Starting phenix.real_space_refine on Sat Jun 6 05:53:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y08_72388/06_2026/9y08_72388.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y08_72388/06_2026/9y08_72388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y08_72388/06_2026/9y08_72388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y08_72388/06_2026/9y08_72388.map" model { file = "/net/cci-nas-00/data/ceres_data/9y08_72388/06_2026/9y08_72388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y08_72388/06_2026/9y08_72388.cif" } resolution = 2.78 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 132 5.16 5 C 16104 2.51 5 N 4512 2.21 5 O 4920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25692 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4228 Classifications: {'peptide': 544} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 26, 'TRANS': 514} Chain breaks: 1 Chain: "B" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4228 Classifications: {'peptide': 544} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 26, 'TRANS': 514} Chain breaks: 1 Chain: "C" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4228 Classifications: {'peptide': 544} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 26, 'TRANS': 514} Chain breaks: 1 Chain: "D" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4228 Classifications: {'peptide': 544} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 26, 'TRANS': 514} Chain breaks: 1 Chain: "E" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4228 Classifications: {'peptide': 544} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 26, 'TRANS': 514} Chain breaks: 1 Chain: "F" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4228 Classifications: {'peptide': 544} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 26, 'TRANS': 514} Chain breaks: 1 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.57, per 1000 atoms: 0.26 Number of scatterers: 25692 At special positions: 0 Unit cell: (139, 143, 95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 24 15.00 O 4920 8.00 N 4512 7.00 C 16104 6.00 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=0, symmetry=0 Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 892.6 milliseconds 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6072 Finding SS restraints... Secondary structure from input PDB file: 191 helices and 12 sheets defined 60.9% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 211 through 220 removed outlier: 3.588A pdb=" N VAL A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.667A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 270 through 277 removed outlier: 3.741A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.571A pdb=" N SER A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.977A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 removed outlier: 3.584A pdb=" N ARG A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 334 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.811A pdb=" N ILE A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 396 through 403 removed outlier: 3.690A pdb=" N ALA A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 426 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 448 through 457 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 506 removed outlier: 3.622A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 557 through 569 removed outlier: 3.745A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.530A pdb=" N ILE A 629 " --> pdb=" O PRO A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 649 through 662 removed outlier: 3.569A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.534A pdb=" N THR A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 705 Processing helix chain 'A' and resid 732 through 742 removed outlier: 3.708A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 763 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.700A pdb=" N VAL B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.788A pdb=" N LEU B 224 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 233 removed outlier: 3.685A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 270 through 277 removed outlier: 3.677A pdb=" N LYS B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.535A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.921A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 removed outlier: 3.612A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 334 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.837A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 396 through 403 removed outlier: 3.728A pdb=" N ALA B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 426 Processing helix chain 'B' and resid 439 through 445 Processing helix chain 'B' and resid 448 through 457 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 removed outlier: 3.544A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 506 removed outlier: 3.642A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 557 through 569 removed outlier: 4.439A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 598 through 610 Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.572A pdb=" N ILE B 629 " --> pdb=" O PRO B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 649 through 662 removed outlier: 3.562A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.542A pdb=" N THR B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 705 Processing helix chain 'B' and resid 732 through 742 removed outlier: 3.721A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 763 Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.506A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 220 removed outlier: 3.516A pdb=" N VAL C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 226 removed outlier: 3.681A pdb=" N LEU C 224 " --> pdb=" O VAL C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 233 removed outlier: 3.653A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 270 through 277 removed outlier: 3.680A pdb=" N LYS C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.644A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.896A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 removed outlier: 3.762A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 334 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.834A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 396 through 403 removed outlier: 3.743A pdb=" N ALA C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 426 Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 448 through 457 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 506 removed outlier: 3.654A pdb=" N PHE C 506 " --> pdb=" O LYS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 Processing helix chain 'C' and resid 543 through 554 Processing helix chain 'C' and resid 557 through 569 removed outlier: 3.803A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 610 Processing helix chain 'C' and resid 625 through 629 removed outlier: 3.568A pdb=" N ILE C 629 " --> pdb=" O PRO C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 649 through 662 removed outlier: 3.584A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.597A pdb=" N THR C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 705 Processing helix chain 'C' and resid 732 through 742 removed outlier: 3.694A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 763 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 211 through 226 removed outlier: 3.616A pdb=" N VAL D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.649A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 270 through 277 removed outlier: 3.734A pdb=" N LYS D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 296 removed outlier: 3.620A pdb=" N SER D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.983A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 326 removed outlier: 3.573A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 334 Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.810A pdb=" N ILE D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 396 through 403 removed outlier: 3.678A pdb=" N ALA D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 426 Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 448 through 457 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 506 removed outlier: 3.619A pdb=" N PHE D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 557 through 569 removed outlier: 3.746A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 610 Processing helix chain 'D' and resid 625 through 629 removed outlier: 3.530A pdb=" N ILE D 629 " --> pdb=" O PRO D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 634 Processing helix chain 'D' and resid 649 through 662 removed outlier: 3.569A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.538A pdb=" N THR D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 705 Processing helix chain 'D' and resid 732 through 742 removed outlier: 3.704A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 763 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 211 through 220 removed outlier: 3.716A pdb=" N VAL E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 226 Processing helix chain 'E' and resid 226 through 233 removed outlier: 3.681A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 270 through 277 removed outlier: 3.676A pdb=" N LYS E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.546A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.918A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 326 removed outlier: 3.826A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 334 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.834A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 396 through 403 removed outlier: 3.780A pdb=" N ALA E 400 " --> pdb=" O LEU E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 426 Processing helix chain 'E' and resid 439 through 445 Processing helix chain 'E' and resid 448 through 457 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 removed outlier: 3.526A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 506 removed outlier: 3.644A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 Processing helix chain 'E' and resid 543 through 553 Processing helix chain 'E' and resid 557 through 569 removed outlier: 4.441A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 610 Processing helix chain 'E' and resid 625 through 629 removed outlier: 3.573A pdb=" N ILE E 629 " --> pdb=" O PRO E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 634 Processing helix chain 'E' and resid 649 through 662 removed outlier: 3.559A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.555A pdb=" N THR E 679 " --> pdb=" O LEU E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 705 Processing helix chain 'E' and resid 732 through 742 removed outlier: 3.696A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 763 Processing helix chain 'F' and resid 202 through 206 removed outlier: 3.513A pdb=" N ILE F 206 " --> pdb=" O TYR F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 220 removed outlier: 3.540A pdb=" N VAL F 220 " --> pdb=" O ILE F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 226 removed outlier: 3.724A pdb=" N LEU F 224 " --> pdb=" O VAL F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 233 removed outlier: 3.647A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 270 through 277 removed outlier: 3.703A pdb=" N LYS F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.572A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.749A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 326 removed outlier: 3.703A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 334 removed outlier: 3.589A pdb=" N LEU F 331 " --> pdb=" O GLN F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.840A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 396 through 403 removed outlier: 3.807A pdb=" N ALA F 400 " --> pdb=" O LEU F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 426 Processing helix chain 'F' and resid 439 through 445 Processing helix chain 'F' and resid 448 through 457 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 506 removed outlier: 3.652A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 543 through 553 Processing helix chain 'F' and resid 557 through 569 removed outlier: 4.027A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 610 Processing helix chain 'F' and resid 625 through 629 removed outlier: 3.578A pdb=" N ILE F 629 " --> pdb=" O PRO F 626 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 634 Processing helix chain 'F' and resid 649 through 662 removed outlier: 3.578A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.586A pdb=" N THR F 679 " --> pdb=" O LEU F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 705 Processing helix chain 'F' and resid 732 through 742 removed outlier: 3.694A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 763 Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 268 removed outlier: 6.184A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.720A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 268 removed outlier: 6.192A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.718A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 268 removed outlier: 6.195A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C 367 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR C 244 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.697A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 268 removed outlier: 6.201A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 367 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.719A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 265 through 268 removed outlier: 6.195A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.732A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 265 through 268 removed outlier: 6.199A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL F 367 " --> pdb=" O LEU F 242 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR F 244 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.693A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) 1244 hydrogen bonds defined for protein. 3516 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: 4.68 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8692 1.34 - 1.46: 2594 1.46 - 1.57: 14584 1.57 - 1.69: 38 1.69 - 1.81: 222 Bond restraints: 26130 Sorted by residual: bond pdb=" C ASN B 460 " pdb=" N PRO B 461 " ideal model delta sigma weight residual 1.339 1.411 -0.071 3.40e-02 8.65e+02 4.41e+00 bond pdb=" C ASN E 460 " pdb=" N PRO E 461 " ideal model delta sigma weight residual 1.339 1.410 -0.071 3.40e-02 8.65e+02 4.34e+00 bond pdb=" C ASN D 460 " pdb=" N PRO D 461 " ideal model delta sigma weight residual 1.339 1.407 -0.068 3.40e-02 8.65e+02 3.97e+00 bond pdb=" CB PRO F 461 " pdb=" CG PRO F 461 " ideal model delta sigma weight residual 1.492 1.588 -0.096 5.00e-02 4.00e+02 3.70e+00 bond pdb=" CB PRO C 461 " pdb=" CG PRO C 461 " ideal model delta sigma weight residual 1.492 1.585 -0.093 5.00e-02 4.00e+02 3.49e+00 ... (remaining 26125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 34152 1.45 - 2.90: 809 2.90 - 4.35: 250 4.35 - 5.80: 111 5.80 - 7.25: 18 Bond angle restraints: 35340 Sorted by residual: angle pdb=" CA PRO C 461 " pdb=" N PRO C 461 " pdb=" CD PRO C 461 " ideal model delta sigma weight residual 112.00 104.75 7.25 1.40e+00 5.10e-01 2.68e+01 angle pdb=" CA PRO F 461 " pdb=" N PRO F 461 " pdb=" CD PRO F 461 " ideal model delta sigma weight residual 112.00 104.79 7.21 1.40e+00 5.10e-01 2.65e+01 angle pdb=" N ILE F 590 " pdb=" CA ILE F 590 " pdb=" C ILE F 590 " ideal model delta sigma weight residual 112.12 108.22 3.90 8.40e-01 1.42e+00 2.15e+01 angle pdb=" N ILE C 590 " pdb=" CA ILE C 590 " pdb=" C ILE C 590 " ideal model delta sigma weight residual 112.12 108.27 3.85 8.40e-01 1.42e+00 2.10e+01 angle pdb=" N ILE A 590 " pdb=" CA ILE A 590 " pdb=" C ILE A 590 " ideal model delta sigma weight residual 112.12 108.39 3.73 8.40e-01 1.42e+00 1.97e+01 ... (remaining 35335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.20: 14844 19.20 - 38.39: 1067 38.39 - 57.59: 140 57.59 - 76.79: 32 76.79 - 95.99: 15 Dihedral angle restraints: 16098 sinusoidal: 6738 harmonic: 9360 Sorted by residual: dihedral pdb=" C5' ADP D 901 " pdb=" O5' ADP D 901 " pdb=" PA ADP D 901 " pdb=" O2A ADP D 901 " ideal model delta sinusoidal sigma weight residual -60.00 -155.98 95.99 1 2.00e+01 2.50e-03 2.65e+01 dihedral pdb=" C5' ADP A 901 " pdb=" O5' ADP A 901 " pdb=" PA ADP A 901 " pdb=" O2A ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 -155.92 95.92 1 2.00e+01 2.50e-03 2.65e+01 dihedral pdb=" C5' ADP B 902 " pdb=" O5' ADP B 902 " pdb=" PA ADP B 902 " pdb=" O2A ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 -155.37 95.38 1 2.00e+01 2.50e-03 2.62e+01 ... (remaining 16095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2833 0.039 - 0.078: 843 0.078 - 0.117: 266 0.117 - 0.156: 24 0.156 - 0.196: 6 Chirality restraints: 3972 Sorted by residual: chirality pdb=" CA ASN A 460 " pdb=" N ASN A 460 " pdb=" C ASN A 460 " pdb=" CB ASN A 460 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.56e-01 chirality pdb=" CA ASN F 460 " pdb=" N ASN F 460 " pdb=" C ASN F 460 " pdb=" CB ASN F 460 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.74e-01 chirality pdb=" CA ASN C 460 " pdb=" N ASN C 460 " pdb=" C ASN C 460 " pdb=" CB ASN C 460 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.77e-01 ... (remaining 3969 not shown) Planarity restraints: 4620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN F 460 " 0.052 5.00e-02 4.00e+02 7.58e-02 9.20e+00 pdb=" N PRO F 461 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO F 461 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 461 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 460 " -0.050 5.00e-02 4.00e+02 7.39e-02 8.73e+00 pdb=" N PRO C 461 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 461 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 461 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 460 " 0.049 5.00e-02 4.00e+02 7.19e-02 8.28e+00 pdb=" N PRO A 461 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 461 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 461 " 0.040 5.00e-02 4.00e+02 ... (remaining 4617 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 589 2.70 - 3.25: 26391 3.25 - 3.80: 40398 3.80 - 4.35: 56883 4.35 - 4.90: 88785 Nonbonded interactions: 213046 Sorted by model distance: nonbonded pdb=" NH1 ARG C 745 " pdb=" O VAL C 747 " model vdw 2.146 3.120 nonbonded pdb=" NH1 ARG F 745 " pdb=" O VAL F 747 " model vdw 2.148 3.120 nonbonded pdb=" NH1 ARG A 745 " pdb=" O VAL A 747 " model vdw 2.153 3.120 nonbonded pdb=" NH1 ARG D 745 " pdb=" O VAL D 747 " model vdw 2.154 3.120 nonbonded pdb=" O ASN E 624 " pdb=" OH TYR E 755 " model vdw 2.226 3.040 ... (remaining 213041 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 23.360 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 26130 Z= 0.118 Angle : 0.648 7.253 35340 Z= 0.320 Chirality : 0.041 0.196 3972 Planarity : 0.004 0.076 4620 Dihedral : 13.406 95.987 10026 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.43 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.15), residues: 3240 helix: 0.56 (0.13), residues: 1698 sheet: 0.20 (0.25), residues: 384 loop : -0.62 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 287 TYR 0.009 0.001 TYR D 244 PHE 0.010 0.001 PHE F 360 TRP 0.014 0.001 TRP B 454 HIS 0.003 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (26130) covalent geometry : angle 0.64806 / 0.32 (35340) hydrogen bonds : bond 0.22212 / 14.99 ( 1244) hydrogen bonds : angle 6.66626 / 4.78 ( 3516) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 522 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8215 (pttm) cc_final: 0.7796 (mmmt) REVERT: A 239 ARG cc_start: 0.7439 (mtt180) cc_final: 0.6770 (mmm160) REVERT: A 560 ARG cc_start: 0.8742 (ttp-110) cc_final: 0.8057 (tpp-160) REVERT: A 651 LYS cc_start: 0.9068 (mppt) cc_final: 0.8799 (tptp) REVERT: A 678 MET cc_start: 0.9160 (mmm) cc_final: 0.8863 (mmm) REVERT: A 752 ILE cc_start: 0.9006 (tp) cc_final: 0.8713 (tp) REVERT: B 239 ARG cc_start: 0.7365 (mtt180) cc_final: 0.6830 (mmp-170) REVERT: B 305 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8408 (mt-10) REVERT: B 324 ILE cc_start: 0.8708 (tp) cc_final: 0.8363 (mp) REVERT: B 449 MET cc_start: 0.8213 (tpt) cc_final: 0.7953 (tpt) REVERT: B 678 MET cc_start: 0.9181 (mmm) cc_final: 0.8954 (mmm) REVERT: B 752 ILE cc_start: 0.9032 (tp) cc_final: 0.8650 (tp) REVERT: C 239 ARG cc_start: 0.7460 (mtt180) cc_final: 0.6776 (mmm160) REVERT: C 454 TRP cc_start: 0.8838 (t60) cc_final: 0.8225 (t60) REVERT: C 560 ARG cc_start: 0.8599 (ttm110) cc_final: 0.8131 (ttt180) REVERT: C 568 GLN cc_start: 0.8469 (tp40) cc_final: 0.8085 (tm-30) REVERT: D 203 TYR cc_start: 0.8732 (m-80) cc_final: 0.8448 (m-80) REVERT: D 236 LYS cc_start: 0.8291 (pttm) cc_final: 0.7875 (mmmt) REVERT: D 239 ARG cc_start: 0.7391 (mtt180) cc_final: 0.6789 (mmm160) REVERT: D 442 MET cc_start: 0.5511 (mpp) cc_final: 0.5193 (mpt) REVERT: D 560 ARG cc_start: 0.8752 (ttp-110) cc_final: 0.8088 (tpp-160) REVERT: D 616 ASN cc_start: 0.8407 (m-40) cc_final: 0.8201 (t160) REVERT: D 651 LYS cc_start: 0.9052 (mppt) cc_final: 0.8801 (tptp) REVERT: D 678 MET cc_start: 0.9170 (mmm) cc_final: 0.8875 (mmm) REVERT: E 239 ARG cc_start: 0.7413 (mtt180) cc_final: 0.6819 (mmp-170) REVERT: E 281 GLU cc_start: 0.8066 (tp30) cc_final: 0.7558 (tp30) REVERT: E 305 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8400 (mt-10) REVERT: E 678 MET cc_start: 0.9161 (mmm) cc_final: 0.8953 (mmm) REVERT: E 752 ILE cc_start: 0.9031 (tp) cc_final: 0.8652 (tp) REVERT: F 239 ARG cc_start: 0.7468 (mtt180) cc_final: 0.6961 (mmp-170) REVERT: F 454 TRP cc_start: 0.8839 (t60) cc_final: 0.8229 (t60) REVERT: F 560 ARG cc_start: 0.8539 (ttm110) cc_final: 0.8041 (ttt180) REVERT: F 561 GLU cc_start: 0.8725 (mp0) cc_final: 0.8440 (mp0) REVERT: F 568 GLN cc_start: 0.8486 (tp40) cc_final: 0.8083 (tm-30) REVERT: F 651 LYS cc_start: 0.9136 (mppt) cc_final: 0.8922 (tptp) REVERT: F 752 ILE cc_start: 0.9012 (tp) cc_final: 0.8693 (tp) outliers start: 0 outliers final: 2 residues processed: 522 average time/residue: 0.8967 time to fit residues: 520.5668 Evaluate side-chains 319 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 317 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 669 ASP Chi-restraints excluded: chain E residue 669 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 0.0870 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN A 750 ASN B 327 GLN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN C 750 ASN D 421 GLN ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN D 750 ASN E 327 GLN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 750 ASN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 538 ASN F 616 ASN F 750 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.116708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.087889 restraints weight = 46646.253| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.62 r_work: 0.3076 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26130 Z= 0.169 Angle : 0.736 9.569 35340 Z= 0.353 Chirality : 0.045 0.192 3972 Planarity : 0.005 0.055 4620 Dihedral : 7.260 92.862 3640 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.96 % Favored : 93.86 % Rotamer: Outliers : 1.74 % Allowed : 8.61 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.15), residues: 3240 helix: 0.92 (0.13), residues: 1692 sheet: 0.27 (0.25), residues: 384 loop : -0.41 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 225 TYR 0.019 0.002 TYR C 203 PHE 0.008 0.001 PHE E 503 TRP 0.020 0.002 TRP B 454 HIS 0.006 0.001 HIS F 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (26130) covalent geometry : angle 0.73575 / 0.35 (35340) hydrogen bonds : bond 0.04644 / 3.13 ( 1244) hydrogen bonds : angle 4.64590 / 3.34 ( 3516) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 342 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.7531 (tpp-160) cc_final: 0.7271 (mpt-90) REVERT: A 236 LYS cc_start: 0.8195 (pttm) cc_final: 0.7808 (mmmt) REVERT: A 239 ARG cc_start: 0.7477 (mtt180) cc_final: 0.6726 (mmm160) REVERT: A 449 MET cc_start: 0.7781 (tpt) cc_final: 0.7198 (tpp) REVERT: A 560 ARG cc_start: 0.8817 (ttp-110) cc_final: 0.7986 (ttt180) REVERT: A 561 GLU cc_start: 0.8586 (mp0) cc_final: 0.8163 (mp0) REVERT: A 651 LYS cc_start: 0.9047 (mppt) cc_final: 0.8713 (tptp) REVERT: A 678 MET cc_start: 0.9118 (mmm) cc_final: 0.8842 (mmm) REVERT: A 753 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8501 (ptp-170) REVERT: B 239 ARG cc_start: 0.7594 (mtt180) cc_final: 0.6926 (mmp-170) REVERT: B 305 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8224 (mt-10) REVERT: B 324 ILE cc_start: 0.8708 (tp) cc_final: 0.8395 (mt) REVERT: B 442 MET cc_start: 0.4388 (mpt) cc_final: 0.4098 (mpt) REVERT: B 454 TRP cc_start: 0.8644 (t60) cc_final: 0.7630 (t60) REVERT: B 561 GLU cc_start: 0.8529 (mp0) cc_final: 0.8263 (mp0) REVERT: B 753 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8540 (ptt-90) REVERT: C 239 ARG cc_start: 0.7329 (mtt180) cc_final: 0.6893 (mmp-170) REVERT: C 454 TRP cc_start: 0.8729 (t60) cc_final: 0.8159 (t60) REVERT: C 560 ARG cc_start: 0.8700 (ttm110) cc_final: 0.7861 (ttt180) REVERT: C 561 GLU cc_start: 0.8595 (mp0) cc_final: 0.8104 (mp0) REVERT: C 565 LYS cc_start: 0.9228 (tttp) cc_final: 0.8991 (ttmm) REVERT: C 568 GLN cc_start: 0.8682 (tp40) cc_final: 0.8304 (tm-30) REVERT: D 236 LYS cc_start: 0.8154 (pttm) cc_final: 0.7854 (mmmt) REVERT: D 239 ARG cc_start: 0.7416 (mtt180) cc_final: 0.6662 (mmm160) REVERT: D 442 MET cc_start: 0.5595 (mpp) cc_final: 0.5366 (mpt) REVERT: D 449 MET cc_start: 0.7743 (tpt) cc_final: 0.7163 (tpp) REVERT: D 560 ARG cc_start: 0.8822 (ttp-110) cc_final: 0.7980 (ttt180) REVERT: D 561 GLU cc_start: 0.8553 (mp0) cc_final: 0.8091 (mp0) REVERT: D 616 ASN cc_start: 0.8477 (m-40) cc_final: 0.8191 (t160) REVERT: D 651 LYS cc_start: 0.9047 (mppt) cc_final: 0.8720 (tptp) REVERT: D 678 MET cc_start: 0.9131 (mmm) cc_final: 0.8873 (mmm) REVERT: D 753 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8380 (ptp-170) REVERT: D 756 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8845 (pt0) REVERT: E 239 ARG cc_start: 0.7412 (mtt180) cc_final: 0.6941 (mmp-170) REVERT: E 305 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8225 (mt-10) REVERT: E 319 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7370 (tm-30) REVERT: E 327 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7787 (tp40) REVERT: E 442 MET cc_start: 0.4329 (mpt) cc_final: 0.4054 (mpt) REVERT: E 449 MET cc_start: 0.7945 (tpt) cc_final: 0.7208 (tpp) REVERT: E 561 GLU cc_start: 0.8569 (mp0) cc_final: 0.8321 (mp0) REVERT: E 753 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8536 (ptt-90) REVERT: F 239 ARG cc_start: 0.7347 (mtt180) cc_final: 0.6910 (mmp-170) REVERT: F 288 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8848 (mtmt) REVERT: F 319 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7077 (tm-30) REVERT: F 454 TRP cc_start: 0.8738 (t60) cc_final: 0.8158 (t60) REVERT: F 560 ARG cc_start: 0.8706 (ttm110) cc_final: 0.7872 (tpt170) REVERT: F 561 GLU cc_start: 0.8712 (mp0) cc_final: 0.8155 (mp0) REVERT: F 565 LYS cc_start: 0.9228 (tttp) cc_final: 0.8967 (ttmm) REVERT: F 568 GLN cc_start: 0.8691 (tp40) cc_final: 0.8304 (tm-30) REVERT: F 651 LYS cc_start: 0.9075 (mppt) cc_final: 0.8765 (tptp) outliers start: 47 outliers final: 17 residues processed: 378 average time/residue: 0.7716 time to fit residues: 329.4592 Evaluate side-chains 307 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 283 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 753 ARG Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 753 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 753 ARG Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 753 ARG Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 634 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 272 optimal weight: 0.5980 chunk 223 optimal weight: 0.6980 chunk 176 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 268 optimal weight: 8.9990 chunk 237 optimal weight: 1.9990 chunk 280 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 203 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN B 327 GLN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.114154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.084843 restraints weight = 46827.061| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.72 r_work: 0.3043 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 26130 Z= 0.190 Angle : 0.711 12.182 35340 Z= 0.337 Chirality : 0.045 0.231 3972 Planarity : 0.005 0.053 4620 Dihedral : 7.362 94.249 3636 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.52 % Favored : 94.29 % Rotamer: Outliers : 1.66 % Allowed : 10.09 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.15), residues: 3240 helix: 0.98 (0.13), residues: 1722 sheet: 0.31 (0.25), residues: 384 loop : -0.20 (0.20), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 560 TYR 0.028 0.002 TYR D 203 PHE 0.009 0.001 PHE E 503 TRP 0.013 0.001 TRP B 454 HIS 0.003 0.001 HIS F 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (26130) covalent geometry : angle 0.71071 / 0.34 (35340) hydrogen bonds : bond 0.04221 / 2.85 ( 1244) hydrogen bonds : angle 4.47349 / 3.21 ( 3516) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 300 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.7504 (tpp-160) cc_final: 0.7160 (mpt-90) REVERT: A 236 LYS cc_start: 0.8352 (pttm) cc_final: 0.7845 (mmmt) REVERT: A 239 ARG cc_start: 0.7361 (mtt180) cc_final: 0.6650 (mmm160) REVERT: A 449 MET cc_start: 0.7841 (tpt) cc_final: 0.7152 (tpp) REVERT: A 560 ARG cc_start: 0.8835 (ttp-110) cc_final: 0.8034 (ttt180) REVERT: A 561 GLU cc_start: 0.8608 (mp0) cc_final: 0.8054 (mp0) REVERT: A 616 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.8051 (t0) REVERT: A 651 LYS cc_start: 0.9079 (mppt) cc_final: 0.8737 (tptp) REVERT: A 678 MET cc_start: 0.9135 (mmm) cc_final: 0.8842 (mmm) REVERT: A 753 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8550 (ptp-170) REVERT: B 219 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7861 (mtt) REVERT: B 239 ARG cc_start: 0.7523 (mtt180) cc_final: 0.6974 (mmp-170) REVERT: B 288 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8867 (mtmt) REVERT: B 305 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8238 (mt-10) REVERT: B 324 ILE cc_start: 0.8764 (tp) cc_final: 0.8437 (mt) REVERT: B 454 TRP cc_start: 0.8666 (t60) cc_final: 0.7715 (t60) REVERT: B 561 GLU cc_start: 0.8670 (mp0) cc_final: 0.8205 (mp0) REVERT: B 753 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8515 (ptt-90) REVERT: C 239 ARG cc_start: 0.7346 (mtt180) cc_final: 0.6896 (mmp-170) REVERT: C 454 TRP cc_start: 0.8792 (t60) cc_final: 0.8157 (t60) REVERT: C 560 ARG cc_start: 0.8709 (ttm110) cc_final: 0.7886 (ttt180) REVERT: C 561 GLU cc_start: 0.8698 (mp0) cc_final: 0.8245 (mp0) REVERT: C 568 GLN cc_start: 0.8691 (tp40) cc_final: 0.8334 (tm-30) REVERT: D 236 LYS cc_start: 0.8264 (pttm) cc_final: 0.7847 (mmmt) REVERT: D 239 ARG cc_start: 0.7302 (mtt180) cc_final: 0.6578 (mmm160) REVERT: D 442 MET cc_start: 0.5668 (mpp) cc_final: 0.5382 (mpt) REVERT: D 449 MET cc_start: 0.7813 (tpt) cc_final: 0.7128 (tpp) REVERT: D 560 ARG cc_start: 0.8852 (ttp-110) cc_final: 0.8038 (ttt180) REVERT: D 561 GLU cc_start: 0.8622 (mp0) cc_final: 0.8072 (mp0) REVERT: D 616 ASN cc_start: 0.8462 (m-40) cc_final: 0.8139 (t160) REVERT: D 651 LYS cc_start: 0.9035 (mppt) cc_final: 0.8693 (tptp) REVERT: D 678 MET cc_start: 0.9145 (mmm) cc_final: 0.8851 (mmm) REVERT: E 239 ARG cc_start: 0.7420 (mtt180) cc_final: 0.6993 (mmp-170) REVERT: E 305 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8241 (mt-10) REVERT: E 449 MET cc_start: 0.8011 (tpt) cc_final: 0.7204 (tpp) REVERT: E 561 GLU cc_start: 0.8677 (mp0) cc_final: 0.8248 (mp0) REVERT: E 753 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8492 (ptt-90) REVERT: F 239 ARG cc_start: 0.7350 (mtt180) cc_final: 0.6945 (mmp-170) REVERT: F 319 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7191 (tm-30) REVERT: F 454 TRP cc_start: 0.8782 (t60) cc_final: 0.8148 (t60) REVERT: F 560 ARG cc_start: 0.8729 (ttm110) cc_final: 0.7865 (tpt170) REVERT: F 561 GLU cc_start: 0.8779 (mp0) cc_final: 0.8253 (mp0) REVERT: F 565 LYS cc_start: 0.9224 (tttp) cc_final: 0.8969 (ttmm) REVERT: F 568 GLN cc_start: 0.8685 (tp40) cc_final: 0.8305 (tm-30) REVERT: F 651 LYS cc_start: 0.9012 (mppt) cc_final: 0.8761 (tptp) outliers start: 45 outliers final: 18 residues processed: 335 average time/residue: 0.7776 time to fit residues: 294.6444 Evaluate side-chains 295 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 271 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 565 LYS Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 753 ARG Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 753 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 753 ARG Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 634 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 1.9990 chunk 241 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 315 optimal weight: 3.9990 chunk 120 optimal weight: 0.3980 chunk 243 optimal weight: 0.0270 chunk 10 optimal weight: 0.9980 chunk 195 optimal weight: 0.0980 chunk 139 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 GLN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 382 GLN ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 382 GLN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.115625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.086577 restraints weight = 46293.903| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.70 r_work: 0.3080 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26130 Z= 0.126 Angle : 0.671 8.902 35340 Z= 0.315 Chirality : 0.043 0.171 3972 Planarity : 0.004 0.052 4620 Dihedral : 7.119 88.915 3636 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.90 % Favored : 93.92 % Rotamer: Outliers : 1.55 % Allowed : 12.38 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.15), residues: 3240 helix: 1.07 (0.13), residues: 1734 sheet: 0.18 (0.25), residues: 384 loop : -0.22 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 745 TYR 0.024 0.002 TYR C 203 PHE 0.011 0.001 PHE F 758 TRP 0.012 0.001 TRP B 454 HIS 0.003 0.000 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (26130) covalent geometry : angle 0.67102 / 0.32 (35340) hydrogen bonds : bond 0.03524 / 2.38 ( 1244) hydrogen bonds : angle 4.22163 / 3.03 ( 3516) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 322 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8362 (pttm) cc_final: 0.7853 (mmmt) REVERT: A 239 ARG cc_start: 0.7341 (mtt180) cc_final: 0.6629 (mmm160) REVERT: A 449 MET cc_start: 0.7864 (tpt) cc_final: 0.7122 (tpp) REVERT: A 560 ARG cc_start: 0.8826 (ttp-110) cc_final: 0.8014 (ttt180) REVERT: A 561 GLU cc_start: 0.8633 (mp0) cc_final: 0.8160 (mp0) REVERT: A 599 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.6545 (mtp85) REVERT: A 651 LYS cc_start: 0.9030 (mppt) cc_final: 0.8701 (tptp) REVERT: A 678 MET cc_start: 0.9136 (mmm) cc_final: 0.8872 (mmm) REVERT: A 753 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8535 (ptp-170) REVERT: B 239 ARG cc_start: 0.7378 (mtt180) cc_final: 0.6890 (mmp-170) REVERT: B 324 ILE cc_start: 0.8815 (tp) cc_final: 0.8388 (mp) REVERT: B 454 TRP cc_start: 0.8671 (t60) cc_final: 0.7844 (t60) REVERT: B 561 GLU cc_start: 0.8746 (mp0) cc_final: 0.8153 (mp0) REVERT: B 568 GLN cc_start: 0.8833 (tp40) cc_final: 0.8142 (tm-30) REVERT: B 753 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8500 (ptt-90) REVERT: C 239 ARG cc_start: 0.7367 (mtt180) cc_final: 0.6743 (mmm160) REVERT: C 449 MET cc_start: 0.8212 (tpt) cc_final: 0.7390 (tpp) REVERT: C 454 TRP cc_start: 0.8821 (t60) cc_final: 0.8260 (t60) REVERT: C 456 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8579 (mt) REVERT: C 560 ARG cc_start: 0.8713 (ttm110) cc_final: 0.7863 (ttt180) REVERT: C 561 GLU cc_start: 0.8750 (mp0) cc_final: 0.8331 (mp0) REVERT: C 568 GLN cc_start: 0.8631 (tp40) cc_final: 0.8311 (tm-30) REVERT: D 236 LYS cc_start: 0.8259 (pttm) cc_final: 0.7866 (mmmt) REVERT: D 239 ARG cc_start: 0.7306 (mtt180) cc_final: 0.6593 (mmm160) REVERT: D 442 MET cc_start: 0.5710 (mpp) cc_final: 0.5399 (mpt) REVERT: D 449 MET cc_start: 0.7849 (tpt) cc_final: 0.7113 (tpp) REVERT: D 560 ARG cc_start: 0.8836 (ttp-110) cc_final: 0.8025 (ttt180) REVERT: D 561 GLU cc_start: 0.8658 (mp0) cc_final: 0.8184 (mp0) REVERT: D 599 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.6503 (mtp85) REVERT: D 616 ASN cc_start: 0.8496 (m-40) cc_final: 0.8191 (t160) REVERT: D 651 LYS cc_start: 0.9032 (mppt) cc_final: 0.8709 (tptp) REVERT: D 678 MET cc_start: 0.9151 (mmm) cc_final: 0.8828 (mmm) REVERT: D 753 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8537 (ptp-170) REVERT: E 239 ARG cc_start: 0.7467 (mtt180) cc_final: 0.7021 (mmp-170) REVERT: E 327 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7653 (tp-100) REVERT: E 449 MET cc_start: 0.7995 (tpt) cc_final: 0.7123 (tpp) REVERT: E 561 GLU cc_start: 0.8761 (mp0) cc_final: 0.8128 (mp0) REVERT: E 753 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8538 (ptp-170) REVERT: F 239 ARG cc_start: 0.7353 (mtt180) cc_final: 0.6762 (mmm160) REVERT: F 319 GLU cc_start: 0.7350 (tm-30) cc_final: 0.6923 (tm-30) REVERT: F 449 MET cc_start: 0.8186 (tpt) cc_final: 0.7429 (tpp) REVERT: F 456 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8536 (mt) REVERT: F 560 ARG cc_start: 0.8722 (ttm110) cc_final: 0.7855 (tpt170) REVERT: F 561 GLU cc_start: 0.8815 (mp0) cc_final: 0.8207 (mp0) REVERT: F 565 LYS cc_start: 0.9229 (tttp) cc_final: 0.8978 (ttmm) outliers start: 42 outliers final: 8 residues processed: 352 average time/residue: 0.7347 time to fit residues: 294.0634 Evaluate side-chains 297 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 280 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 753 ARG Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 753 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 624 ASN Chi-restraints excluded: chain D residue 753 ARG Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 753 ARG Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 456 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 118 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 chunk 218 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 179 optimal weight: 0.8980 chunk 290 optimal weight: 2.9990 chunk 294 optimal weight: 5.9990 chunk 191 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 272 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.115694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.085755 restraints weight = 45608.260| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.68 r_work: 0.3055 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26130 Z= 0.160 Angle : 0.694 14.418 35340 Z= 0.324 Chirality : 0.044 0.176 3972 Planarity : 0.005 0.053 4620 Dihedral : 7.118 86.546 3636 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.43 % Favored : 94.38 % Rotamer: Outliers : 1.63 % Allowed : 13.71 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.15), residues: 3240 helix: 1.09 (0.13), residues: 1788 sheet: 0.18 (0.25), residues: 384 loop : -0.09 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 210 TYR 0.023 0.002 TYR C 244 PHE 0.008 0.001 PHE E 503 TRP 0.008 0.001 TRP B 454 HIS 0.003 0.000 HIS F 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (26130) covalent geometry : angle 0.69377 / 0.32 (35340) hydrogen bonds : bond 0.03566 / 2.41 ( 1244) hydrogen bonds : angle 4.16923 / 3.00 ( 3516) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 286 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8437 (pttm) cc_final: 0.7911 (mmmt) REVERT: A 239 ARG cc_start: 0.7358 (mtt180) cc_final: 0.6591 (mmm160) REVERT: A 449 MET cc_start: 0.7828 (tpt) cc_final: 0.7114 (tpp) REVERT: A 560 ARG cc_start: 0.8836 (ttp-110) cc_final: 0.8009 (ttt180) REVERT: A 561 GLU cc_start: 0.8642 (mp0) cc_final: 0.8170 (mp0) REVERT: A 616 ASN cc_start: 0.8661 (t0) cc_final: 0.8424 (t0) REVERT: A 651 LYS cc_start: 0.9087 (mppt) cc_final: 0.8720 (tptp) REVERT: A 678 MET cc_start: 0.9159 (mmm) cc_final: 0.8818 (mmm) REVERT: A 753 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8555 (ptp-170) REVERT: B 239 ARG cc_start: 0.7393 (mtt180) cc_final: 0.6893 (mmp-170) REVERT: B 324 ILE cc_start: 0.8872 (tp) cc_final: 0.8432 (mp) REVERT: B 454 TRP cc_start: 0.8655 (t60) cc_final: 0.7840 (t60) REVERT: B 561 GLU cc_start: 0.8665 (mp0) cc_final: 0.8046 (mp0) REVERT: B 568 GLN cc_start: 0.8834 (tp40) cc_final: 0.8083 (tm-30) REVERT: B 753 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8515 (ptt-90) REVERT: C 239 ARG cc_start: 0.7226 (mtt180) cc_final: 0.6892 (mmp-170) REVERT: C 449 MET cc_start: 0.8232 (tpt) cc_final: 0.7431 (tpp) REVERT: C 456 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8564 (mt) REVERT: C 560 ARG cc_start: 0.8725 (ttm110) cc_final: 0.7850 (ttt180) REVERT: C 561 GLU cc_start: 0.8741 (mp0) cc_final: 0.8255 (mp0) REVERT: C 568 GLN cc_start: 0.8599 (tp40) cc_final: 0.8286 (tm-30) REVERT: D 236 LYS cc_start: 0.8261 (pttm) cc_final: 0.7865 (mmmt) REVERT: D 239 ARG cc_start: 0.7348 (mtt180) cc_final: 0.6605 (mmm160) REVERT: D 442 MET cc_start: 0.5869 (mpp) cc_final: 0.5558 (mpt) REVERT: D 449 MET cc_start: 0.7826 (tpt) cc_final: 0.7102 (tpp) REVERT: D 560 ARG cc_start: 0.8854 (ttp-110) cc_final: 0.8023 (ttt180) REVERT: D 561 GLU cc_start: 0.8660 (mp0) cc_final: 0.8193 (mp0) REVERT: D 616 ASN cc_start: 0.8529 (m-40) cc_final: 0.8188 (t160) REVERT: D 651 LYS cc_start: 0.9040 (mppt) cc_final: 0.8699 (tptp) REVERT: D 678 MET cc_start: 0.9152 (mmm) cc_final: 0.8807 (mmm) REVERT: D 753 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8574 (ptp-170) REVERT: E 239 ARG cc_start: 0.7441 (mtt180) cc_final: 0.6994 (mmp-170) REVERT: E 449 MET cc_start: 0.7960 (tpt) cc_final: 0.7061 (tpp) REVERT: E 561 GLU cc_start: 0.8689 (mp0) cc_final: 0.8048 (mp0) REVERT: E 753 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8517 (ptt-90) REVERT: F 239 ARG cc_start: 0.7278 (mtt180) cc_final: 0.6821 (mmp-170) REVERT: F 288 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8778 (mtmt) REVERT: F 319 GLU cc_start: 0.7367 (tm-30) cc_final: 0.6930 (tm-30) REVERT: F 449 MET cc_start: 0.8136 (tpt) cc_final: 0.7376 (tpp) REVERT: F 456 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8520 (mt) REVERT: F 560 ARG cc_start: 0.8713 (ttm110) cc_final: 0.7837 (tpt170) REVERT: F 561 GLU cc_start: 0.8760 (mp0) cc_final: 0.8153 (mp0) REVERT: F 565 LYS cc_start: 0.9199 (tttp) cc_final: 0.8938 (ttmm) outliers start: 44 outliers final: 13 residues processed: 319 average time/residue: 0.7513 time to fit residues: 273.2222 Evaluate side-chains 287 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 267 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 565 LYS Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 753 ARG Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 753 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 753 ARG Chi-restraints excluded: chain E residue 753 ARG Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 634 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 234 optimal weight: 2.9990 chunk 173 optimal weight: 0.0670 chunk 260 optimal weight: 0.9980 chunk 310 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 19 optimal weight: 0.0010 chunk 84 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 overall best weight: 0.5124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 GLN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.116801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.087032 restraints weight = 45614.610| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.73 r_work: 0.3064 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26130 Z= 0.132 Angle : 0.684 10.042 35340 Z= 0.320 Chirality : 0.043 0.171 3972 Planarity : 0.004 0.052 4620 Dihedral : 6.994 82.590 3636 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.86 % Favored : 93.95 % Rotamer: Outliers : 1.59 % Allowed : 14.38 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.15), residues: 3240 helix: 1.16 (0.13), residues: 1788 sheet: 0.11 (0.26), residues: 384 loop : -0.05 (0.21), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 210 TYR 0.025 0.002 TYR C 244 PHE 0.010 0.001 PHE F 742 TRP 0.009 0.001 TRP B 454 HIS 0.002 0.000 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (26130) covalent geometry : angle 0.68392 / 0.32 (35340) hydrogen bonds : bond 0.03344 / 2.27 ( 1244) hydrogen bonds : angle 4.10911 / 2.95 ( 3516) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 297 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8451 (pttm) cc_final: 0.7907 (mmmt) REVERT: A 239 ARG cc_start: 0.7405 (mtt180) cc_final: 0.6598 (mmm160) REVERT: A 449 MET cc_start: 0.7823 (tpt) cc_final: 0.7114 (tpp) REVERT: A 560 ARG cc_start: 0.8826 (ttp-110) cc_final: 0.7937 (tpp-160) REVERT: A 561 GLU cc_start: 0.8644 (mp0) cc_final: 0.8022 (mp0) REVERT: A 565 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8832 (ttpp) REVERT: A 599 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.6525 (mtp85) REVERT: A 616 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8381 (t0) REVERT: A 651 LYS cc_start: 0.9078 (mppt) cc_final: 0.8723 (tptp) REVERT: A 678 MET cc_start: 0.9161 (mmm) cc_final: 0.8792 (mmm) REVERT: A 753 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8547 (ptp-170) REVERT: B 239 ARG cc_start: 0.7274 (mtt180) cc_final: 0.6876 (mmp-170) REVERT: B 324 ILE cc_start: 0.8869 (tp) cc_final: 0.8435 (mp) REVERT: B 449 MET cc_start: 0.8119 (tpt) cc_final: 0.7345 (tpp) REVERT: B 454 TRP cc_start: 0.8673 (t60) cc_final: 0.7761 (t60) REVERT: B 560 ARG cc_start: 0.7568 (ttt-90) cc_final: 0.7290 (ttt180) REVERT: B 561 GLU cc_start: 0.8663 (mp0) cc_final: 0.8025 (mp0) REVERT: B 568 GLN cc_start: 0.8797 (tp40) cc_final: 0.8084 (tm-30) REVERT: B 753 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8521 (ptt-90) REVERT: C 239 ARG cc_start: 0.7289 (mtt180) cc_final: 0.6727 (mmm160) REVERT: C 449 MET cc_start: 0.8224 (tpt) cc_final: 0.7456 (tpp) REVERT: C 456 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8523 (mt) REVERT: C 560 ARG cc_start: 0.8711 (ttm110) cc_final: 0.7822 (ttt180) REVERT: C 561 GLU cc_start: 0.8743 (mp0) cc_final: 0.8146 (mp0) REVERT: C 568 GLN cc_start: 0.8587 (tp40) cc_final: 0.8261 (tm-30) REVERT: D 236 LYS cc_start: 0.8221 (pttm) cc_final: 0.7844 (mmmt) REVERT: D 239 ARG cc_start: 0.7370 (mtt180) cc_final: 0.6607 (mmm160) REVERT: D 449 MET cc_start: 0.7815 (tpt) cc_final: 0.7094 (tpp) REVERT: D 560 ARG cc_start: 0.8845 (ttp-110) cc_final: 0.7958 (tpp-160) REVERT: D 561 GLU cc_start: 0.8679 (mp0) cc_final: 0.8070 (mp0) REVERT: D 565 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8862 (ttpp) REVERT: D 599 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.6533 (mtp85) REVERT: D 616 ASN cc_start: 0.8537 (m-40) cc_final: 0.8202 (t160) REVERT: D 651 LYS cc_start: 0.9057 (mppt) cc_final: 0.8713 (tptp) REVERT: D 678 MET cc_start: 0.9142 (mmm) cc_final: 0.8786 (mmm) REVERT: D 753 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8585 (ptp-170) REVERT: E 203 TYR cc_start: 0.8173 (m-80) cc_final: 0.7968 (m-80) REVERT: E 239 ARG cc_start: 0.7476 (mtt180) cc_final: 0.7012 (mmp-170) REVERT: E 449 MET cc_start: 0.7943 (tpt) cc_final: 0.7045 (tpp) REVERT: E 561 GLU cc_start: 0.8700 (mp0) cc_final: 0.8029 (mp0) REVERT: E 753 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8535 (ptt-90) REVERT: F 239 ARG cc_start: 0.7303 (mtt180) cc_final: 0.6707 (mmm160) REVERT: F 319 GLU cc_start: 0.7358 (tm-30) cc_final: 0.6943 (tm-30) REVERT: F 449 MET cc_start: 0.8225 (tpt) cc_final: 0.7491 (tpp) REVERT: F 456 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8538 (mt) REVERT: F 560 ARG cc_start: 0.8697 (ttm110) cc_final: 0.7801 (tpt170) REVERT: F 561 GLU cc_start: 0.8783 (mp0) cc_final: 0.8095 (mp0) REVERT: F 565 LYS cc_start: 0.9198 (tttp) cc_final: 0.8936 (ttmm) outliers start: 43 outliers final: 14 residues processed: 327 average time/residue: 0.7730 time to fit residues: 287.6088 Evaluate side-chains 298 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 273 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 565 LYS Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 753 ARG Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 753 ARG Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 753 ARG Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 753 ARG Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 634 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 238 optimal weight: 0.9990 chunk 268 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 chunk 285 optimal weight: 0.5980 chunk 246 optimal weight: 2.9990 chunk 273 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 167 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.115308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.085491 restraints weight = 45910.025| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.70 r_work: 0.3056 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26130 Z= 0.160 Angle : 0.701 10.838 35340 Z= 0.326 Chirality : 0.044 0.256 3972 Planarity : 0.004 0.053 4620 Dihedral : 7.020 81.161 3636 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.59 % Favored : 94.23 % Rotamer: Outliers : 1.55 % Allowed : 15.19 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.15), residues: 3240 helix: 1.16 (0.13), residues: 1794 sheet: 0.17 (0.26), residues: 384 loop : 0.07 (0.21), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 210 TYR 0.024 0.002 TYR C 244 PHE 0.009 0.001 PHE B 363 TRP 0.007 0.001 TRP B 454 HIS 0.003 0.001 HIS C 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (26130) covalent geometry : angle 0.70087 / 0.33 (35340) hydrogen bonds : bond 0.03436 / 2.33 ( 1244) hydrogen bonds : angle 4.09948 / 2.95 ( 3516) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 276 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8490 (pttm) cc_final: 0.7973 (mmmt) REVERT: A 239 ARG cc_start: 0.7254 (mtt180) cc_final: 0.6637 (mmp-170) REVERT: A 288 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8771 (mtmt) REVERT: A 449 MET cc_start: 0.7866 (tpt) cc_final: 0.7111 (tpp) REVERT: A 560 ARG cc_start: 0.8845 (ttp-110) cc_final: 0.8019 (ttt180) REVERT: A 561 GLU cc_start: 0.8670 (mp0) cc_final: 0.8073 (mp0) REVERT: A 565 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8824 (ttpp) REVERT: A 616 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8420 (t0) REVERT: A 651 LYS cc_start: 0.9088 (mppt) cc_final: 0.8728 (tptp) REVERT: A 678 MET cc_start: 0.9156 (mmm) cc_final: 0.8769 (mmm) REVERT: A 753 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8595 (ptp-170) REVERT: B 203 TYR cc_start: 0.8105 (m-80) cc_final: 0.7862 (m-80) REVERT: B 239 ARG cc_start: 0.7417 (mtt180) cc_final: 0.6863 (mmp-170) REVERT: B 449 MET cc_start: 0.8173 (tpt) cc_final: 0.7386 (tpp) REVERT: B 454 TRP cc_start: 0.8722 (t60) cc_final: 0.7715 (t60) REVERT: B 561 GLU cc_start: 0.8714 (mp0) cc_final: 0.8040 (mp0) REVERT: B 568 GLN cc_start: 0.8841 (tp40) cc_final: 0.8066 (tm-30) REVERT: B 753 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8501 (ptt-90) REVERT: C 239 ARG cc_start: 0.7280 (mtt180) cc_final: 0.6710 (mmm160) REVERT: C 449 MET cc_start: 0.8224 (tpt) cc_final: 0.7410 (tpp) REVERT: C 456 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8504 (mt) REVERT: C 560 ARG cc_start: 0.8728 (ttm110) cc_final: 0.7850 (ttt180) REVERT: C 561 GLU cc_start: 0.8740 (mp0) cc_final: 0.8108 (mp0) REVERT: C 568 GLN cc_start: 0.8626 (tp40) cc_final: 0.8307 (tm-30) REVERT: D 236 LYS cc_start: 0.8273 (pttm) cc_final: 0.7856 (mmmt) REVERT: D 239 ARG cc_start: 0.7236 (mtt180) cc_final: 0.6545 (mmm160) REVERT: D 449 MET cc_start: 0.7818 (tpt) cc_final: 0.7042 (tpp) REVERT: D 560 ARG cc_start: 0.8856 (ttp-110) cc_final: 0.8026 (ttt180) REVERT: D 561 GLU cc_start: 0.8682 (mp0) cc_final: 0.8050 (mp0) REVERT: D 565 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8815 (ttpp) REVERT: D 651 LYS cc_start: 0.9069 (mppt) cc_final: 0.8720 (tptp) REVERT: D 678 MET cc_start: 0.9162 (mmm) cc_final: 0.8773 (mmm) REVERT: D 753 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8603 (ptp-170) REVERT: E 239 ARG cc_start: 0.7402 (mtt180) cc_final: 0.6947 (mmp-170) REVERT: E 449 MET cc_start: 0.7959 (tpt) cc_final: 0.7023 (tpp) REVERT: E 561 GLU cc_start: 0.8731 (mp0) cc_final: 0.8051 (mp0) REVERT: E 753 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8518 (ptt-90) REVERT: F 219 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7733 (mtm) REVERT: F 239 ARG cc_start: 0.7316 (mtt180) cc_final: 0.6868 (mmp-170) REVERT: F 319 GLU cc_start: 0.7364 (tm-30) cc_final: 0.6971 (tm-30) REVERT: F 449 MET cc_start: 0.8213 (tpt) cc_final: 0.7409 (tpp) REVERT: F 456 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8504 (mt) REVERT: F 560 ARG cc_start: 0.8716 (ttm110) cc_final: 0.7825 (tpt170) REVERT: F 561 GLU cc_start: 0.8819 (mp0) cc_final: 0.8197 (mp0) outliers start: 42 outliers final: 16 residues processed: 308 average time/residue: 0.7863 time to fit residues: 274.6783 Evaluate side-chains 297 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 270 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 565 LYS Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 753 ARG Chi-restraints excluded: chain B residue 753 ARG Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 753 ARG Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 753 ARG Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 634 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 88 optimal weight: 0.5980 chunk 254 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 232 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.116104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.086229 restraints weight = 45776.451| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.72 r_work: 0.3068 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26130 Z= 0.138 Angle : 0.702 11.373 35340 Z= 0.326 Chirality : 0.044 0.250 3972 Planarity : 0.005 0.053 4620 Dihedral : 6.934 79.047 3636 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.80 % Favored : 94.01 % Rotamer: Outliers : 1.52 % Allowed : 15.85 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.15), residues: 3240 helix: 1.20 (0.13), residues: 1794 sheet: 0.29 (0.26), residues: 366 loop : 0.17 (0.21), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 210 TYR 0.024 0.002 TYR C 244 PHE 0.013 0.001 PHE F 742 TRP 0.008 0.001 TRP B 454 HIS 0.003 0.000 HIS F 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (26130) covalent geometry : angle 0.70203 / 0.33 (35340) hydrogen bonds : bond 0.03301 / 2.24 ( 1244) hydrogen bonds : angle 4.05558 / 2.92 ( 3516) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 284 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8406 (pttm) cc_final: 0.7913 (mmmt) REVERT: A 239 ARG cc_start: 0.7282 (mtt180) cc_final: 0.6609 (mmp-170) REVERT: A 288 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8765 (mtmt) REVERT: A 449 MET cc_start: 0.7857 (tpt) cc_final: 0.7041 (tpp) REVERT: A 560 ARG cc_start: 0.8836 (ttp-110) cc_final: 0.7965 (tpp-160) REVERT: A 561 GLU cc_start: 0.8685 (mp0) cc_final: 0.7991 (mp0) REVERT: A 565 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8835 (ttpp) REVERT: A 599 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8084 (mtp85) REVERT: A 651 LYS cc_start: 0.9090 (mppt) cc_final: 0.8719 (tptp) REVERT: A 678 MET cc_start: 0.9147 (mmm) cc_final: 0.8764 (mmm) REVERT: A 753 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8604 (ptp-170) REVERT: B 203 TYR cc_start: 0.8204 (m-80) cc_final: 0.7916 (m-80) REVERT: B 239 ARG cc_start: 0.7392 (mtt180) cc_final: 0.6836 (mmp-170) REVERT: B 561 GLU cc_start: 0.8715 (mp0) cc_final: 0.8025 (mp0) REVERT: B 568 GLN cc_start: 0.8818 (tp40) cc_final: 0.8051 (tm-30) REVERT: B 753 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8524 (ptt-90) REVERT: C 239 ARG cc_start: 0.7337 (mtt180) cc_final: 0.6740 (mmm160) REVERT: C 456 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8502 (mt) REVERT: C 560 ARG cc_start: 0.8707 (ttm110) cc_final: 0.7845 (ttt180) REVERT: C 561 GLU cc_start: 0.8756 (mp0) cc_final: 0.8173 (mp0) REVERT: C 568 GLN cc_start: 0.8603 (tp40) cc_final: 0.8270 (tm-30) REVERT: D 236 LYS cc_start: 0.8277 (pttm) cc_final: 0.7854 (mmmt) REVERT: D 239 ARG cc_start: 0.7255 (mtt180) cc_final: 0.6520 (mmm160) REVERT: D 449 MET cc_start: 0.7849 (tpt) cc_final: 0.7012 (tpp) REVERT: D 560 ARG cc_start: 0.8847 (ttp-110) cc_final: 0.7969 (tpp-160) REVERT: D 561 GLU cc_start: 0.8703 (mp0) cc_final: 0.8100 (mp0) REVERT: D 565 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8859 (ttpp) REVERT: D 599 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.6635 (mtp85) REVERT: D 651 LYS cc_start: 0.9075 (mppt) cc_final: 0.8721 (tptp) REVERT: D 678 MET cc_start: 0.9147 (mmm) cc_final: 0.8787 (mmm) REVERT: D 753 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8571 (ptp-170) REVERT: E 239 ARG cc_start: 0.7367 (mtt180) cc_final: 0.6903 (mmp-170) REVERT: E 449 MET cc_start: 0.7966 (tpt) cc_final: 0.7041 (tpp) REVERT: E 561 GLU cc_start: 0.8743 (mp0) cc_final: 0.8061 (mp0) REVERT: E 753 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8534 (ptt-90) REVERT: F 239 ARG cc_start: 0.7291 (mtt180) cc_final: 0.6844 (mmp-170) REVERT: F 319 GLU cc_start: 0.7360 (tm-30) cc_final: 0.6976 (tm-30) REVERT: F 449 MET cc_start: 0.8239 (tpt) cc_final: 0.7489 (tpp) REVERT: F 456 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8483 (mt) REVERT: F 560 ARG cc_start: 0.8713 (ttm110) cc_final: 0.7842 (ttt180) REVERT: F 561 GLU cc_start: 0.8819 (mp0) cc_final: 0.8239 (mp0) outliers start: 41 outliers final: 18 residues processed: 315 average time/residue: 0.7774 time to fit residues: 278.4595 Evaluate side-chains 294 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 265 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 565 LYS Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 753 ARG Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 753 ARG Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 753 ARG Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 753 ARG Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 634 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 227 optimal weight: 0.0570 chunk 249 optimal weight: 0.6980 chunk 311 optimal weight: 0.9980 chunk 56 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 chunk 244 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 300 optimal weight: 1.9990 chunk 269 optimal weight: 0.9980 chunk 223 optimal weight: 3.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.116496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.086670 restraints weight = 45818.851| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.71 r_work: 0.3060 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26130 Z= 0.133 Angle : 0.710 11.922 35340 Z= 0.330 Chirality : 0.044 0.254 3972 Planarity : 0.005 0.052 4620 Dihedral : 6.843 74.881 3636 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.52 % Favored : 94.29 % Rotamer: Outliers : 1.40 % Allowed : 16.33 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.15), residues: 3240 helix: 1.24 (0.13), residues: 1788 sheet: 0.29 (0.27), residues: 366 loop : 0.19 (0.21), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 210 TYR 0.024 0.002 TYR C 244 PHE 0.008 0.001 PHE E 742 TRP 0.021 0.001 TRP B 454 HIS 0.003 0.000 HIS F 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (26130) covalent geometry : angle 0.71002 / 0.33 (35340) hydrogen bonds : bond 0.03235 / 2.19 ( 1244) hydrogen bonds : angle 4.04572 / 2.92 ( 3516) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 279 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8412 (pttm) cc_final: 0.7908 (mmmt) REVERT: A 239 ARG cc_start: 0.7288 (mtt180) cc_final: 0.6628 (mmp-170) REVERT: A 288 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8748 (mtmt) REVERT: A 449 MET cc_start: 0.7826 (tpt) cc_final: 0.6983 (tpp) REVERT: A 560 ARG cc_start: 0.8837 (ttp-110) cc_final: 0.7954 (tpp-160) REVERT: A 561 GLU cc_start: 0.8697 (mp0) cc_final: 0.7995 (mp0) REVERT: A 565 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8844 (ttpp) REVERT: A 599 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.6488 (mtp85) REVERT: A 616 ASN cc_start: 0.8684 (t0) cc_final: 0.8420 (t0) REVERT: A 651 LYS cc_start: 0.9087 (mppt) cc_final: 0.8716 (tptp) REVERT: A 678 MET cc_start: 0.9157 (mmm) cc_final: 0.8781 (mmm) REVERT: A 753 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8624 (ptp-170) REVERT: B 203 TYR cc_start: 0.8218 (m-80) cc_final: 0.7903 (m-80) REVERT: B 239 ARG cc_start: 0.7335 (mtt180) cc_final: 0.6813 (mmp-170) REVERT: B 449 MET cc_start: 0.8127 (tpt) cc_final: 0.7313 (tpp) REVERT: B 561 GLU cc_start: 0.8731 (mp0) cc_final: 0.8019 (mp0) REVERT: B 568 GLN cc_start: 0.8808 (tp40) cc_final: 0.8056 (tm-30) REVERT: B 651 LYS cc_start: 0.9066 (tptp) cc_final: 0.8824 (mppt) REVERT: B 753 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8525 (ptt-90) REVERT: C 239 ARG cc_start: 0.7321 (mtt180) cc_final: 0.6711 (mmm160) REVERT: C 449 MET cc_start: 0.7979 (tpp) cc_final: 0.7734 (tpp) REVERT: C 560 ARG cc_start: 0.8704 (ttm110) cc_final: 0.7826 (ttt180) REVERT: C 561 GLU cc_start: 0.8740 (mp0) cc_final: 0.8224 (mp0) REVERT: C 568 GLN cc_start: 0.8606 (tp40) cc_final: 0.8280 (tm-30) REVERT: D 236 LYS cc_start: 0.8286 (pttm) cc_final: 0.7881 (mmmt) REVERT: D 239 ARG cc_start: 0.7259 (mtt180) cc_final: 0.6529 (mmm160) REVERT: D 449 MET cc_start: 0.7844 (tpt) cc_final: 0.6975 (tpp) REVERT: D 560 ARG cc_start: 0.8853 (ttp-110) cc_final: 0.7978 (tpp-160) REVERT: D 561 GLU cc_start: 0.8721 (mp0) cc_final: 0.8036 (mp0) REVERT: D 565 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8871 (ttpp) REVERT: D 599 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.6523 (mtp85) REVERT: D 651 LYS cc_start: 0.9082 (mppt) cc_final: 0.8718 (tptp) REVERT: D 678 MET cc_start: 0.9175 (mmm) cc_final: 0.8844 (mmm) REVERT: D 753 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8617 (ptp-170) REVERT: E 239 ARG cc_start: 0.7416 (mtt180) cc_final: 0.6951 (mmp-170) REVERT: E 449 MET cc_start: 0.7963 (tpt) cc_final: 0.7019 (tpp) REVERT: E 561 GLU cc_start: 0.8749 (mp0) cc_final: 0.8060 (mp0) REVERT: E 651 LYS cc_start: 0.9077 (tptp) cc_final: 0.8825 (mppt) REVERT: E 753 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8552 (ptt-90) REVERT: F 239 ARG cc_start: 0.7271 (mtt180) cc_final: 0.6825 (mmp-170) REVERT: F 319 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6982 (tm-30) REVERT: F 449 MET cc_start: 0.8203 (tpt) cc_final: 0.7491 (tpp) REVERT: F 560 ARG cc_start: 0.8709 (ttm110) cc_final: 0.7828 (ttt180) REVERT: F 561 GLU cc_start: 0.8821 (mp0) cc_final: 0.8384 (mp0) outliers start: 38 outliers final: 21 residues processed: 308 average time/residue: 0.7555 time to fit residues: 265.9151 Evaluate side-chains 301 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 271 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 565 LYS Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 753 ARG Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 753 ARG Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 753 ARG Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 753 ARG Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 634 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 175 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 322 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.115382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.085635 restraints weight = 45756.601| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.70 r_work: 0.3037 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26130 Z= 0.158 Angle : 0.717 12.393 35340 Z= 0.334 Chirality : 0.045 0.244 3972 Planarity : 0.005 0.053 4620 Dihedral : 6.893 74.486 3636 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.62 % Favored : 94.20 % Rotamer: Outliers : 1.22 % Allowed : 16.59 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.15), residues: 3240 helix: 1.21 (0.12), residues: 1794 sheet: 0.40 (0.27), residues: 360 loop : 0.23 (0.21), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 349 TYR 0.025 0.002 TYR C 244 PHE 0.014 0.001 PHE C 742 TRP 0.018 0.001 TRP B 454 HIS 0.003 0.001 HIS F 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (26130) covalent geometry : angle 0.71651 / 0.33 (35340) hydrogen bonds : bond 0.03337 / 2.26 ( 1244) hydrogen bonds : angle 4.07504 / 2.94 ( 3516) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 271 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8479 (pttm) cc_final: 0.7955 (mmmt) REVERT: A 239 ARG cc_start: 0.7260 (mtt180) cc_final: 0.6637 (mmp-170) REVERT: A 288 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8741 (mtmt) REVERT: A 449 MET cc_start: 0.7806 (tpt) cc_final: 0.6938 (tpp) REVERT: A 560 ARG cc_start: 0.8856 (ttp-110) cc_final: 0.8032 (ttt180) REVERT: A 561 GLU cc_start: 0.8685 (mp0) cc_final: 0.8009 (mp0) REVERT: A 565 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8825 (ttpp) REVERT: A 651 LYS cc_start: 0.9097 (mppt) cc_final: 0.8723 (tptp) REVERT: A 678 MET cc_start: 0.9180 (mmm) cc_final: 0.8839 (mmm) REVERT: B 239 ARG cc_start: 0.7365 (mtt180) cc_final: 0.6806 (mmp-170) REVERT: B 449 MET cc_start: 0.8105 (tpt) cc_final: 0.7277 (tpp) REVERT: B 561 GLU cc_start: 0.8735 (mp0) cc_final: 0.8015 (mp0) REVERT: B 568 GLN cc_start: 0.8841 (tp40) cc_final: 0.8073 (tm-30) REVERT: B 753 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8535 (ptt-90) REVERT: C 239 ARG cc_start: 0.7318 (mtt180) cc_final: 0.6712 (mmm160) REVERT: C 560 ARG cc_start: 0.8716 (ttm110) cc_final: 0.7847 (ttt180) REVERT: C 561 GLU cc_start: 0.8765 (mp0) cc_final: 0.8113 (mp0) REVERT: C 568 GLN cc_start: 0.8650 (tp40) cc_final: 0.8303 (tm-30) REVERT: D 236 LYS cc_start: 0.8329 (pttm) cc_final: 0.7916 (mmmt) REVERT: D 239 ARG cc_start: 0.7242 (mtt180) cc_final: 0.6658 (mmp-170) REVERT: D 449 MET cc_start: 0.7849 (tpt) cc_final: 0.7036 (tpp) REVERT: D 560 ARG cc_start: 0.8867 (ttp-110) cc_final: 0.8035 (ttt180) REVERT: D 561 GLU cc_start: 0.8715 (mp0) cc_final: 0.8095 (mp0) REVERT: D 565 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8856 (ttpp) REVERT: D 651 LYS cc_start: 0.9089 (mppt) cc_final: 0.8724 (tptp) REVERT: D 678 MET cc_start: 0.9171 (mmm) cc_final: 0.8809 (mmm) REVERT: D 753 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8621 (ptp-170) REVERT: E 203 TYR cc_start: 0.8001 (m-80) cc_final: 0.7680 (m-80) REVERT: E 239 ARG cc_start: 0.7393 (mtt180) cc_final: 0.6887 (mmp-170) REVERT: E 449 MET cc_start: 0.7957 (tpt) cc_final: 0.7027 (tpp) REVERT: E 561 GLU cc_start: 0.8755 (mp0) cc_final: 0.8064 (mp0) REVERT: E 753 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8557 (ptt-90) REVERT: F 239 ARG cc_start: 0.7305 (mtt180) cc_final: 0.6836 (mmp-170) REVERT: F 319 GLU cc_start: 0.7363 (tm-30) cc_final: 0.7004 (tm-30) REVERT: F 449 MET cc_start: 0.8190 (tpt) cc_final: 0.7459 (tpp) REVERT: F 560 ARG cc_start: 0.8708 (ttm110) cc_final: 0.7820 (ttt180) REVERT: F 561 GLU cc_start: 0.8814 (mp0) cc_final: 0.8234 (mp0) outliers start: 33 outliers final: 22 residues processed: 298 average time/residue: 0.7522 time to fit residues: 254.9518 Evaluate side-chains 292 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 264 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 565 LYS Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 753 ARG Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 753 ARG Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 753 ARG Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 634 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 271 optimal weight: 0.6980 chunk 252 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 262 optimal weight: 0.0470 chunk 191 optimal weight: 0.8980 chunk 283 optimal weight: 1.9990 chunk 317 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.115804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.086118 restraints weight = 45619.495| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.70 r_work: 0.3045 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26130 Z= 0.140 Angle : 0.714 12.446 35340 Z= 0.332 Chirality : 0.044 0.244 3972 Planarity : 0.005 0.052 4620 Dihedral : 6.838 73.487 3636 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.43 % Favored : 94.38 % Rotamer: Outliers : 1.22 % Allowed : 16.85 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.15), residues: 3240 helix: 1.21 (0.12), residues: 1800 sheet: 0.56 (0.28), residues: 330 loop : 0.32 (0.21), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 210 TYR 0.025 0.002 TYR D 244 PHE 0.008 0.001 PHE E 742 TRP 0.018 0.001 TRP B 454 HIS 0.003 0.001 HIS F 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (26130) covalent geometry : angle 0.71362 / 0.33 (35340) hydrogen bonds : bond 0.03249 / 2.20 ( 1244) hydrogen bonds : angle 4.04178 / 2.92 ( 3516) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8748.47 seconds wall clock time: 149 minutes 45.99 seconds (8985.99 seconds total)