE A 529 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N PHE A 571 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 604 through 606 removed outlier: 6.529A pdb=" N ALA A 605 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN A 642 " --> pdb=" O HIS A 670 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N TYR A 672 " --> pdb=" O GLN A 642 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL A 644 " --> pdb=" O TYR A 672 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL A 674 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU A 646 " --> pdb=" O VAL A 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 609 through 610 Processing sheet with id=AC4, first strand: chain 'G' and resid 266 through 269 removed outlier: 6.586A pdb=" N VAL G 267 " --> pdb=" O ILE G 311 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ASP G 313 " --> pdb=" O VAL G 267 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N GLU G 269 " --> pdb=" O ASP G 313 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU G 310 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL G 361 " --> pdb=" O LEU G 310 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU G 312 " --> pdb=" O VAL G 361 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 77 through 82 Processing sheet with id=AC6, first strand: chain 'G' and resid 156 through 159 Processing sheet with id=AC7, first strand: chain 'G' and resid 284 through 286 Processing sheet with id=AC8, first strand: chain 'G' and resid 334 through 335 Processing sheet with id=AC9, first strand: chain 'G' and resid 389 through 391 Processing sheet with id=AD1, first strand: chain 'G' and resid 410 through 411 removed outlier: 7.252A pdb=" N GLN G 410 " --> pdb=" O LEU G 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 494 through 496 Processing sheet with id=AD3, first strand: chain 'G' and resid 498 through 504 removed outlier: 6.755A pdb=" N ILE G 529 " --> pdb=" O LEU G 569 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N PHE G 571 " --> pdb=" O ILE G 529 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 604 through 606 removed outlier: 6.523A pdb=" N ALA G 605 " --> pdb=" O ILE G 645 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 609 through 610 Processing sheet with id=AD6, first strand: chain 'F' and resid 266 through 269 removed outlier: 6.593A pdb=" N VAL F 267 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ASP F 313 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N GLU F 269 " --> pdb=" O ASP F 313 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU F 310 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL F 361 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU F 312 " --> pdb=" O VAL F 361 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 77 through 82 Processing sheet with id=AD8, first strand: chain 'F' and resid 156 through 159 Processing sheet with id=AD9, first strand: chain 'F' and resid 284 through 286 Processing sheet with id=AE1, first strand: chain 'F' and resid 334 through 335 Processing sheet with id=AE2, first strand: chain 'F' and resid 389 through 391 Processing sheet with id=AE3, first strand: chain 'F' and resid 410 through 411 removed outlier: 7.283A pdb=" N GLN F 410 " --> pdb=" O LEU F 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'F' and resid 494 through 496 Processing sheet with id=AE5, first strand: chain 'F' and resid 498 through 504 removed outlier: 6.708A pdb=" N ILE F 529 " --> pdb=" O LEU F 569 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N PHE F 571 " --> pdb=" O ILE F 529 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 604 through 606 removed outlier: 6.533A pdb=" N ALA F 605 " --> pdb=" O ILE F 645 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLN F 642 " --> pdb=" O HIS F 670 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N TYR F 672 " --> pdb=" O GLN F 642 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL F 644 " --> pdb=" O TYR F 672 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL F 674 " --> pdb=" O VAL F 644 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU F 646 " --> pdb=" O VAL F 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'F' and resid 609 through 610 Processing sheet with id=AE8, first strand: chain 'E' and resid 266 through 269 removed outlier: 6.586A pdb=" N VAL E 267 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N ASP E 313 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLU E 269 " --> pdb=" O ASP E 313 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU E 310 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL E 361 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU E 312 " --> pdb=" O VAL E 361 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 77 through 82 Processing sheet with id=AF1, first strand: chain 'E' and resid 156 through 159 Processing sheet with id=AF2, first strand: chain 'E' and resid 284 through 286 Processing sheet with id=AF3, first strand: chain 'E' and resid 334 through 335 Processing sheet with id=AF4, first strand: chain 'E' and resid 389 through 391 Processing sheet with id=AF5, first strand: chain 'E' and resid 410 through 411 removed outlier: 7.271A pdb=" N GLN E 410 " --> pdb=" O LEU E 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'E' and resid 494 through 496 Processing sheet with id=AF7, first strand: chain 'E' and resid 498 through 504 removed outlier: 6.633A pdb=" N ILE E 529 " --> pdb=" O LEU E 569 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N PHE E 571 " --> pdb=" O ILE E 529 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 604 through 606 removed outlier: 6.541A pdb=" N ALA E 605 " --> pdb=" O ILE E 645 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN E 642 " --> pdb=" O HIS E 670 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N TYR E 672 " --> pdb=" O GLN E 642 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL E 644 " --> pdb=" O TYR E 672 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL E 674 " --> pdb=" O VAL E 644 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU E 646 " --> pdb=" O VAL E 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'E' and resid 609 through 610 Processing sheet with id=AG1, first strand: chain 'D' and resid 266 through 269 removed outlier: 6.426A pdb=" N VAL D 267 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ASP D 313 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N GLU D 269 " --> pdb=" O ASP D 313 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU D 310 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL D 361 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU D 312 " --> pdb=" O VAL D 361 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 77 through 82 Processing sheet with id=AG3, first strand: chain 'D' and resid 156 through 159 Processing sheet with id=AG4, first strand: chain 'D' and resid 284 through 286 Processing sheet with id=AG5, first strand: chain 'D' and resid 334 through 335 Processing sheet with id=AG6, first strand: chain 'D' and resid 389 through 391 Processing sheet with id=AG7, first strand: chain 'D' and resid 410 through 411 removed outlier: 7.263A pdb=" N GLN D 410 " --> pdb=" O LEU D 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'D' and resid 494 through 496 Processing sheet with id=AG9, first strand: chain 'D' and resid 498 through 504 removed outlier: 6.718A pdb=" N ILE D 529 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N PHE D 571 " --> pdb=" O ILE D 529 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 604 through 606 removed outlier: 6.535A pdb=" N ALA D 605 " --> pdb=" O ILE D 645 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLN D 642 " --> pdb=" O HIS D 670 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N TYR D 672 " --> pdb=" O GLN D 642 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL D 644 " --> pdb=" O TYR D 672 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL D 674 " --> pdb=" O VAL D 644 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU D 646 " --> pdb=" O VAL D 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'D' and resid 609 through 610 Processing sheet with id=AH3, first strand: chain 'C' and resid 266 through 269 removed outlier: 6.590A pdb=" N VAL C 267 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ASP C 313 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N GLU C 269 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU C 310 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL C 361 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU C 312 " --> pdb=" O VAL C 361 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 77 through 82 Processing sheet with id=AH5, first strand: chain 'C' and resid 156 through 159 Processing sheet with id=AH6, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AH7, first strand: chain 'C' and resid 334 through 335 Processing sheet with id=AH8, first strand: chain 'C' and resid 389 through 391 Processing sheet with id=AH9, first strand: chain 'C' and resid 410 through 411 removed outlier: 7.287A pdb=" N GLN C 410 " --> pdb=" O LEU C 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'C' and resid 494 through 496 Processing sheet with id=AI2, first strand: chain 'C' and resid 498 through 504 removed outlier: 6.743A pdb=" N ILE C 529 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N PHE C 571 " --> pdb=" O ILE C 529 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'C' and resid 604 through 606 removed outlier: 6.526A pdb=" N ALA C 605 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLN C 642 " --> pdb=" O HIS C 670 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N TYR C 672 " --> pdb=" O GLN C 642 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL C 644 " --> pdb=" O TYR C 672 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL C 674 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU C 646 " --> pdb=" O VAL C 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'C' and resid 609 through 610 2190 hydrogen bonds defined for protein. 6300 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: 8.92 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 13874 1.37 - 1.52: 11359 1.52 - 1.66: 14716 1.66 - 1.80: 77 1.80 - 1.95: 14 Bond restraints: 40040 Sorted by residual: bond pdb=" O4 PO4 E 801 " pdb=" P PO4 E 801 " ideal model delta sigma weight residual 1.568 1.949 -0.381 2.00e-02 2.50e+03 3.63e+02 bond pdb=" O4 PO4 G 801 " pdb=" P PO4 G 801 " ideal model delta sigma weight residual 1.568 1.949 -0.381 2.00e-02 2.50e+03 3.62e+02 bond pdb=" O4 PO4 D 801 " pdb=" P PO4 D 801 " ideal model delta sigma weight residual 1.568 1.949 -0.381 2.00e-02 2.50e+03 3.62e+02 bond pdb=" O4 PO4 A 801 " pdb=" P PO4 A 801 " ideal model delta sigma weight residual 1.568 1.948 -0.380 2.00e-02 2.50e+03 3.62e+02 bond pdb=" O4 PO4 B 801 " pdb=" P PO4 B 801 " ideal model delta sigma weight residual 1.568 1.948 -0.380 2.00e-02 2.50e+03 3.62e+02 ... (remaining 40035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 52946 1.47 - 2.95: 1127 2.95 - 4.42: 187 4.42 - 5.89: 71 5.89 - 7.37: 24 Bond angle restraints: 54355 Sorted by residual: angle pdb=" C ALA F 427 " pdb=" N GLU F 428 " pdb=" CA GLU F 428 " ideal model delta sigma weight residual 121.54 127.01 -5.47 1.91e+00 2.74e-01 8.21e+00 angle pdb=" C ALA G 427 " pdb=" N GLU G 428 " pdb=" CA GLU G 428 " ideal model delta sigma weight residual 121.54 126.99 -5.45 1.91e+00 2.74e-01 8.13e+00 angle pdb=" C ALA A 427 " pdb=" N GLU A 428 " pdb=" CA GLU A 428 " ideal model delta sigma weight residual 121.54 126.98 -5.44 1.91e+00 2.74e-01 8.10e+00 angle pdb=" N GLU C 140 " pdb=" CA GLU C 140 " pdb=" CB GLU C 140 " ideal model delta sigma weight residual 110.16 114.32 -4.16 1.48e+00 4.57e-01 7.90e+00 angle pdb=" C ALA B 427 " pdb=" N GLU B 428 " pdb=" CA GLU B 428 " ideal model delta sigma weight residual 121.54 126.89 -5.35 1.91e+00 2.74e-01 7.85e+00 ... (remaining 54350 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 22002 17.98 - 35.96: 1766 35.96 - 53.94: 330 53.94 - 71.92: 111 71.92 - 89.90: 102 Dihedral angle restraints: 24311 sinusoidal: 9926 harmonic: 14385 Sorted by residual: dihedral pdb=" CA PHE F 692 " pdb=" C PHE F 692 " pdb=" N ARG F 693 " pdb=" CA ARG F 693 " ideal model delta harmonic sigma weight residual -180.00 -158.12 -21.88 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ILE B 558 " pdb=" C ILE B 558 " pdb=" N GLU B 559 " pdb=" CA GLU B 559 " ideal model delta harmonic sigma weight residual 180.00 158.44 21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ILE E 558 " pdb=" C ILE E 558 " pdb=" N GLU E 559 " pdb=" CA GLU E 559 " ideal model delta harmonic sigma weight residual 180.00 158.45 21.55 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 24308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 5402 0.063 - 0.126: 611 0.126 - 0.189: 21 0.189 - 0.251: 3 0.251 - 0.314: 4 Chirality restraints: 6041 Sorted by residual: chirality pdb=" C10 BO2 D 802 " pdb=" C11 BO2 D 802 " pdb=" C18 BO2 D 802 " pdb=" N9 BO2 D 802 " both_signs ideal model delta sigma weight residual False -2.57 -2.25 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C10 BO2 F 802 " pdb=" C11 BO2 F 802 " pdb=" C18 BO2 F 802 " pdb=" N9 BO2 F 802 " both_signs ideal model delta sigma weight residual False -2.57 -2.26 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C10 BO2 G 802 " pdb=" C11 BO2 G 802 " pdb=" C18 BO2 G 802 " pdb=" N9 BO2 G 802 " both_signs ideal model delta sigma weight residual False -2.57 -2.26 -0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 6038 not shown) Planarity restraints: 7245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 BO2 D 802 " -0.250 2.00e-02 2.50e+03 2.10e-01 5.53e+02 pdb=" C2 BO2 D 802 " -0.171 2.00e-02 2.50e+03 pdb=" C7 BO2 D 802 " 0.070 2.00e-02 2.50e+03 pdb=" N9 BO2 D 802 " 0.353 2.00e-02 2.50e+03 pdb=" O8 BO2 D 802 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BO2 G 802 " -0.245 2.00e-02 2.50e+03 2.06e-01 5.28e+02 pdb=" C2 BO2 G 802 " -0.168 2.00e-02 2.50e+03 pdb=" C7 BO2 G 802 " 0.069 2.00e-02 2.50e+03 pdb=" N9 BO2 G 802 " 0.344 2.00e-02 2.50e+03 pdb=" O8 BO2 G 802 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BO2 F 802 " -0.244 2.00e-02 2.50e+03 2.05e-01 5.23e+02 pdb=" C2 BO2 F 802 " -0.168 2.00e-02 2.50e+03 pdb=" C7 BO2 F 802 " 0.069 2.00e-02 2.50e+03 pdb=" N9 BO2 F 802 " 0.342 2.00e-02 2.50e+03 pdb=" O8 BO2 F 802 " 0.001 2.00e-02 2.50e+03 ... (remaining 7242 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 9 2.08 - 2.79: 8819 2.79 - 3.49: 58853 3.49 - 4.20: 97671 4.20 - 4.90: 172510 Nonbonded interactions: 337862 Sorted by model distance: nonbonded pdb=" OG SER D 582 " pdb=" O27 BO2 D 802 " model vdw 1.378 3.040 nonbonded pdb=" OG SER F 582 " pdb=" O27 BO2 F 802 " model vdw 1.395 3.040 nonbonded pdb=" OG SER G 582 " pdb=" O27 BO2 G 802 " model vdw 1.403 3.040 nonbonded pdb=" OG SER D 582 " pdb=" B26 BO2 D 802 " model vdw 1.442 2.370 nonbonded pdb=" OG SER F 582 " pdb=" B26 BO2 F 802 " model vdw 1.443 2.370 ... (remaining 337857 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 35.570 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5838 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 : 0.006 0.381 40044 Z= 0.276 Angle : 0.566 7.367 54355 Z= 0.284 Chirality : 0.040 0.314 6041 Planarity : 0.008 0.210 7245 Dihedral : 15.286 89.896 15071 Min Nonbonded Distance : 1.378 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.77 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.12), residues: 5019 helix: 1.71 (0.11), residues: 2562 sheet: 0.66 (0.22), residues: 630 loop : 0.21 (0.15), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 120 TYR 0.013 0.001 TYR A 575 PHE 0.029 0.001 PHE F 692 TRP 0.007 0.001 TRP G 10 HIS 0.005 0.001 HIS G 543 Details of bonding type rmsd covalent geometry : bond 0.00556 (40040) covalent geometry : angle 0.56638 (54355) hydrogen bonds : bond 0.15959 ( 2190) hydrogen bonds : angle 6.20563 ( 6300) Misc. bond : bond 0.00165 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 788 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5450 (tpt) cc_final: 0.4951 (ptt) REVERT: B 86 ARG cc_start: 0.6176 (tpp-160) cc_final: 0.5973 (tpt170) REVERT: B 213 ARG cc_start: 0.6410 (mmm160) cc_final: 0.6177 (mtp180) REVERT: B 225 ARG cc_start: 0.6577 (tpp80) cc_final: 0.6192 (tpp80) REVERT: B 249 GLN cc_start: 0.7573 (mt0) cc_final: 0.7294 (mt0) REVERT: B 278 PHE cc_start: 0.7017 (m-10) cc_final: 0.6267 (m-80) REVERT: B 373 ASP cc_start: 0.6188 (t0) cc_final: 0.5405 (m-30) REVERT: B 385 GLU cc_start: 0.6664 (tt0) cc_final: 0.6008 (tp30) REVERT: B 395 GLU cc_start: 0.6043 (mp0) cc_final: 0.5779 (pm20) REVERT: B 410 GLN cc_start: 0.5181 (mp10) cc_final: 0.4799 (mm-40) REVERT: B 498 GLU cc_start: 0.7462 (pt0) cc_final: 0.6201 (pm20) REVERT: B 560 HIS cc_start: 0.6055 (m-70) cc_final: 0.5509 (m90) REVERT: B 648 GLU cc_start: 0.6343 (tt0) cc_final: 0.6041 (tt0) REVERT: B 665 ARG cc_start: 0.6258 (ttp-170) cc_final: 0.5905 (ttp80) REVERT: B 688 ARG cc_start: 0.5498 (mpp-170) cc_final: 0.4923 (ttm110) REVERT: A 1 MET cc_start: 0.5601 (tpt) cc_final: 0.4998 (ptt) REVERT: A 223 GLN cc_start: 0.7387 (mp10) cc_final: 0.7157 (mp10) REVERT: A 225 ARG cc_start: 0.6587 (tpp80) cc_final: 0.6267 (tpp-160) REVERT: A 229 GLU cc_start: 0.5573 (mm-30) cc_final: 0.5128 (mt-10) REVERT: A 249 GLN cc_start: 0.7641 (mt0) cc_final: 0.7377 (mt0) REVERT: A 355 GLN cc_start: 0.7254 (mt0) cc_final: 0.7014 (mp10) REVERT: A 385 GLU cc_start: 0.6630 (tt0) cc_final: 0.6010 (tp30) REVERT: A 410 GLN cc_start: 0.5339 (mp10) cc_final: 0.5069 (mm-40) REVERT: A 429 GLN cc_start: 0.6788 (mt0) cc_final: 0.6512 (mp10) REVERT: A 498 GLU cc_start: 0.7392 (pt0) cc_final: 0.6109 (pm20) REVERT: A 560 HIS cc_start: 0.6100 (m-70) cc_final: 0.5212 (m90) REVERT: A 603 ASP cc_start: 0.6612 (p0) cc_final: 0.5336 (p0) REVERT: A 615 LYS cc_start: 0.5078 (ttmt) cc_final: 0.4822 (ptpt) REVERT: A 648 GLU cc_start: 0.6817 (tt0) cc_final: 0.6367 (tt0) REVERT: A 665 ARG cc_start: 0.6014 (ttp-170) cc_final: 0.5564 (ttp80) REVERT: A 688 ARG cc_start: 0.5410 (mpp-170) cc_final: 0.4753 (ttm-80) REVERT: G 1 MET cc_start: 0.5149 (tpt) cc_final: 0.4489 (ptt) REVERT: G 225 ARG cc_start: 0.6435 (tpp80) cc_final: 0.6016 (tpp80) REVERT: G 229 GLU cc_start: 0.5526 (mm-30) cc_final: 0.5196 (mt-10) REVERT: G 249 GLN cc_start: 0.7642 (mt0) cc_final: 0.7360 (mt0) REVERT: G 373 ASP cc_start: 0.6060 (t0) cc_final: 0.5380 (m-30) REVERT: G 385 GLU cc_start: 0.6674 (tt0) cc_final: 0.6000 (tp30) REVERT: G 410 GLN cc_start: 0.5410 (mp10) cc_final: 0.5084 (mm-40) REVERT: G 429 GLN cc_start: 0.6812 (mt0) cc_final: 0.6589 (mp10) REVERT: G 498 GLU cc_start: 0.7295 (pt0) cc_final: 0.6158 (pm20) REVERT: G 560 HIS cc_start: 0.6187 (m-70) cc_final: 0.5645 (m90) REVERT: G 603 ASP cc_start: 0.6599 (p0) cc_final: 0.5335 (p0) REVERT: G 613 THR cc_start: 0.6628 (m) cc_final: 0.6312 (p) REVERT: G 615 LYS cc_start: 0.4802 (ttmt) cc_final: 0.4369 (ptpt) REVERT: G 665 ARG cc_start: 0.6128 (ttp-170) cc_final: 0.5882 (ttp80) REVERT: G 675 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6910 (mm-30) REVERT: G 688 ARG cc_start: 0.5314 (mpp-170) cc_final: 0.4555 (ttm-80) REVERT: F 1 MET cc_start: 0.5557 (tpt) cc_final: 0.4860 (ptt) REVERT: F 86 ARG cc_start: 0.6221 (tpp-160) cc_final: 0.5958 (tpt170) REVERT: F 225 ARG cc_start: 0.6374 (tpp80) cc_final: 0.5986 (tpp80) REVERT: F 249 GLN cc_start: 0.7838 (mt0) cc_final: 0.7580 (mt0) REVERT: F 385 GLU cc_start: 0.6639 (tt0) cc_final: 0.6001 (tp30) REVERT: F 410 GLN cc_start: 0.5341 (mp10) cc_final: 0.5022 (mm-40) REVERT: F 429 GLN cc_start: 0.6804 (mt0) cc_final: 0.6581 (mp10) REVERT: F 498 GLU cc_start: 0.7476 (pt0) cc_final: 0.6328 (pm20) REVERT: F 560 HIS cc_start: 0.6130 (m-70) cc_final: 0.5383 (m90) REVERT: F 603 ASP cc_start: 0.6600 (p0) cc_final: 0.5452 (p0) REVERT: F 648 GLU cc_start: 0.6904 (tt0) cc_final: 0.6632 (mt-10) REVERT: F 665 ARG cc_start: 0.6230 (ttp-170) cc_final: 0.5790 (ttp80) REVERT: F 688 ARG cc_start: 0.5566 (mpp-170) cc_final: 0.5013 (ttm110) REVERT: F 697 GLU cc_start: 0.5645 (pp20) cc_final: 0.5079 (pp20) REVERT: E 1 MET cc_start: 0.5402 (tpt) cc_final: 0.4866 (ptt) REVERT: E 249 GLN cc_start: 0.7619 (mt0) cc_final: 0.7346 (mt0) REVERT: E 355 GLN cc_start: 0.7073 (mt0) cc_final: 0.6845 (mp10) REVERT: E 373 ASP cc_start: 0.6283 (t0) cc_final: 0.5649 (m-30) REVERT: E 378 GLU cc_start: 0.5945 (pm20) cc_final: 0.5682 (pm20) REVERT: E 385 GLU cc_start: 0.6580 (tt0) cc_final: 0.5954 (tp30) REVERT: E 395 GLU cc_start: 0.6104 (mp0) cc_final: 0.5886 (pm20) REVERT: E 410 GLN cc_start: 0.5185 (mp10) cc_final: 0.4743 (mm-40) REVERT: E 498 GLU cc_start: 0.7452 (pt0) cc_final: 0.6133 (pm20) REVERT: E 560 HIS cc_start: 0.6148 (m-70) cc_final: 0.5606 (m90) REVERT: E 603 ASP cc_start: 0.6680 (p0) cc_final: 0.5480 (p0) REVERT: E 665 ARG cc_start: 0.6164 (ttp-170) cc_final: 0.5593 (ttp80) REVERT: E 688 ARG cc_start: 0.5361 (mpp-170) cc_final: 0.4911 (ttm-80) REVERT: D 1 MET cc_start: 0.5537 (tpt) cc_final: 0.4949 (ptt) REVERT: D 86 ARG cc_start: 0.6037 (tpp-160) cc_final: 0.5804 (tpt170) REVERT: D 249 GLN cc_start: 0.7685 (mt0) cc_final: 0.7377 (mt0) REVERT: D 355 GLN cc_start: 0.7349 (mt0) cc_final: 0.7125 (mp10) REVERT: D 385 GLU cc_start: 0.6765 (tt0) cc_final: 0.6164 (tp30) REVERT: D 410 GLN cc_start: 0.5293 (mp10) cc_final: 0.4976 (mm-40) REVERT: D 476 GLU cc_start: 0.5724 (tt0) cc_final: 0.4934 (tp30) REVERT: D 498 GLU cc_start: 0.7520 (pt0) cc_final: 0.7168 (pt0) REVERT: D 560 HIS cc_start: 0.6166 (m-70) cc_final: 0.5637 (m90) REVERT: D 603 ASP cc_start: 0.6590 (p0) cc_final: 0.5339 (p0) REVERT: D 648 GLU cc_start: 0.6722 (tt0) cc_final: 0.6378 (tt0) REVERT: D 665 ARG cc_start: 0.6158 (ttp-170) cc_final: 0.5819 (ttp80) REVERT: D 688 ARG cc_start: 0.5665 (mpp-170) cc_final: 0.4973 (ttm-80) REVERT: D 697 GLU cc_start: 0.5623 (pp20) cc_final: 0.5149 (pp20) REVERT: C 1 MET cc_start: 0.5436 (tpt) cc_final: 0.4910 (ptt) REVERT: C 225 ARG cc_start: 0.6350 (tpp80) cc_final: 0.5991 (tpp80) REVERT: C 249 GLN cc_start: 0.7627 (mt0) cc_final: 0.7347 (mt0) REVERT: C 355 GLN cc_start: 0.7115 (mt0) cc_final: 0.6875 (mp10) REVERT: C 373 ASP cc_start: 0.6277 (t0) cc_final: 0.5473 (m-30) REVERT: C 385 GLU cc_start: 0.6599 (tt0) cc_final: 0.5941 (tp30) REVERT: C 395 GLU cc_start: 0.5999 (mp0) cc_final: 0.5747 (pm20) REVERT: C 410 GLN cc_start: 0.5122 (mp10) cc_final: 0.4789 (mm-40) REVERT: C 429 GLN cc_start: 0.6768 (mt0) cc_final: 0.6514 (mp10) REVERT: C 498 GLU cc_start: 0.7280 (tt0) cc_final: 0.6593 (tt0) REVERT: C 560 HIS cc_start: 0.6331 (m-70) cc_final: 0.5585 (m90) REVERT: C 603 ASP cc_start: 0.6614 (p0) cc_final: 0.5266 (p0) REVERT: C 648 GLU cc_start: 0.6764 (tt0) cc_final: 0.6394 (tt0) REVERT: C 688 ARG cc_start: 0.5393 (mpp-170) cc_final: 0.4689 (ttm-80) outliers start: 0 outliers final: 1 residues processed: 788 average time/residue: 0.7208 time to fit residues: 675.3271 Evaluate side-chains 499 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 498 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 547 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 0.1980 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 0.0060 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 494 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 overall best weight: 1.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 303 HIS B 642 GLN A 303 HIS G 303 HIS F 303 HIS E 303 HIS E 543 HIS E 573 GLN E 612 GLN D 303 HIS C 303 HIS C 612 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.223725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.185117 restraints weight = 44471.559| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 1.82 r_work: 0.3882 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 40044 Z= 0.156 Angle : 0.647 9.412 54355 Z= 0.313 Chirality : 0.043 0.425 6041 Planarity : 0.005 0.063 7245 Dihedral : 6.970 85.020 5735 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.45 % Favored : 97.41 % Rotamer: Outliers : 1.96 % Allowed : 11.37 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.12), residues: 5019 helix: 1.41 (0.10), residues: 2625 sheet: 0.53 (0.21), residues: 595 loop : 0.24 (0.15), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 280 TYR 0.019 0.002 TYR E 557 PHE 0.020 0.002 PHE F 692 TRP 0.009 0.001 TRP B 250 HIS 0.003 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00354 (40040) covalent geometry : angle 0.64741 (54355) hydrogen bonds : bond 0.04406 ( 2190) hydrogen bonds : angle 4.97786 ( 6300) Misc. bond : bond 0.00066 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 522 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 GLU cc_start: 0.5752 (mt-10) cc_final: 0.5528 (mt-10) REVERT: B 204 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.7080 (p0) REVERT: B 225 ARG cc_start: 0.8014 (tpp80) cc_final: 0.7564 (tpp80) REVERT: B 278 PHE cc_start: 0.7164 (m-10) cc_final: 0.6544 (m-80) REVERT: B 373 ASP cc_start: 0.6796 (t0) cc_final: 0.6587 (m-30) REVERT: B 385 GLU cc_start: 0.7869 (tt0) cc_final: 0.7667 (tt0) REVERT: B 498 GLU cc_start: 0.8387 (pt0) cc_final: 0.7873 (pm20) REVERT: B 556 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6965 (tmt170) REVERT: B 566 THR cc_start: 0.7933 (t) cc_final: 0.7661 (m) REVERT: B 603 ASP cc_start: 0.8450 (p0) cc_final: 0.8033 (p0) REVERT: B 651 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8056 (mt) REVERT: B 688 ARG cc_start: 0.7141 (mpp-170) cc_final: 0.6712 (ttm-80) REVERT: A 204 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6938 (p0) REVERT: A 207 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7354 (mm) REVERT: A 212 ASN cc_start: 0.7874 (m110) cc_final: 0.7568 (m-40) REVERT: A 225 ARG cc_start: 0.7980 (tpp80) cc_final: 0.7453 (tpp-160) REVERT: A 249 GLN cc_start: 0.8458 (mt0) cc_final: 0.8233 (mt0) REVERT: A 566 THR cc_start: 0.7960 (t) cc_final: 0.7699 (m) REVERT: A 603 ASP cc_start: 0.8440 (p0) cc_final: 0.7926 (p0) REVERT: A 651 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8147 (mt) REVERT: A 688 ARG cc_start: 0.6871 (mpp-170) cc_final: 0.6382 (ttm-80) REVERT: G 204 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.6933 (p0) REVERT: G 212 ASN cc_start: 0.7686 (m110) cc_final: 0.7477 (m-40) REVERT: G 225 ARG cc_start: 0.7949 (tpp80) cc_final: 0.7563 (tpp80) REVERT: G 229 GLU cc_start: 0.6820 (mm-30) cc_final: 0.6617 (mt-10) REVERT: G 237 ARG cc_start: 0.7732 (ttt180) cc_final: 0.7515 (ttp-110) REVERT: G 249 GLN cc_start: 0.8380 (mt0) cc_final: 0.8152 (mt0) REVERT: G 385 GLU cc_start: 0.7999 (tt0) cc_final: 0.7732 (tt0) REVERT: G 498 GLU cc_start: 0.8386 (pt0) cc_final: 0.7929 (pm20) REVERT: G 556 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7225 (tpt90) REVERT: G 566 THR cc_start: 0.7871 (t) cc_final: 0.7552 (m) REVERT: G 651 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8079 (mt) REVERT: G 688 ARG cc_start: 0.7193 (mpp-170) cc_final: 0.6645 (ttm-80) REVERT: F 72 VAL cc_start: 0.7799 (p) cc_final: 0.7544 (m) REVERT: F 127 GLU cc_start: 0.5732 (mt-10) cc_final: 0.5524 (mt-10) REVERT: F 204 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6808 (p0) REVERT: F 207 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7302 (mm) REVERT: F 225 ARG cc_start: 0.7997 (tpp80) cc_final: 0.7564 (tpp80) REVERT: F 249 GLN cc_start: 0.8457 (mt0) cc_final: 0.8204 (mt0) REVERT: F 385 GLU cc_start: 0.7925 (tt0) cc_final: 0.7646 (tp30) REVERT: F 566 THR cc_start: 0.7926 (t) cc_final: 0.7699 (m) REVERT: F 603 ASP cc_start: 0.8349 (p0) cc_final: 0.8007 (p0) REVERT: F 688 ARG cc_start: 0.7337 (mpp-170) cc_final: 0.6928 (ttm-80) REVERT: E 83 LEU cc_start: 0.7820 (mm) cc_final: 0.7615 (mp) REVERT: E 127 GLU cc_start: 0.5663 (OUTLIER) cc_final: 0.5299 (mt-10) REVERT: E 204 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6910 (p0) REVERT: E 207 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7243 (mm) REVERT: E 212 ASN cc_start: 0.7841 (m110) cc_final: 0.7640 (m-40) REVERT: E 249 GLN cc_start: 0.8398 (mt0) cc_final: 0.8194 (mt0) REVERT: E 385 GLU cc_start: 0.7890 (tt0) cc_final: 0.7655 (tt0) REVERT: E 498 GLU cc_start: 0.8340 (pt0) cc_final: 0.8033 (pt0) REVERT: E 566 THR cc_start: 0.8066 (t) cc_final: 0.7773 (m) REVERT: E 603 ASP cc_start: 0.8386 (p0) cc_final: 0.7717 (p0) REVERT: E 651 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7945 (mt) REVERT: E 688 ARG cc_start: 0.7258 (mpp-170) cc_final: 0.6848 (ttm-80) REVERT: E 698 LYS cc_start: 0.8252 (mttp) cc_final: 0.7997 (mtpt) REVERT: D 72 VAL cc_start: 0.7744 (p) cc_final: 0.7492 (m) REVERT: D 127 GLU cc_start: 0.5822 (mt-10) cc_final: 0.5557 (mt-10) REVERT: D 204 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.7031 (p0) REVERT: D 207 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7178 (mm) REVERT: D 212 ASN cc_start: 0.7668 (m110) cc_final: 0.7372 (m-40) REVERT: D 249 GLN cc_start: 0.8455 (mt0) cc_final: 0.8198 (mt0) REVERT: D 257 SER cc_start: 0.6761 (m) cc_final: 0.6481 (t) REVERT: D 358 VAL cc_start: 0.9030 (p) cc_final: 0.8828 (t) REVERT: D 498 GLU cc_start: 0.8361 (pt0) cc_final: 0.8038 (pt0) REVERT: D 566 THR cc_start: 0.7976 (t) cc_final: 0.7619 (m) REVERT: D 651 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8242 (mt) REVERT: D 688 ARG cc_start: 0.7129 (mpp-170) cc_final: 0.6701 (ttm-80) REVERT: D 697 GLU cc_start: 0.7716 (pp20) cc_final: 0.7312 (pp20) REVERT: C 86 ARG cc_start: 0.6745 (tpm170) cc_final: 0.6516 (tpt170) REVERT: C 204 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6905 (p0) REVERT: C 207 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7347 (mm) REVERT: C 225 ARG cc_start: 0.7861 (tpp80) cc_final: 0.7448 (tpp80) REVERT: C 249 GLN cc_start: 0.8437 (mt0) cc_final: 0.8209 (mt0) REVERT: C 385 GLU cc_start: 0.7854 (tt0) cc_final: 0.7612 (tt0) REVERT: C 534 GLU cc_start: 0.6166 (OUTLIER) cc_final: 0.5731 (mt-10) REVERT: C 603 ASP cc_start: 0.8467 (p0) cc_final: 0.8223 (p0) REVERT: C 651 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8097 (mt) REVERT: C 688 ARG cc_start: 0.6926 (mpp-170) cc_final: 0.6484 (ttm-80) REVERT: C 698 LYS cc_start: 0.8262 (mttp) cc_final: 0.7965 (mtpt) outliers start: 78 outliers final: 26 residues processed: 548 average time/residue: 0.7081 time to fit residues: 463.3655 Evaluate side-chains 451 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 403 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 556 ARG Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 556 ARG Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 651 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 450 optimal weight: 0.7980 chunk 207 optimal weight: 4.9990 chunk 123 optimal weight: 0.0030 chunk 493 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 496 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 261 optimal weight: 4.9990 chunk 235 optimal weight: 10.0000 chunk 196 optimal weight: 0.9980 chunk 464 optimal weight: 4.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN G 573 GLN G 642 GLN F 429 GLN E 573 GLN D 113 ASN D 642 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.223819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.185738 restraints weight = 44278.270| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 1.87 r_work: 0.3887 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 40044 Z= 0.134 Angle : 0.604 8.778 54355 Z= 0.291 Chirality : 0.041 0.444 6041 Planarity : 0.004 0.054 7245 Dihedral : 6.913 83.731 5735 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.65 % Favored : 97.21 % Rotamer: Outliers : 2.44 % Allowed : 15.69 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.12), residues: 5019 helix: 1.40 (0.10), residues: 2597 sheet: 0.36 (0.21), residues: 595 loop : 0.38 (0.15), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 280 TYR 0.021 0.002 TYR A 557 PHE 0.015 0.001 PHE F 692 TRP 0.010 0.001 TRP B 250 HIS 0.004 0.001 HIS C 543 Details of bonding type rmsd covalent geometry : bond 0.00300 (40040) covalent geometry : angle 0.60400 (54355) hydrogen bonds : bond 0.04050 ( 2190) hydrogen bonds : angle 4.69257 ( 6300) Misc. bond : bond 0.00011 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 442 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 204 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7002 (p0) REVERT: B 212 ASN cc_start: 0.7894 (m110) cc_final: 0.7686 (m-40) REVERT: B 225 ARG cc_start: 0.8064 (tpp80) cc_final: 0.7590 (tpp80) REVERT: B 385 GLU cc_start: 0.7881 (tt0) cc_final: 0.7641 (tt0) REVERT: B 556 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.7016 (tmt170) REVERT: B 566 THR cc_start: 0.7959 (t) cc_final: 0.7671 (m) REVERT: B 603 ASP cc_start: 0.8365 (p0) cc_final: 0.7944 (p0) REVERT: B 651 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8053 (mt) REVERT: B 688 ARG cc_start: 0.7072 (mpp-170) cc_final: 0.6693 (ttm-80) REVERT: B 697 GLU cc_start: 0.7778 (pp20) cc_final: 0.7344 (pp20) REVERT: B 698 LYS cc_start: 0.8384 (mttp) cc_final: 0.7927 (mtpt) REVERT: A 117 GLU cc_start: 0.7405 (pp20) cc_final: 0.7154 (pp20) REVERT: A 204 ASP cc_start: 0.7213 (OUTLIER) cc_final: 0.6793 (p0) REVERT: A 217 LEU cc_start: 0.8195 (mp) cc_final: 0.7990 (mt) REVERT: A 225 ARG cc_start: 0.7965 (tpp80) cc_final: 0.7494 (tpp-160) REVERT: A 249 GLN cc_start: 0.8445 (mt0) cc_final: 0.8226 (mt0) REVERT: A 488 ARG cc_start: 0.8195 (mtt90) cc_final: 0.7928 (mtt90) REVERT: A 566 THR cc_start: 0.8030 (t) cc_final: 0.7713 (m) REVERT: A 603 ASP cc_start: 0.8421 (p0) cc_final: 0.8184 (p0) REVERT: A 651 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8133 (mt) REVERT: A 665 ARG cc_start: 0.7512 (ttm110) cc_final: 0.7097 (ttp80) REVERT: A 688 ARG cc_start: 0.6934 (mpp-170) cc_final: 0.6552 (ttm-80) REVERT: G 204 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6773 (p0) REVERT: G 225 ARG cc_start: 0.7986 (tpp80) cc_final: 0.7570 (tpp80) REVERT: G 229 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6586 (mt-10) REVERT: G 237 ARG cc_start: 0.7757 (ttt180) cc_final: 0.7455 (ttp-110) REVERT: G 249 GLN cc_start: 0.8426 (mt0) cc_final: 0.8203 (mt0) REVERT: G 385 GLU cc_start: 0.7948 (tt0) cc_final: 0.7694 (mm-30) REVERT: G 498 GLU cc_start: 0.8496 (pt0) cc_final: 0.7977 (pm20) REVERT: G 556 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7127 (tmt170) REVERT: G 566 THR cc_start: 0.8007 (t) cc_final: 0.7666 (m) REVERT: G 648 GLU cc_start: 0.7912 (tt0) cc_final: 0.7695 (mt-10) REVERT: G 651 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8084 (mt) REVERT: G 665 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7613 (ttp80) REVERT: G 675 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7594 (mm-30) REVERT: G 688 ARG cc_start: 0.7192 (mpp-170) cc_final: 0.6659 (ttm-80) REVERT: F 72 VAL cc_start: 0.7785 (p) cc_final: 0.7560 (m) REVERT: F 117 GLU cc_start: 0.7396 (pp20) cc_final: 0.7138 (pp20) REVERT: F 127 GLU cc_start: 0.5764 (mt-10) cc_final: 0.5503 (mt-10) REVERT: F 204 ASP cc_start: 0.7266 (OUTLIER) cc_final: 0.6789 (p0) REVERT: F 207 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7270 (mm) REVERT: F 225 ARG cc_start: 0.8025 (tpp80) cc_final: 0.7546 (tpp80) REVERT: F 249 GLN cc_start: 0.8490 (mt0) cc_final: 0.8242 (mt0) REVERT: F 385 GLU cc_start: 0.7879 (tt0) cc_final: 0.7653 (tt0) REVERT: F 559 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6565 (mt-10) REVERT: F 566 THR cc_start: 0.7979 (t) cc_final: 0.7745 (m) REVERT: F 688 ARG cc_start: 0.7248 (mpp-170) cc_final: 0.6953 (ttm110) REVERT: E 117 GLU cc_start: 0.7381 (pp20) cc_final: 0.7157 (pp20) REVERT: E 127 GLU cc_start: 0.5687 (tt0) cc_final: 0.5351 (mt-10) REVERT: E 204 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6744 (p0) REVERT: E 207 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7175 (mm) REVERT: E 212 ASN cc_start: 0.7688 (m110) cc_final: 0.7472 (m-40) REVERT: E 249 GLN cc_start: 0.8427 (mt0) cc_final: 0.8219 (mt0) REVERT: E 385 GLU cc_start: 0.7860 (tt0) cc_final: 0.7636 (tt0) REVERT: E 556 ARG cc_start: 0.7407 (tmt170) cc_final: 0.7122 (tpt90) REVERT: E 566 THR cc_start: 0.8117 (t) cc_final: 0.7776 (m) REVERT: E 603 ASP cc_start: 0.8277 (p0) cc_final: 0.7826 (p0) REVERT: E 651 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7979 (mt) REVERT: E 665 ARG cc_start: 0.7642 (ttm110) cc_final: 0.7381 (ttp80) REVERT: E 688 ARG cc_start: 0.7185 (mpp-170) cc_final: 0.6852 (ttm-80) REVERT: E 698 LYS cc_start: 0.8267 (mttp) cc_final: 0.8025 (mtpt) REVERT: D 72 VAL cc_start: 0.7742 (p) cc_final: 0.7498 (m) REVERT: D 127 GLU cc_start: 0.5810 (mt-10) cc_final: 0.5576 (mt-10) REVERT: D 204 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.6915 (p0) REVERT: D 207 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7145 (mm) REVERT: D 212 ASN cc_start: 0.7616 (m110) cc_final: 0.7338 (m-40) REVERT: D 249 GLN cc_start: 0.8496 (mt0) cc_final: 0.8244 (mt0) REVERT: D 257 SER cc_start: 0.6774 (m) cc_final: 0.6480 (t) REVERT: D 498 GLU cc_start: 0.8462 (pt0) cc_final: 0.8143 (pt0) REVERT: D 566 THR cc_start: 0.8071 (t) cc_final: 0.7695 (m) REVERT: D 651 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8261 (mt) REVERT: D 688 ARG cc_start: 0.7144 (mpp-170) cc_final: 0.6707 (ttm-80) REVERT: D 697 GLU cc_start: 0.7728 (pp20) cc_final: 0.7306 (pp20) REVERT: C 72 VAL cc_start: 0.7850 (p) cc_final: 0.7635 (m) REVERT: C 86 ARG cc_start: 0.6706 (tpm170) cc_final: 0.6466 (tpt170) REVERT: C 117 GLU cc_start: 0.7395 (pp20) cc_final: 0.7182 (pp20) REVERT: C 135 PHE cc_start: 0.5026 (m-10) cc_final: 0.4822 (m-10) REVERT: C 204 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.6887 (p0) REVERT: C 207 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7380 (mm) REVERT: C 212 ASN cc_start: 0.7822 (m110) cc_final: 0.7570 (m-40) REVERT: C 249 GLN cc_start: 0.8460 (mt0) cc_final: 0.8241 (mt0) REVERT: C 385 GLU cc_start: 0.7830 (tt0) cc_final: 0.7610 (tt0) REVERT: C 534 GLU cc_start: 0.6212 (mm-30) cc_final: 0.5790 (mt-10) REVERT: C 572 GLU cc_start: 0.6803 (pt0) cc_final: 0.6553 (pt0) REVERT: C 651 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8087 (mt) REVERT: C 688 ARG cc_start: 0.6872 (mpp-170) cc_final: 0.6599 (ttm-80) REVERT: C 697 GLU cc_start: 0.7700 (pp20) cc_final: 0.7129 (pp20) REVERT: C 698 LYS cc_start: 0.8290 (mttp) cc_final: 0.7872 (mtpt) outliers start: 97 outliers final: 31 residues processed: 490 average time/residue: 0.7343 time to fit residues: 428.7060 Evaluate side-chains 439 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 389 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 556 ARG Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 530 SER Chi-restraints excluded: chain G residue 556 ARG Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 560 HIS Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 651 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 369 optimal weight: 5.9990 chunk 352 optimal weight: 0.7980 chunk 210 optimal weight: 0.9990 chunk 405 optimal weight: 0.8980 chunk 238 optimal weight: 5.9990 chunk 479 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 322 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 398 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN B 573 GLN A 121 GLN F 696 GLN E 573 GLN C 121 GLN C 413 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.220050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.180867 restraints weight = 44068.348| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 1.70 r_work: 0.3863 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3738 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 40044 Z= 0.174 Angle : 0.626 8.852 54355 Z= 0.303 Chirality : 0.042 0.384 6041 Planarity : 0.005 0.057 7245 Dihedral : 6.870 77.735 5735 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.33 % Favored : 97.53 % Rotamer: Outliers : 3.57 % Allowed : 16.17 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.12), residues: 5019 helix: 1.26 (0.10), residues: 2597 sheet: 0.21 (0.21), residues: 602 loop : 0.26 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 280 TYR 0.023 0.002 TYR A 557 PHE 0.017 0.002 PHE A 135 TRP 0.010 0.002 TRP B 250 HIS 0.004 0.001 HIS C 543 Details of bonding type rmsd covalent geometry : bond 0.00406 (40040) covalent geometry : angle 0.62582 (54355) hydrogen bonds : bond 0.04072 ( 2190) hydrogen bonds : angle 4.66210 ( 6300) Misc. bond : bond 0.00084 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 423 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.6540 (tpt) REVERT: B 204 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.6869 (p0) REVERT: B 237 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.5587 (ttp-110) REVERT: B 385 GLU cc_start: 0.7853 (tt0) cc_final: 0.7629 (tt0) REVERT: B 556 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7267 (tmt170) REVERT: B 566 THR cc_start: 0.8146 (t) cc_final: 0.7854 (m) REVERT: B 651 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8086 (mt) REVERT: B 688 ARG cc_start: 0.7035 (mpp-170) cc_final: 0.6719 (ttm-80) REVERT: B 697 GLU cc_start: 0.7817 (pp20) cc_final: 0.7303 (pp20) REVERT: B 698 LYS cc_start: 0.8439 (mttp) cc_final: 0.7976 (mtpt) REVERT: A 204 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6774 (p0) REVERT: A 212 ASN cc_start: 0.7859 (m110) cc_final: 0.7643 (m-40) REVERT: A 225 ARG cc_start: 0.7953 (tpp80) cc_final: 0.7497 (tpp-160) REVERT: A 237 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.5841 (ttp-110) REVERT: A 249 GLN cc_start: 0.8494 (mt0) cc_final: 0.8269 (mt0) REVERT: A 566 THR cc_start: 0.8134 (t) cc_final: 0.7803 (m) REVERT: A 651 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8172 (mt) REVERT: A 665 ARG cc_start: 0.7613 (ttm110) cc_final: 0.7212 (ttp80) REVERT: A 688 ARG cc_start: 0.6993 (mpp-170) cc_final: 0.6762 (mtp85) REVERT: G 1 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.6327 (tpt) REVERT: G 117 GLU cc_start: 0.7345 (pp20) cc_final: 0.7070 (pp20) REVERT: G 204 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.6754 (p0) REVERT: G 229 GLU cc_start: 0.6696 (mm-30) cc_final: 0.6495 (mt-10) REVERT: G 237 ARG cc_start: 0.7703 (ttt180) cc_final: 0.7327 (ttp-110) REVERT: G 249 GLN cc_start: 0.8454 (mt0) cc_final: 0.8222 (mt0) REVERT: G 385 GLU cc_start: 0.7994 (tt0) cc_final: 0.7748 (tt0) REVERT: G 498 GLU cc_start: 0.8561 (pt0) cc_final: 0.8348 (pt0) REVERT: G 556 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7442 (tpt90) REVERT: G 566 THR cc_start: 0.8089 (t) cc_final: 0.7776 (m) REVERT: G 651 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8096 (mt) REVERT: G 688 ARG cc_start: 0.7195 (mpp-170) cc_final: 0.6713 (ttm-80) REVERT: F 127 GLU cc_start: 0.5910 (mt-10) cc_final: 0.5636 (mt-10) REVERT: F 204 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6722 (p0) REVERT: F 207 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7304 (mm) REVERT: F 212 ASN cc_start: 0.7778 (m110) cc_final: 0.7462 (m-40) REVERT: F 225 ARG cc_start: 0.7986 (tpp80) cc_final: 0.7538 (tpp-160) REVERT: F 237 ARG cc_start: 0.7631 (ttt180) cc_final: 0.7277 (ttp-110) REVERT: F 249 GLN cc_start: 0.8528 (mt0) cc_final: 0.8306 (mt0) REVERT: F 385 GLU cc_start: 0.7980 (tt0) cc_final: 0.7658 (tt0) REVERT: F 566 THR cc_start: 0.8080 (t) cc_final: 0.7806 (m) REVERT: F 651 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8205 (mt) REVERT: F 688 ARG cc_start: 0.7181 (mpp-170) cc_final: 0.6963 (ttm-80) REVERT: E 72 VAL cc_start: 0.7867 (p) cc_final: 0.7622 (m) REVERT: E 113 ASN cc_start: 0.7882 (m-40) cc_final: 0.7676 (m110) REVERT: E 127 GLU cc_start: 0.5671 (OUTLIER) cc_final: 0.5354 (mt-10) REVERT: E 204 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6625 (p0) REVERT: E 237 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.5569 (ttp-110) REVERT: E 249 GLN cc_start: 0.8486 (mt0) cc_final: 0.8269 (mt0) REVERT: E 385 GLU cc_start: 0.7908 (tt0) cc_final: 0.7659 (tt0) REVERT: E 498 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8084 (pt0) REVERT: E 566 THR cc_start: 0.8269 (t) cc_final: 0.7901 (m) REVERT: E 603 ASP cc_start: 0.8269 (p0) cc_final: 0.7904 (p0) REVERT: E 651 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8015 (mt) REVERT: E 665 ARG cc_start: 0.7709 (ttm110) cc_final: 0.7392 (ttp80) REVERT: E 688 ARG cc_start: 0.7180 (mpp-170) cc_final: 0.6960 (ttm110) REVERT: E 698 LYS cc_start: 0.8282 (mttp) cc_final: 0.8028 (mtpt) REVERT: D 72 VAL cc_start: 0.7859 (p) cc_final: 0.7643 (m) REVERT: D 117 GLU cc_start: 0.7407 (pp20) cc_final: 0.7198 (pp20) REVERT: D 127 GLU cc_start: 0.5776 (mt-10) cc_final: 0.5525 (mt-10) REVERT: D 204 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.6867 (p0) REVERT: D 237 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.5785 (ttp-110) REVERT: D 249 GLN cc_start: 0.8498 (mt0) cc_final: 0.8265 (mt0) REVERT: D 498 GLU cc_start: 0.8496 (pt0) cc_final: 0.8257 (pt0) REVERT: D 566 THR cc_start: 0.8156 (t) cc_final: 0.7736 (m) REVERT: D 651 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8306 (mt) REVERT: D 688 ARG cc_start: 0.7190 (mpp-170) cc_final: 0.6959 (mtp85) REVERT: D 697 GLU cc_start: 0.7845 (pp20) cc_final: 0.7516 (pp20) REVERT: C 86 ARG cc_start: 0.6697 (tpm170) cc_final: 0.6453 (tpt170) REVERT: C 117 GLU cc_start: 0.7377 (pp20) cc_final: 0.7156 (pp20) REVERT: C 204 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.6868 (p0) REVERT: C 207 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7390 (mm) REVERT: C 237 ARG cc_start: 0.7611 (ttt180) cc_final: 0.7288 (ttp-110) REVERT: C 249 GLN cc_start: 0.8484 (mt0) cc_final: 0.8258 (mt0) REVERT: C 385 GLU cc_start: 0.7878 (tt0) cc_final: 0.7609 (tt0) REVERT: C 534 GLU cc_start: 0.6269 (mm-30) cc_final: 0.5935 (mt-10) REVERT: C 651 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8167 (mt) REVERT: C 665 ARG cc_start: 0.7733 (ttm110) cc_final: 0.7193 (ttp80) REVERT: C 697 GLU cc_start: 0.7751 (pp20) cc_final: 0.7157 (pp20) REVERT: C 698 LYS cc_start: 0.8313 (mttp) cc_final: 0.7913 (mtpt) outliers start: 142 outliers final: 47 residues processed: 502 average time/residue: 0.7891 time to fit residues: 468.2922 Evaluate side-chains 448 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 375 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 556 ARG Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 492 THR Chi-restraints excluded: chain G residue 530 SER Chi-restraints excluded: chain G residue 556 ARG Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 498 GLU Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 651 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 26 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 288 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 88 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 428 optimal weight: 3.9990 chunk 491 optimal weight: 0.9990 chunk 217 optimal weight: 0.7980 chunk 302 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN B 355 GLN B 642 GLN A 16 ASN A 113 ASN A 121 GLN A 642 GLN G 113 ASN G 121 GLN G 597 ASN E 355 GLN D 121 GLN D 355 GLN C 113 ASN C 121 GLN C 355 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.217068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.175835 restraints weight = 43530.225| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 1.86 r_work: 0.3803 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 40044 Z= 0.127 Angle : 0.599 11.864 54355 Z= 0.286 Chirality : 0.040 0.371 6041 Planarity : 0.004 0.048 7245 Dihedral : 6.594 77.507 5735 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.37 % Favored : 97.49 % Rotamer: Outliers : 3.22 % Allowed : 18.16 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.12), residues: 5019 helix: 1.34 (0.10), residues: 2597 sheet: 0.35 (0.21), residues: 595 loop : 0.36 (0.15), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 488 TYR 0.020 0.002 TYR A 557 PHE 0.016 0.001 PHE C 352 TRP 0.008 0.001 TRP A 250 HIS 0.005 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00284 (40040) covalent geometry : angle 0.59937 (54355) hydrogen bonds : bond 0.03845 ( 2190) hydrogen bonds : angle 4.52431 ( 6300) Misc. bond : bond 0.00012 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 407 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 204 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.6788 (p0) REVERT: B 385 GLU cc_start: 0.7961 (tt0) cc_final: 0.7705 (tt0) REVERT: B 556 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7172 (tmt170) REVERT: B 566 THR cc_start: 0.8216 (t) cc_final: 0.7888 (m) REVERT: B 651 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8063 (mt) REVERT: B 688 ARG cc_start: 0.7125 (mpp-170) cc_final: 0.6519 (ttm-80) REVERT: B 698 LYS cc_start: 0.8307 (mttp) cc_final: 0.7954 (mtpt) REVERT: A 204 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6842 (p0) REVERT: A 212 ASN cc_start: 0.7898 (m110) cc_final: 0.7634 (m-40) REVERT: A 225 ARG cc_start: 0.7983 (tpp80) cc_final: 0.7546 (tpp-160) REVERT: A 249 GLN cc_start: 0.8521 (mt0) cc_final: 0.8302 (mt0) REVERT: A 566 THR cc_start: 0.8192 (t) cc_final: 0.7848 (m) REVERT: A 651 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8147 (mt) REVERT: A 665 ARG cc_start: 0.7612 (ttm110) cc_final: 0.7198 (ttp80) REVERT: A 688 ARG cc_start: 0.6974 (mpp-170) cc_final: 0.6624 (mtp85) REVERT: G 204 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6621 (p0) REVERT: G 229 GLU cc_start: 0.6769 (mm-30) cc_final: 0.6511 (mt-10) REVERT: G 237 ARG cc_start: 0.7605 (ttt180) cc_final: 0.7196 (ttp-110) REVERT: G 249 GLN cc_start: 0.8443 (mt0) cc_final: 0.8188 (mt0) REVERT: G 320 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: G 385 GLU cc_start: 0.8025 (tt0) cc_final: 0.7741 (mm-30) REVERT: G 498 GLU cc_start: 0.8629 (pt0) cc_final: 0.8426 (pt0) REVERT: G 572 GLU cc_start: 0.7360 (pt0) cc_final: 0.7144 (pt0) REVERT: G 651 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8059 (mt) REVERT: G 688 ARG cc_start: 0.7242 (mpp-170) cc_final: 0.6861 (mtp85) REVERT: G 696 GLN cc_start: 0.8269 (tp-100) cc_final: 0.8066 (tp40) REVERT: F 127 GLU cc_start: 0.5944 (mt-10) cc_final: 0.5677 (mt-10) REVERT: F 204 ASP cc_start: 0.7138 (OUTLIER) cc_final: 0.6634 (p0) REVERT: F 207 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7143 (mm) REVERT: F 212 ASN cc_start: 0.7755 (m110) cc_final: 0.7521 (m-40) REVERT: F 249 GLN cc_start: 0.8553 (mt0) cc_final: 0.8317 (mt0) REVERT: F 320 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: F 385 GLU cc_start: 0.7996 (tt0) cc_final: 0.7693 (tt0) REVERT: F 566 THR cc_start: 0.8150 (t) cc_final: 0.7859 (m) REVERT: F 651 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8218 (mt) REVERT: F 688 ARG cc_start: 0.7157 (mpp-170) cc_final: 0.6904 (ttm110) REVERT: E 1 MET cc_start: 0.7482 (ptt) cc_final: 0.6360 (tpt) REVERT: E 72 VAL cc_start: 0.7756 (p) cc_final: 0.7517 (m) REVERT: E 127 GLU cc_start: 0.5485 (OUTLIER) cc_final: 0.5217 (mt-10) REVERT: E 204 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6585 (p0) REVERT: E 320 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: E 385 GLU cc_start: 0.7942 (tt0) cc_final: 0.7692 (mm-30) REVERT: E 566 THR cc_start: 0.8285 (t) cc_final: 0.7881 (m) REVERT: E 603 ASP cc_start: 0.8297 (p0) cc_final: 0.7944 (p0) REVERT: E 648 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7720 (mt-10) REVERT: E 651 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7991 (mt) REVERT: E 665 ARG cc_start: 0.7679 (ttm110) cc_final: 0.7352 (ttp80) REVERT: E 688 ARG cc_start: 0.7236 (mpp-170) cc_final: 0.6805 (ttm110) REVERT: E 698 LYS cc_start: 0.8204 (mttp) cc_final: 0.7961 (mtpt) REVERT: D 72 VAL cc_start: 0.7921 (p) cc_final: 0.7661 (m) REVERT: D 127 GLU cc_start: 0.5911 (mt-10) cc_final: 0.5646 (mt-10) REVERT: D 204 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.6957 (p0) REVERT: D 207 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7169 (mm) REVERT: D 249 GLN cc_start: 0.8511 (mt0) cc_final: 0.8288 (mt0) REVERT: D 651 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8332 (mt) REVERT: D 688 ARG cc_start: 0.7190 (mpp-170) cc_final: 0.6885 (mtp85) REVERT: D 697 GLU cc_start: 0.7872 (pp20) cc_final: 0.7524 (pp20) REVERT: C 86 ARG cc_start: 0.6763 (tpm170) cc_final: 0.6508 (tpt170) REVERT: C 113 ASN cc_start: 0.7850 (m-40) cc_final: 0.7638 (m110) REVERT: C 117 GLU cc_start: 0.7299 (pp20) cc_final: 0.7062 (pp20) REVERT: C 121 GLN cc_start: 0.6851 (mm-40) cc_final: 0.6648 (mm110) REVERT: C 204 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6858 (p0) REVERT: C 207 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7360 (mm) REVERT: C 225 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7334 (tpt-90) REVERT: C 237 ARG cc_start: 0.7577 (ttt180) cc_final: 0.7223 (ttp-110) REVERT: C 249 GLN cc_start: 0.8505 (mt0) cc_final: 0.8285 (mt0) REVERT: C 385 GLU cc_start: 0.7934 (tt0) cc_final: 0.7545 (mm-30) REVERT: C 534 GLU cc_start: 0.6083 (mm-30) cc_final: 0.5776 (mt-10) REVERT: C 651 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8162 (mt) REVERT: C 665 ARG cc_start: 0.7704 (ttm110) cc_final: 0.7179 (ttp80) REVERT: C 697 GLU cc_start: 0.7803 (pp20) cc_final: 0.7358 (pp20) REVERT: C 698 LYS cc_start: 0.8268 (mttp) cc_final: 0.8012 (mttt) outliers start: 128 outliers final: 42 residues processed: 481 average time/residue: 0.7154 time to fit residues: 410.8978 Evaluate side-chains 429 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 363 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 556 ARG Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 320 GLU Chi-restraints excluded: chain G residue 433 MET Chi-restraints excluded: chain G residue 530 SER Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 648 GLU Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 225 ARG Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 651 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 17 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 325 optimal weight: 0.7980 chunk 280 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 195 optimal weight: 0.0370 chunk 444 optimal weight: 9.9990 chunk 457 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 306 optimal weight: 2.9990 overall best weight: 2.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 642 GLN A 113 ASN G 113 ASN F 573 GLN E 113 ASN E 121 GLN E 413 GLN D 16 ASN D 121 GLN D 573 GLN C 696 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.212097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.170973 restraints weight = 43712.562| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 1.92 r_work: 0.3768 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 40044 Z= 0.220 Angle : 0.667 13.112 54355 Z= 0.323 Chirality : 0.043 0.353 6041 Planarity : 0.005 0.065 7245 Dihedral : 6.636 70.771 5735 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.41 % Favored : 97.45 % Rotamer: Outliers : 3.57 % Allowed : 19.29 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.12), residues: 5019 helix: 1.08 (0.10), residues: 2597 sheet: 0.21 (0.20), residues: 602 loop : 0.14 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 556 TYR 0.021 0.002 TYR G 557 PHE 0.017 0.002 PHE A 380 TRP 0.011 0.002 TRP E 250 HIS 0.004 0.001 HIS B 670 Details of bonding type rmsd covalent geometry : bond 0.00524 (40040) covalent geometry : angle 0.66691 (54355) hydrogen bonds : bond 0.04130 ( 2190) hydrogen bonds : angle 4.73794 ( 6300) Misc. bond : bond 0.00134 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 381 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.6564 (tpt) REVERT: B 204 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6570 (p0) REVERT: B 205 TRP cc_start: 0.8279 (m100) cc_final: 0.7899 (m100) REVERT: B 237 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.5552 (ttp-110) REVERT: B 385 GLU cc_start: 0.7916 (tt0) cc_final: 0.7627 (tt0) REVERT: B 566 THR cc_start: 0.8310 (t) cc_final: 0.7959 (m) REVERT: B 651 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8123 (mt) REVERT: B 688 ARG cc_start: 0.7107 (mpp-170) cc_final: 0.6754 (mtp85) REVERT: B 698 LYS cc_start: 0.8209 (mttp) cc_final: 0.7837 (mtpt) REVERT: A 204 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6710 (p0) REVERT: A 212 ASN cc_start: 0.8073 (m110) cc_final: 0.7867 (m-40) REVERT: A 225 ARG cc_start: 0.7953 (tpp80) cc_final: 0.7668 (tpp-160) REVERT: A 237 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.5653 (ttp-110) REVERT: A 566 THR cc_start: 0.8233 (t) cc_final: 0.7861 (m) REVERT: A 651 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8190 (mt) REVERT: A 665 ARG cc_start: 0.7641 (ttm110) cc_final: 0.7254 (ttp80) REVERT: A 688 ARG cc_start: 0.6996 (mpp-170) cc_final: 0.6651 (mtp85) REVERT: G 204 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6506 (p0) REVERT: G 205 TRP cc_start: 0.8321 (m100) cc_final: 0.8034 (m100) REVERT: G 229 GLU cc_start: 0.6635 (mm-30) cc_final: 0.6383 (mt-10) REVERT: G 237 ARG cc_start: 0.7504 (ttt180) cc_final: 0.7025 (ttp-110) REVERT: G 267 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8388 (p) REVERT: G 319 ARG cc_start: 0.6696 (OUTLIER) cc_final: 0.6323 (ttp-170) REVERT: G 385 GLU cc_start: 0.8110 (tt0) cc_final: 0.7784 (tt0) REVERT: G 566 THR cc_start: 0.8102 (t) cc_final: 0.7803 (m) REVERT: G 572 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7016 (pt0) REVERT: G 651 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8094 (mt) REVERT: G 688 ARG cc_start: 0.7197 (mpp-170) cc_final: 0.6782 (mtp85) REVERT: F 127 GLU cc_start: 0.5985 (mt-10) cc_final: 0.5714 (mt-10) REVERT: F 204 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6562 (p0) REVERT: F 237 ARG cc_start: 0.7519 (ttt180) cc_final: 0.7071 (ttp-110) REVERT: F 385 GLU cc_start: 0.8044 (tt0) cc_final: 0.7761 (tt0) REVERT: F 566 THR cc_start: 0.8270 (t) cc_final: 0.7925 (m) REVERT: F 651 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8227 (mt) REVERT: F 688 ARG cc_start: 0.7079 (mpp-170) cc_final: 0.6828 (ttm-80) REVERT: E 127 GLU cc_start: 0.5617 (OUTLIER) cc_final: 0.5301 (mt-10) REVERT: E 204 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6490 (p0) REVERT: E 237 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.5479 (ttp-110) REVERT: E 385 GLU cc_start: 0.8017 (tt0) cc_final: 0.7704 (tt0) REVERT: E 566 THR cc_start: 0.8435 (t) cc_final: 0.8001 (m) REVERT: E 603 ASP cc_start: 0.8331 (p0) cc_final: 0.7981 (p0) REVERT: E 651 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8058 (mt) REVERT: E 665 ARG cc_start: 0.7684 (ttm110) cc_final: 0.7326 (ttp80) REVERT: E 688 ARG cc_start: 0.7112 (mpp-170) cc_final: 0.6860 (mtp85) REVERT: E 698 LYS cc_start: 0.8124 (mttp) cc_final: 0.7855 (mtpt) REVERT: D 127 GLU cc_start: 0.5801 (mt-10) cc_final: 0.5549 (mt-10) REVERT: D 204 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6811 (p0) REVERT: D 237 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.5650 (ttp-110) REVERT: D 249 GLN cc_start: 0.8524 (mt0) cc_final: 0.8268 (mt0) REVERT: D 651 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8247 (mt) REVERT: D 688 ARG cc_start: 0.7129 (mpp-170) cc_final: 0.6853 (mtp85) REVERT: D 697 GLU cc_start: 0.7820 (pp20) cc_final: 0.7454 (pp20) REVERT: C 86 ARG cc_start: 0.6685 (tpm170) cc_final: 0.6482 (tpt170) REVERT: C 117 GLU cc_start: 0.7266 (pp20) cc_final: 0.6992 (pp20) REVERT: C 121 GLN cc_start: 0.6900 (mm-40) cc_final: 0.6644 (mm110) REVERT: C 204 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6795 (p0) REVERT: C 225 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7496 (tpt-90) REVERT: C 237 ARG cc_start: 0.7535 (ttt180) cc_final: 0.7084 (ttp-110) REVERT: C 249 GLN cc_start: 0.8534 (mt0) cc_final: 0.8290 (mt0) REVERT: C 385 GLU cc_start: 0.7975 (tt0) cc_final: 0.7685 (tt0) REVERT: C 534 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.5864 (mt-10) REVERT: C 651 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8225 (mt) REVERT: C 665 ARG cc_start: 0.7683 (ttm110) cc_final: 0.7138 (ttp80) REVERT: C 697 GLU cc_start: 0.7876 (pp20) cc_final: 0.7327 (pp20) REVERT: C 698 LYS cc_start: 0.8216 (mttp) cc_final: 0.7892 (mtpt) outliers start: 142 outliers final: 58 residues processed: 473 average time/residue: 0.7350 time to fit residues: 412.9968 Evaluate side-chains 432 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 349 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 319 ARG Chi-restraints excluded: chain G residue 433 MET Chi-restraints excluded: chain G residue 530 SER Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 572 GLU Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain F residue 619 VAL Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 619 VAL Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain D residue 16 ASN Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 225 ARG Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 651 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 309 optimal weight: 9.9990 chunk 467 optimal weight: 2.9990 chunk 364 optimal weight: 0.9980 chunk 198 optimal weight: 5.9990 chunk 393 optimal weight: 0.5980 chunk 352 optimal weight: 0.8980 chunk 338 optimal weight: 7.9990 chunk 416 optimal weight: 2.9990 chunk 319 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN G 113 ASN G 121 GLN E 355 GLN D 113 ASN D 121 GLN C 113 ASN C 573 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.213849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.172987 restraints weight = 43419.447| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.88 r_work: 0.3771 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 40044 Z= 0.162 Angle : 0.634 15.444 54355 Z= 0.305 Chirality : 0.041 0.343 6041 Planarity : 0.005 0.055 7245 Dihedral : 6.468 70.561 5735 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.57 % Favored : 97.29 % Rotamer: Outliers : 2.99 % Allowed : 20.57 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.12), residues: 5019 helix: 1.15 (0.10), residues: 2597 sheet: 0.19 (0.20), residues: 602 loop : 0.16 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 533 TYR 0.021 0.002 TYR G 557 PHE 0.018 0.002 PHE D 380 TRP 0.009 0.002 TRP E 250 HIS 0.004 0.001 HIS C 543 Details of bonding type rmsd covalent geometry : bond 0.00376 (40040) covalent geometry : angle 0.63379 (54355) hydrogen bonds : bond 0.03961 ( 2190) hydrogen bonds : angle 4.64420 ( 6300) Misc. bond : bond 0.00049 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 370 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.6665 (tpt) REVERT: B 204 ASP cc_start: 0.7218 (OUTLIER) cc_final: 0.6639 (p0) REVERT: B 205 TRP cc_start: 0.8332 (OUTLIER) cc_final: 0.7981 (m100) REVERT: B 212 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7415 (t0) REVERT: B 237 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.5505 (ttp-110) REVERT: B 385 GLU cc_start: 0.7917 (tt0) cc_final: 0.7667 (tt0) REVERT: B 566 THR cc_start: 0.8273 (t) cc_final: 0.7954 (m) REVERT: B 651 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8127 (mt) REVERT: B 688 ARG cc_start: 0.7224 (mpp-170) cc_final: 0.6895 (mtp85) REVERT: B 698 LYS cc_start: 0.8306 (mttp) cc_final: 0.7957 (mtpt) REVERT: A 204 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.6798 (p0) REVERT: A 566 THR cc_start: 0.8215 (t) cc_final: 0.7863 (m) REVERT: A 651 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8198 (mt) REVERT: A 665 ARG cc_start: 0.7678 (ttm110) cc_final: 0.7332 (ttp80) REVERT: A 688 ARG cc_start: 0.7144 (mpp-170) cc_final: 0.6774 (mtp85) REVERT: G 204 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6552 (p0) REVERT: G 205 TRP cc_start: 0.8350 (m100) cc_final: 0.8097 (m100) REVERT: G 229 GLU cc_start: 0.6707 (mm-30) cc_final: 0.6485 (mt-10) REVERT: G 237 ARG cc_start: 0.7691 (ttt180) cc_final: 0.7206 (ttp-110) REVERT: G 385 GLU cc_start: 0.8112 (tt0) cc_final: 0.7862 (tt0) REVERT: G 566 THR cc_start: 0.8058 (t) cc_final: 0.7784 (m) REVERT: G 572 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7025 (pt0) REVERT: G 651 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8121 (mt) REVERT: G 688 ARG cc_start: 0.7359 (mpp-170) cc_final: 0.6877 (mtp85) REVERT: F 127 GLU cc_start: 0.5998 (mt-10) cc_final: 0.5736 (mt-10) REVERT: F 204 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6655 (p0) REVERT: F 237 ARG cc_start: 0.7637 (ttt180) cc_final: 0.7185 (ttp-110) REVERT: F 385 GLU cc_start: 0.8048 (tt0) cc_final: 0.7742 (tt0) REVERT: F 566 THR cc_start: 0.8220 (t) cc_final: 0.7885 (m) REVERT: F 651 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8229 (mt) REVERT: F 688 ARG cc_start: 0.7157 (mpp-170) cc_final: 0.6902 (ttm110) REVERT: E 127 GLU cc_start: 0.5535 (OUTLIER) cc_final: 0.5265 (mt-10) REVERT: E 204 ASP cc_start: 0.7156 (OUTLIER) cc_final: 0.6636 (p0) REVERT: E 212 ASN cc_start: 0.7684 (OUTLIER) cc_final: 0.7139 (t0) REVERT: E 237 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.5568 (ttp-110) REVERT: E 385 GLU cc_start: 0.7999 (tt0) cc_final: 0.7754 (tt0) REVERT: E 566 THR cc_start: 0.8386 (t) cc_final: 0.7980 (m) REVERT: E 603 ASP cc_start: 0.8313 (p0) cc_final: 0.7981 (p0) REVERT: E 651 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8122 (mt) REVERT: E 665 ARG cc_start: 0.7702 (ttm110) cc_final: 0.7385 (ttp80) REVERT: E 688 ARG cc_start: 0.7306 (mpp-170) cc_final: 0.7008 (mtp85) REVERT: E 698 LYS cc_start: 0.8249 (mttp) cc_final: 0.7991 (mtpt) REVERT: D 86 ARG cc_start: 0.6861 (mmp-170) cc_final: 0.6570 (tpt170) REVERT: D 127 GLU cc_start: 0.5846 (mt-10) cc_final: 0.5573 (mt-10) REVERT: D 204 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.6944 (p0) REVERT: D 207 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7221 (mm) REVERT: D 237 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.5626 (ttp-110) REVERT: D 249 GLN cc_start: 0.8536 (mt0) cc_final: 0.8300 (mt0) REVERT: D 285 VAL cc_start: 0.4084 (OUTLIER) cc_final: 0.3882 (m) REVERT: D 651 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8323 (mt) REVERT: D 688 ARG cc_start: 0.7237 (mpp-170) cc_final: 0.6936 (mtp85) REVERT: D 697 GLU cc_start: 0.7897 (pp20) cc_final: 0.7567 (pp20) REVERT: C 117 GLU cc_start: 0.7362 (pp20) cc_final: 0.7108 (pp20) REVERT: C 121 GLN cc_start: 0.6938 (mm-40) cc_final: 0.6709 (mm110) REVERT: C 204 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.6867 (p0) REVERT: C 207 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7367 (mm) REVERT: C 237 ARG cc_start: 0.7634 (ttt180) cc_final: 0.7177 (ttp-110) REVERT: C 249 GLN cc_start: 0.8529 (mt0) cc_final: 0.8277 (mt0) REVERT: C 385 GLU cc_start: 0.7999 (tt0) cc_final: 0.7737 (tt0) REVERT: C 534 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.5867 (mt-10) REVERT: C 651 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8257 (mt) REVERT: C 665 ARG cc_start: 0.7735 (ttm110) cc_final: 0.7253 (ttp80) REVERT: C 697 GLU cc_start: 0.7912 (pp20) cc_final: 0.7271 (pp20) REVERT: C 698 LYS cc_start: 0.8301 (mttp) cc_final: 0.8005 (mttt) outliers start: 119 outliers final: 59 residues processed: 441 average time/residue: 0.7031 time to fit residues: 370.3466 Evaluate side-chains 428 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 342 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 205 TRP Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 433 MET Chi-restraints excluded: chain G residue 530 SER Chi-restraints excluded: chain G residue 572 GLU Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain F residue 619 VAL Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 212 ASN Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 619 VAL Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 651 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 393 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 271 optimal weight: 1.9990 chunk 265 optimal weight: 4.9990 chunk 474 optimal weight: 3.9990 chunk 317 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 326 optimal weight: 2.9990 chunk 331 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN A 597 ASN G 113 ASN G 121 GLN F 113 ASN D 113 ASN D 121 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.215418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.177253 restraints weight = 43208.478| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 1.60 r_work: 0.3807 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 40044 Z= 0.250 Angle : 0.692 10.018 54355 Z= 0.337 Chirality : 0.044 0.349 6041 Planarity : 0.005 0.075 7245 Dihedral : 6.601 63.678 5735 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.77 % Favored : 97.09 % Rotamer: Outliers : 3.19 % Allowed : 21.03 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.12), residues: 5019 helix: 0.92 (0.10), residues: 2590 sheet: -0.07 (0.20), residues: 609 loop : -0.01 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 533 TYR 0.024 0.002 TYR F 557 PHE 0.020 0.002 PHE G 380 TRP 0.011 0.002 TRP E 250 HIS 0.003 0.001 HIS A 670 Details of bonding type rmsd covalent geometry : bond 0.00595 (40040) covalent geometry : angle 0.69202 (54355) hydrogen bonds : bond 0.04252 ( 2190) hydrogen bonds : angle 4.86390 ( 6300) Misc. bond : bond 0.00131 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 341 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.6677 (tpt) REVERT: B 135 PHE cc_start: 0.4582 (m-10) cc_final: 0.4328 (m-10) REVERT: B 204 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.6796 (p0) REVERT: B 212 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7682 (t0) REVERT: B 237 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.5633 (ttp-110) REVERT: B 385 GLU cc_start: 0.7951 (tt0) cc_final: 0.7713 (tt0) REVERT: B 566 THR cc_start: 0.8200 (t) cc_final: 0.7933 (m) REVERT: B 648 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: B 651 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8156 (mt) REVERT: B 688 ARG cc_start: 0.7359 (mpp-170) cc_final: 0.7141 (mtp85) REVERT: B 698 LYS cc_start: 0.8447 (mttp) cc_final: 0.8107 (mtpt) REVERT: A 204 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.6821 (p0) REVERT: A 237 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.5833 (ttp-110) REVERT: A 566 THR cc_start: 0.8161 (t) cc_final: 0.7817 (m) REVERT: A 651 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8236 (mt) REVERT: A 665 ARG cc_start: 0.7623 (ttm110) cc_final: 0.7337 (ttp80) REVERT: A 688 ARG cc_start: 0.7285 (mpp-170) cc_final: 0.6971 (mtp85) REVERT: G 204 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6673 (p0) REVERT: G 237 ARG cc_start: 0.7753 (ttt180) cc_final: 0.7238 (ttp-110) REVERT: G 267 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8434 (p) REVERT: G 385 GLU cc_start: 0.8144 (tt0) cc_final: 0.7878 (tt0) REVERT: G 566 THR cc_start: 0.8098 (t) cc_final: 0.7836 (m) REVERT: G 572 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6991 (pt0) REVERT: G 651 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8156 (mp) REVERT: G 688 ARG cc_start: 0.7322 (mpp-170) cc_final: 0.6967 (mtp85) REVERT: F 127 GLU cc_start: 0.5987 (mt-10) cc_final: 0.5706 (mt-10) REVERT: F 204 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6710 (p0) REVERT: F 237 ARG cc_start: 0.7689 (ttt180) cc_final: 0.7148 (ttp-110) REVERT: F 385 GLU cc_start: 0.8031 (tt0) cc_final: 0.7781 (tt0) REVERT: F 566 THR cc_start: 0.8201 (t) cc_final: 0.7877 (m) REVERT: F 651 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8278 (mt) REVERT: E 127 GLU cc_start: 0.5674 (OUTLIER) cc_final: 0.5376 (mt-10) REVERT: E 204 ASP cc_start: 0.7250 (OUTLIER) cc_final: 0.6702 (p0) REVERT: E 212 ASN cc_start: 0.7891 (OUTLIER) cc_final: 0.7345 (t0) REVERT: E 237 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.5639 (ttp-110) REVERT: E 385 GLU cc_start: 0.8017 (tt0) cc_final: 0.7791 (tt0) REVERT: E 566 THR cc_start: 0.8272 (t) cc_final: 0.7899 (m) REVERT: E 651 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8151 (mt) REVERT: E 665 ARG cc_start: 0.7658 (ttm110) cc_final: 0.7405 (ttp80) REVERT: E 698 LYS cc_start: 0.8392 (mttp) cc_final: 0.8167 (mtpt) REVERT: D 127 GLU cc_start: 0.5955 (mt-10) cc_final: 0.5695 (mt-10) REVERT: D 204 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.6938 (p0) REVERT: D 237 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.5780 (ttp-110) REVERT: D 249 GLN cc_start: 0.8583 (mt0) cc_final: 0.8359 (mt0) REVERT: D 566 THR cc_start: 0.8272 (t) cc_final: 0.7999 (m) REVERT: D 651 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8292 (mt) REVERT: D 688 ARG cc_start: 0.7330 (mpp-170) cc_final: 0.7101 (mtp85) REVERT: D 697 GLU cc_start: 0.7929 (pp20) cc_final: 0.7645 (pp20) REVERT: C 117 GLU cc_start: 0.7476 (pp20) cc_final: 0.7186 (pp20) REVERT: C 121 GLN cc_start: 0.7054 (mm-40) cc_final: 0.6799 (mm110) REVERT: C 204 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.6883 (p0) REVERT: C 237 ARG cc_start: 0.7741 (ttt180) cc_final: 0.7204 (ttp-110) REVERT: C 249 GLN cc_start: 0.8583 (mt0) cc_final: 0.8326 (mt0) REVERT: C 385 GLU cc_start: 0.8028 (tt0) cc_final: 0.7774 (tt0) REVERT: C 534 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.6177 (mp0) REVERT: C 651 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8302 (mt) REVERT: C 665 ARG cc_start: 0.7720 (ttm110) cc_final: 0.7495 (ttp80) REVERT: C 697 GLU cc_start: 0.7939 (pp20) cc_final: 0.7451 (pp20) REVERT: C 698 LYS cc_start: 0.8399 (mttp) cc_final: 0.8170 (mtpt) outliers start: 127 outliers final: 64 residues processed: 420 average time/residue: 0.7023 time to fit residues: 352.8119 Evaluate side-chains 420 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 330 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 269 GLU Chi-restraints excluded: chain G residue 433 MET Chi-restraints excluded: chain G residue 530 SER Chi-restraints excluded: chain G residue 572 GLU Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain F residue 619 VAL Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 212 ASN Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 619 VAL Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 651 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 351 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 265 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 371 optimal weight: 40.0000 chunk 267 optimal weight: 0.9980 chunk 405 optimal weight: 0.9990 chunk 315 optimal weight: 3.9990 chunk 463 optimal weight: 4.9990 chunk 195 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN G 113 ASN G 121 GLN F 113 ASN ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.215270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.176579 restraints weight = 43276.484| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 1.61 r_work: 0.3810 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 40044 Z= 0.242 Angle : 0.696 10.129 54355 Z= 0.339 Chirality : 0.044 0.358 6041 Planarity : 0.005 0.072 7245 Dihedral : 6.615 60.496 5735 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.75 % Favored : 97.11 % Rotamer: Outliers : 2.82 % Allowed : 21.81 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.12), residues: 5019 helix: 0.84 (0.10), residues: 2590 sheet: -0.06 (0.19), residues: 602 loop : -0.05 (0.15), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 331 TYR 0.021 0.002 TYR G 557 PHE 0.023 0.002 PHE G 380 TRP 0.011 0.002 TRP E 250 HIS 0.004 0.001 HIS G 543 Details of bonding type rmsd covalent geometry : bond 0.00576 (40040) covalent geometry : angle 0.69563 (54355) hydrogen bonds : bond 0.04237 ( 2190) hydrogen bonds : angle 4.88627 ( 6300) Misc. bond : bond 0.00109 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 338 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.6707 (tpt) REVERT: B 135 PHE cc_start: 0.4731 (m-10) cc_final: 0.4317 (m-10) REVERT: B 204 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.6779 (p0) REVERT: B 212 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7678 (t0) REVERT: B 237 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.5595 (ttp-110) REVERT: B 385 GLU cc_start: 0.7915 (tt0) cc_final: 0.7665 (tt0) REVERT: B 566 THR cc_start: 0.8199 (t) cc_final: 0.7936 (m) REVERT: B 648 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7642 (mt-10) REVERT: B 651 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8163 (mt) REVERT: B 688 ARG cc_start: 0.7443 (mpp-170) cc_final: 0.7182 (mtp85) REVERT: B 698 LYS cc_start: 0.8435 (mttp) cc_final: 0.8098 (mtpt) REVERT: A 204 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.6873 (p0) REVERT: A 212 ASN cc_start: 0.8015 (m-40) cc_final: 0.7478 (t0) REVERT: A 237 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.5873 (ttp-110) REVERT: A 566 THR cc_start: 0.8143 (t) cc_final: 0.7807 (m) REVERT: A 651 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8238 (mt) REVERT: A 665 ARG cc_start: 0.7657 (ttm110) cc_final: 0.7341 (ttp80) REVERT: A 688 ARG cc_start: 0.7405 (mpp-170) cc_final: 0.7056 (mtp85) REVERT: G 135 PHE cc_start: 0.4747 (m-10) cc_final: 0.4505 (m-10) REVERT: G 204 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6697 (p0) REVERT: G 237 ARG cc_start: 0.7761 (ttt180) cc_final: 0.7186 (ttp-110) REVERT: G 385 GLU cc_start: 0.8135 (tt0) cc_final: 0.7881 (tt0) REVERT: G 566 THR cc_start: 0.8114 (t) cc_final: 0.7811 (m) REVERT: G 572 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7030 (pt0) REVERT: G 651 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8176 (mp) REVERT: G 688 ARG cc_start: 0.7338 (mpp-170) cc_final: 0.6968 (mtp85) REVERT: F 100 HIS cc_start: 0.7813 (m90) cc_final: 0.7369 (m-70) REVERT: F 127 GLU cc_start: 0.5915 (mt-10) cc_final: 0.5636 (mt-10) REVERT: F 204 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.6703 (p0) REVERT: F 207 LEU cc_start: 0.7759 (mm) cc_final: 0.7479 (mm) REVERT: F 229 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6261 (mm-30) REVERT: F 237 ARG cc_start: 0.7742 (ttt180) cc_final: 0.7194 (ttp-110) REVERT: F 385 GLU cc_start: 0.8020 (tt0) cc_final: 0.7781 (tt0) REVERT: F 566 THR cc_start: 0.8226 (t) cc_final: 0.7891 (m) REVERT: F 651 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8294 (mt) REVERT: E 127 GLU cc_start: 0.5644 (OUTLIER) cc_final: 0.5338 (mt-10) REVERT: E 204 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6686 (p0) REVERT: E 212 ASN cc_start: 0.7961 (OUTLIER) cc_final: 0.7418 (t0) REVERT: E 237 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.5598 (ttp-110) REVERT: E 385 GLU cc_start: 0.8043 (tt0) cc_final: 0.7821 (tt0) REVERT: E 566 THR cc_start: 0.8285 (t) cc_final: 0.7957 (m) REVERT: E 651 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8170 (mt) REVERT: E 665 ARG cc_start: 0.7635 (ttm110) cc_final: 0.7391 (ttp80) REVERT: E 688 ARG cc_start: 0.7405 (mtp85) cc_final: 0.6853 (mtm-85) REVERT: E 698 LYS cc_start: 0.8433 (mttp) cc_final: 0.8216 (mtpt) REVERT: D 127 GLU cc_start: 0.5995 (mt-10) cc_final: 0.5733 (mt-10) REVERT: D 204 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.6896 (p0) REVERT: D 207 LEU cc_start: 0.7607 (mm) cc_final: 0.7254 (mm) REVERT: D 212 ASN cc_start: 0.8092 (m-40) cc_final: 0.7592 (t0) REVERT: D 237 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.5686 (ttp-110) REVERT: D 249 GLN cc_start: 0.8578 (mt0) cc_final: 0.8340 (mt0) REVERT: D 566 THR cc_start: 0.8288 (t) cc_final: 0.8047 (m) REVERT: D 651 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8298 (mt) REVERT: D 697 GLU cc_start: 0.7935 (pp20) cc_final: 0.7651 (pp20) REVERT: C 117 GLU cc_start: 0.7405 (pp20) cc_final: 0.7131 (pp20) REVERT: C 121 GLN cc_start: 0.7067 (mm-40) cc_final: 0.6826 (mm110) REVERT: C 204 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.6865 (p0) REVERT: C 237 ARG cc_start: 0.7721 (ttt180) cc_final: 0.7167 (ttp-110) REVERT: C 249 GLN cc_start: 0.8589 (mt0) cc_final: 0.8336 (mt0) REVERT: C 385 GLU cc_start: 0.8063 (tt0) cc_final: 0.7784 (tt0) REVERT: C 534 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6182 (mp0) REVERT: C 651 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8333 (mt) REVERT: C 665 ARG cc_start: 0.7713 (ttm110) cc_final: 0.7320 (ttp80) REVERT: C 697 GLU cc_start: 0.7927 (pp20) cc_final: 0.7420 (pp20) REVERT: C 698 LYS cc_start: 0.8374 (mttp) cc_final: 0.8143 (mtpt) outliers start: 112 outliers final: 56 residues processed: 409 average time/residue: 0.6963 time to fit residues: 340.4825 Evaluate side-chains 407 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 326 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 269 GLU Chi-restraints excluded: chain G residue 433 MET Chi-restraints excluded: chain G residue 530 SER Chi-restraints excluded: chain G residue 560 HIS Chi-restraints excluded: chain G residue 572 GLU Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain F residue 619 VAL Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 212 ASN Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 619 VAL Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 651 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 120 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 287 optimal weight: 0.6980 chunk 181 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 chunk 457 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN A 113 ASN A 642 GLN G 113 ASN G 642 GLN F 113 ASN D 113 ASN D 121 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.212262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.171343 restraints weight = 43458.782| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 1.88 r_work: 0.3766 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 40044 Z= 0.170 Angle : 0.663 11.248 54355 Z= 0.321 Chirality : 0.042 0.350 6041 Planarity : 0.005 0.060 7245 Dihedral : 6.409 60.268 5735 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.77 % Favored : 97.09 % Rotamer: Outliers : 2.19 % Allowed : 22.41 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.12), residues: 5019 helix: 1.03 (0.10), residues: 2597 sheet: -0.10 (0.19), residues: 609 loop : -0.03 (0.15), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 331 TYR 0.021 0.002 TYR G 557 PHE 0.027 0.002 PHE F 380 TRP 0.020 0.002 TRP G 205 HIS 0.003 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00397 (40040) covalent geometry : angle 0.66298 (54355) hydrogen bonds : bond 0.04023 ( 2190) hydrogen bonds : angle 4.71604 ( 6300) Misc. bond : bond 0.00070 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 344 time to evaluate : 1.008 Fit side-chains REVERT: B 1 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.6625 (tpt) REVERT: B 204 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6165 (m-30) REVERT: B 212 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7599 (t0) REVERT: B 237 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.5533 (ttp-110) REVERT: B 385 GLU cc_start: 0.7921 (tt0) cc_final: 0.7667 (tt0) REVERT: B 566 THR cc_start: 0.8245 (t) cc_final: 0.7966 (m) REVERT: B 648 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: B 651 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8135 (mt) REVERT: B 688 ARG cc_start: 0.7418 (mpp-170) cc_final: 0.7004 (mtp85) REVERT: B 696 GLN cc_start: 0.8198 (tp-100) cc_final: 0.7983 (tp40) REVERT: B 698 LYS cc_start: 0.8336 (mttp) cc_final: 0.8004 (mtpt) REVERT: A 204 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.6826 (p0) REVERT: A 212 ASN cc_start: 0.7937 (m-40) cc_final: 0.7467 (t0) REVERT: A 237 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.5798 (ttp-110) REVERT: A 566 THR cc_start: 0.8219 (t) cc_final: 0.7865 (m) REVERT: A 651 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8224 (mt) REVERT: A 665 ARG cc_start: 0.7639 (ttm110) cc_final: 0.7313 (ttp80) REVERT: A 688 ARG cc_start: 0.7293 (mpp-170) cc_final: 0.6849 (mtp85) REVERT: G 135 PHE cc_start: 0.4665 (m-10) cc_final: 0.4441 (m-10) REVERT: G 204 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6533 (p0) REVERT: G 205 TRP cc_start: 0.8335 (m100) cc_final: 0.7976 (m100) REVERT: G 237 ARG cc_start: 0.7659 (ttt180) cc_final: 0.7092 (ttp-110) REVERT: G 319 ARG cc_start: 0.6674 (OUTLIER) cc_final: 0.6247 (ttp-170) REVERT: G 385 GLU cc_start: 0.8138 (tt0) cc_final: 0.7838 (tt0) REVERT: G 566 THR cc_start: 0.7997 (t) cc_final: 0.7735 (m) REVERT: G 572 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7121 (pt0) REVERT: G 651 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8126 (mp) REVERT: G 688 ARG cc_start: 0.7372 (mpp-170) cc_final: 0.6901 (mtp85) REVERT: F 100 HIS cc_start: 0.7764 (m90) cc_final: 0.7299 (m-70) REVERT: F 127 GLU cc_start: 0.5955 (mt-10) cc_final: 0.5684 (mt-10) REVERT: F 204 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6626 (p0) REVERT: F 207 LEU cc_start: 0.7631 (mm) cc_final: 0.7330 (mm) REVERT: F 225 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7427 (tpt-90) REVERT: F 229 GLU cc_start: 0.6794 (mm-30) cc_final: 0.6225 (mm-30) REVERT: F 237 ARG cc_start: 0.7602 (ttt180) cc_final: 0.7106 (ttp-110) REVERT: F 385 GLU cc_start: 0.7975 (tt0) cc_final: 0.7692 (tt0) REVERT: F 566 THR cc_start: 0.8283 (t) cc_final: 0.7917 (m) REVERT: F 651 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8303 (mt) REVERT: E 127 GLU cc_start: 0.5569 (OUTLIER) cc_final: 0.5306 (mt-10) REVERT: E 204 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6649 (p0) REVERT: E 212 ASN cc_start: 0.7874 (m-40) cc_final: 0.7334 (t0) REVERT: E 385 GLU cc_start: 0.8042 (tt0) cc_final: 0.7762 (tt0) REVERT: E 566 THR cc_start: 0.8343 (t) cc_final: 0.7985 (m) REVERT: E 651 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8141 (mt) REVERT: E 665 ARG cc_start: 0.7611 (ttm110) cc_final: 0.7371 (ttp80) REVERT: E 698 LYS cc_start: 0.8306 (mttp) cc_final: 0.8085 (mtpt) REVERT: D 86 ARG cc_start: 0.6816 (mmp-170) cc_final: 0.6544 (tpt170) REVERT: D 127 GLU cc_start: 0.5987 (mt-10) cc_final: 0.5694 (mt-10) REVERT: D 204 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6844 (p0) REVERT: D 212 ASN cc_start: 0.8010 (m-40) cc_final: 0.7494 (t0) REVERT: D 237 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.5601 (ttp-110) REVERT: D 249 GLN cc_start: 0.8517 (mt0) cc_final: 0.8274 (mt0) REVERT: D 566 THR cc_start: 0.8237 (t) cc_final: 0.7982 (m) REVERT: D 651 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8284 (mt) REVERT: D 688 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6881 (mtm-85) REVERT: D 697 GLU cc_start: 0.7942 (pp20) cc_final: 0.7613 (pp20) REVERT: C 117 GLU cc_start: 0.7322 (pp20) cc_final: 0.7046 (pp20) REVERT: C 121 GLN cc_start: 0.7001 (mm-40) cc_final: 0.6756 (mm110) REVERT: C 204 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6868 (p0) REVERT: C 207 LEU cc_start: 0.7712 (mm) cc_final: 0.7381 (mm) REVERT: C 237 ARG cc_start: 0.7651 (ttt180) cc_final: 0.7085 (ttp-110) REVERT: C 249 GLN cc_start: 0.8571 (mt0) cc_final: 0.8337 (mt0) REVERT: C 385 GLU cc_start: 0.8044 (tt0) cc_final: 0.7775 (tt0) REVERT: C 534 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.5959 (mp0) REVERT: C 651 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8311 (mt) REVERT: C 665 ARG cc_start: 0.7683 (ttm110) cc_final: 0.7286 (ttp80) REVERT: C 697 GLU cc_start: 0.7951 (pp20) cc_final: 0.7376 (pp20) REVERT: C 698 LYS cc_start: 0.8271 (mttp) cc_final: 0.8030 (mttt) outliers start: 87 outliers final: 47 residues processed: 397 average time/residue: 0.7304 time to fit residues: 347.3231 Evaluate side-chains 396 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 323 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 319 ARG Chi-restraints excluded: chain G residue 433 MET Chi-restraints excluded: chain G residue 530 SER Chi-restraints excluded: chain G residue 572 GLU Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain F residue 619 VAL Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 619 VAL Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 688 ARG Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 651 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 472 optimal weight: 5.9990 chunk 372 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 401 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 205 optimal weight: 0.8980 chunk 246 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 423 optimal weight: 0.3980 chunk 38 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 642 GLN D 642 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.212237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.171409 restraints weight = 43413.458| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.92 r_work: 0.3765 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 40044 Z= 0.176 Angle : 0.662 10.805 54355 Z= 0.320 Chirality : 0.042 0.349 6041 Planarity : 0.005 0.062 7245 Dihedral : 6.298 59.505 5735 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.69 % Favored : 97.17 % Rotamer: Outliers : 2.44 % Allowed : 22.33 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.12), residues: 5019 helix: 1.08 (0.10), residues: 2590 sheet: -0.08 (0.19), residues: 609 loop : 0.02 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 331 TYR 0.022 0.002 TYR G 557 PHE 0.027 0.002 PHE F 380 TRP 0.010 0.002 TRP E 250 HIS 0.003 0.001 HIS C 543 Details of bonding type rmsd covalent geometry : bond 0.00413 (40040) covalent geometry : angle 0.66154 (54355) hydrogen bonds : bond 0.04006 ( 2190) hydrogen bonds : angle 4.69982 ( 6300) Misc. bond : bond 0.00082 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13551.45 seconds wall clock time: 230 minutes 46.80 seconds (13846.80 seconds total)