Starting phenix.real_space_refine on Fri Aug 7 15:37:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13lk_77135/08_2026/13lk_77135.cif Found real_map, /net/cci-nas-00/data/ceres_data/13lk_77135/08_2026/13lk_77135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/13lk_77135/08_2026/13lk_77135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13lk_77135/08_2026/13lk_77135.map" model { file = "/net/cci-nas-00/data/ceres_data/13lk_77135/08_2026/13lk_77135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13lk_77135/08_2026/13lk_77135.cif" } resolution = 3.18 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= 0.002 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: 6 Type Number sf(0) Gaussians P 28 5.49 5 S 136 5.16 5 Na 4 4.78 5 C 14520 2.51 5 N 3404 2.21 5 O 3896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21988 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 5123 Classifications: {'peptide': 630} Link IDs: {'PTRANS': 16, 'TRANS': 613} Chain breaks: 3 Chain: "B" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 5123 Classifications: {'peptide': 630} Link IDs: {'PTRANS': 16, 'TRANS': 613} Chain breaks: 3 Chain: "C" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 5123 Classifications: {'peptide': 630} Link IDs: {'PTRANS': 16, 'TRANS': 613} Chain breaks: 3 Chain: "D" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 5123 Classifications: {'peptide': 630} Link IDs: {'PTRANS': 16, 'TRANS': 613} Chain breaks: 3 Chain: "A" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 367 Unusual residues: {' NA': 3, 'POV': 7} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 365 Unusual residues: {' NA': 1, 'POV': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 364 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 364 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 4.95, per 1000 atoms: 0.23 Number of scatterers: 21988 At special positions: 0 Unit cell: (153.972, 154.818, 126.054, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 136 16.00 P 28 15.00 Na 4 11.00 O 3896 8.00 N 3404 7.00 C 14520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 731 " distance=2.04 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 721 " - pdb=" SG CYS D 731 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 886.0 milliseconds 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4832 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 60.8% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 119 through 130 removed outlier: 4.013A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 removed outlier: 4.183A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N CYS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 removed outlier: 3.745A pdb=" N HIS A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.530A pdb=" N ILE A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.666A pdb=" N ALA A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 258 removed outlier: 3.615A pdb=" N GLU A 257 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY A 258 " --> pdb=" O GLN A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 254 through 258' Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 282 Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.516A pdb=" N LEU A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.548A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.540A pdb=" N ALA A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.605A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.703A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 461 removed outlier: 3.612A pdb=" N TYR A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 454 " --> pdb=" O PHE A 450 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 507 removed outlier: 3.678A pdb=" N LEU A 485 " --> pdb=" O TRP A 481 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.546A pdb=" N SER A 518 " --> pdb=" O SER A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 543 removed outlier: 3.688A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 530 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 561 removed outlier: 3.764A pdb=" N ALA A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 586 removed outlier: 3.620A pdb=" N ILE A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 595 removed outlier: 4.396A pdb=" N PHE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 606 removed outlier: 4.044A pdb=" N PHE A 601 " --> pdb=" O PHE A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 removed outlier: 3.638A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU A 631 " --> pdb=" O ASP A 627 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 removed outlier: 3.821A pdb=" N LEU A 658 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 676 through 685 removed outlier: 3.534A pdb=" N THR A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 706 removed outlier: 3.615A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 Processing helix chain 'A' and resid 714 through 716 No H-bonds generated for 'chain 'A' and resid 714 through 716' Processing helix chain 'A' and resid 738 through 750 removed outlier: 3.647A pdb=" N LYS A 743 " --> pdb=" O TRP A 739 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN A 750 " --> pdb=" O VAL A 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 130 removed outlier: 4.013A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 126 " --> pdb=" O ARG B 122 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 146 removed outlier: 4.183A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N CYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.745A pdb=" N HIS B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.530A pdb=" N ILE B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 227 through 237 removed outlier: 3.665A pdb=" N ALA B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 removed outlier: 3.615A pdb=" N GLU B 257 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY B 258 " --> pdb=" O GLN B 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 254 through 258' Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.516A pdb=" N LEU B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.548A pdb=" N ARG B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR B 321 " --> pdb=" O VAL B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.539A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.606A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.702A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 461 removed outlier: 3.612A pdb=" N TYR B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR B 454 " --> pdb=" O PHE B 450 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 507 removed outlier: 3.678A pdb=" N LEU B 485 " --> pdb=" O TRP B 481 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.546A pdb=" N SER B 518 " --> pdb=" O SER B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 543 removed outlier: 3.689A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 530 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 561 removed outlier: 3.763A pdb=" N ALA B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 586 removed outlier: 3.621A pdb=" N ILE B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 595 removed outlier: 4.395A pdb=" N PHE B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 606 removed outlier: 4.044A pdb=" N PHE B 601 " --> pdb=" O PHE B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 removed outlier: 3.639A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 631 " --> pdb=" O ASP B 627 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 666 removed outlier: 3.822A pdb=" N LEU B 658 " --> pdb=" O PHE B 654 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 674 Processing helix chain 'B' and resid 676 through 685 removed outlier: 3.533A pdb=" N THR B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU B 682 " --> pdb=" O GLY B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 706 removed outlier: 3.614A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 Processing helix chain 'B' and resid 714 through 716 No H-bonds generated for 'chain 'B' and resid 714 through 716' Processing helix chain 'B' and resid 738 through 750 removed outlier: 3.647A pdb=" N LYS B 743 " --> pdb=" O TRP B 739 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN B 750 " --> pdb=" O VAL B 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 130 removed outlier: 4.012A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA C 126 " --> pdb=" O ARG C 122 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 146 removed outlier: 4.183A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N CYS C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 removed outlier: 3.746A pdb=" N HIS C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.530A pdb=" N ILE C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 227 through 237 removed outlier: 3.666A pdb=" N ALA C 231 " --> pdb=" O GLN C 227 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 258 removed outlier: 3.614A pdb=" N GLU C 257 " --> pdb=" O TYR C 254 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY C 258 " --> pdb=" O GLN C 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 254 through 258' Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 282 Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.516A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.548A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR C 321 " --> pdb=" O VAL C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.539A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.605A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.703A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 461 removed outlier: 3.611A pdb=" N TYR C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 453 " --> pdb=" O PHE C 449 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR C 454 " --> pdb=" O PHE C 450 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR C 461 " --> pdb=" O LEU C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 507 removed outlier: 3.677A pdb=" N LEU C 485 " --> pdb=" O TRP C 481 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.547A pdb=" N SER C 518 " --> pdb=" O SER C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 543 removed outlier: 3.689A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE C 526 " --> pdb=" O PHE C 522 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 530 " --> pdb=" O PHE C 526 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 561 removed outlier: 3.763A pdb=" N ALA C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 586 removed outlier: 3.620A pdb=" N ILE C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 595 removed outlier: 4.396A pdb=" N PHE C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 606 removed outlier: 4.044A pdb=" N PHE C 601 " --> pdb=" O PHE C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 removed outlier: 3.638A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU C 631 " --> pdb=" O ASP C 627 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 666 removed outlier: 3.822A pdb=" N LEU C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C 662 " --> pdb=" O LEU C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 676 through 685 removed outlier: 3.533A pdb=" N THR C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU C 682 " --> pdb=" O GLY C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 706 removed outlier: 3.614A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU C 704 " --> pdb=" O ILE C 700 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 705 " --> pdb=" O LEU C 701 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 Processing helix chain 'C' and resid 714 through 716 No H-bonds generated for 'chain 'C' and resid 714 through 716' Processing helix chain 'C' and resid 738 through 750 removed outlier: 3.647A pdb=" N LYS C 743 " --> pdb=" O TRP C 739 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN C 750 " --> pdb=" O VAL C 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 removed outlier: 4.013A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA D 126 " --> pdb=" O ARG D 122 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 146 removed outlier: 4.184A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 145 " --> pdb=" O GLU D 141 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N CYS D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 160 removed outlier: 3.745A pdb=" N HIS D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 182 through 195 removed outlier: 3.529A pdb=" N ILE D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 227 through 237 removed outlier: 3.667A pdb=" N ALA D 231 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 258 removed outlier: 3.614A pdb=" N GLU D 257 " --> pdb=" O TYR D 254 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY D 258 " --> pdb=" O GLN D 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 254 through 258' Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 282 Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.516A pdb=" N LEU D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.548A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR D 321 " --> pdb=" O VAL D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 removed outlier: 3.539A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.606A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.703A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 461 removed outlier: 3.612A pdb=" N TYR D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D 453 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR D 454 " --> pdb=" O PHE D 450 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR D 461 " --> pdb=" O LEU D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 507 removed outlier: 3.677A pdb=" N LEU D 485 " --> pdb=" O TRP D 481 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY D 486 " --> pdb=" O LEU D 482 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.546A pdb=" N SER D 518 " --> pdb=" O SER D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 543 removed outlier: 3.689A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE D 526 " --> pdb=" O PHE D 522 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA D 530 " --> pdb=" O PHE D 526 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 561 removed outlier: 3.763A pdb=" N ALA D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 586 removed outlier: 3.620A pdb=" N ILE D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 584 " --> pdb=" O GLN D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 595 removed outlier: 4.395A pdb=" N PHE D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 606 removed outlier: 4.043A pdb=" N PHE D 601 " --> pdb=" O PHE D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 removed outlier: 3.639A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU D 631 " --> pdb=" O ASP D 627 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 666 removed outlier: 3.822A pdb=" N LEU D 658 " --> pdb=" O PHE D 654 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 662 " --> pdb=" O LEU D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 674 Processing helix chain 'D' and resid 676 through 685 removed outlier: 3.534A pdb=" N THR D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU D 682 " --> pdb=" O GLY D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 706 removed outlier: 3.614A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU D 704 " --> pdb=" O ILE D 700 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 Processing helix chain 'D' and resid 714 through 716 No H-bonds generated for 'chain 'D' and resid 714 through 716' Processing helix chain 'D' and resid 738 through 750 removed outlier: 3.647A pdb=" N LYS D 743 " --> pdb=" O TRP D 739 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN D 750 " --> pdb=" O VAL D 746 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 74 removed outlier: 3.628A pdb=" N ARG A 73 " --> pdb=" O LYS D 722 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG D 729 " --> pdb=" O CYS D 721 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 376 through 382 removed outlier: 5.052A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 720 through 723 removed outlier: 3.559A pdb=" N ARG A 729 " --> pdb=" O CYS A 721 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 376 through 382 removed outlier: 5.052A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 727 through 730 removed outlier: 3.770A pdb=" N ASP B 727 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 729 " --> pdb=" O CYS B 721 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG C 73 " --> pdb=" O LYS B 722 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 376 through 382 removed outlier: 5.052A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 720 through 723 removed outlier: 3.559A pdb=" N ARG C 729 " --> pdb=" O CYS C 721 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 376 through 382 removed outlier: 5.052A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) 774 hydrogen bonds defined for protein. 2274 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.47 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3430 1.32 - 1.44: 5686 1.44 - 1.57: 12968 1.57 - 1.69: 56 1.69 - 1.81: 220 Bond restraints: 22360 Sorted by residual: bond pdb=" O12 POV C1105 " pdb=" P POV C1105 " ideal model delta sigma weight residual 1.657 1.590 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" O12 POV D1107 " pdb=" P POV D1107 " ideal model delta sigma weight residual 1.657 1.591 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" O12 POV A1104 " pdb=" P POV A1104 " ideal model delta sigma weight residual 1.657 1.591 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" O12 POV D1103 " pdb=" P POV D1103 " ideal model delta sigma weight residual 1.657 1.592 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" O12 POV B1101 " pdb=" P POV B1101 " ideal model delta sigma weight residual 1.657 1.592 0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 22355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 28438 2.41 - 4.83: 1338 4.83 - 7.24: 122 7.24 - 9.65: 55 9.65 - 12.06: 3 Bond angle restraints: 29956 Sorted by residual: angle pdb=" N ILE D 199 " pdb=" CA ILE D 199 " pdb=" C ILE D 199 " ideal model delta sigma weight residual 113.20 107.36 5.84 9.60e-01 1.09e+00 3.70e+01 angle pdb=" C LYS D 368 " pdb=" N ARG D 369 " pdb=" CA ARG D 369 " ideal model delta sigma weight residual 126.45 135.74 -9.29 1.77e+00 3.19e-01 2.75e+01 angle pdb=" C LYS B 368 " pdb=" N ARG B 369 " pdb=" CA ARG B 369 " ideal model delta sigma weight residual 126.45 135.67 -9.22 1.77e+00 3.19e-01 2.72e+01 angle pdb=" C LYS C 368 " pdb=" N ARG C 369 " pdb=" CA ARG C 369 " ideal model delta sigma weight residual 126.45 135.66 -9.21 1.77e+00 3.19e-01 2.71e+01 angle pdb=" N PRO C 613 " pdb=" CA PRO C 613 " pdb=" C PRO C 613 " ideal model delta sigma weight residual 112.47 119.61 -7.14 2.06e+00 2.36e-01 1.20e+01 ... (remaining 29951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 13319 35.33 - 70.66: 316 70.66 - 105.99: 37 105.99 - 141.32: 32 141.32 - 176.65: 24 Dihedral angle restraints: 13728 sinusoidal: 6300 harmonic: 7428 Sorted by residual: dihedral pdb=" CB CYS B 612 " pdb=" SG CYS B 612 " pdb=" SG CYS B 619 " pdb=" CB CYS B 619 " ideal model delta sinusoidal sigma weight residual -86.00 -166.75 80.75 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS D 612 " pdb=" SG CYS D 612 " pdb=" SG CYS D 619 " pdb=" CB CYS D 619 " ideal model delta sinusoidal sigma weight residual -86.00 -166.75 80.75 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS C 612 " pdb=" SG CYS C 612 " pdb=" SG CYS C 619 " pdb=" CB CYS C 619 " ideal model delta sinusoidal sigma weight residual -86.00 -166.73 80.73 1 1.00e+01 1.00e-02 8.05e+01 ... (remaining 13725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2697 0.071 - 0.141: 494 0.141 - 0.212: 41 0.212 - 0.283: 21 0.283 - 0.353: 11 Chirality restraints: 3264 Sorted by residual: chirality pdb=" CG LEU A 429 " pdb=" CB LEU A 429 " pdb=" CD1 LEU A 429 " pdb=" CD2 LEU A 429 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CG LEU C 429 " pdb=" CB LEU C 429 " pdb=" CD1 LEU C 429 " pdb=" CD2 LEU C 429 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CG LEU B 429 " pdb=" CB LEU B 429 " pdb=" CD1 LEU B 429 " pdb=" CD2 LEU B 429 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 3261 not shown) Planarity restraints: 3600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 376 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C LYS D 376 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS D 376 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE D 377 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 376 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.72e+00 pdb=" C LYS A 376 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS A 376 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE A 377 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 376 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C LYS B 376 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS B 376 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE B 377 " 0.015 2.00e-02 2.50e+03 ... (remaining 3597 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5046 2.78 - 3.31: 18413 3.31 - 3.84: 32835 3.84 - 4.37: 41735 4.37 - 4.90: 72173 Nonbonded interactions: 170202 Sorted by model distance: nonbonded pdb=" OH TYR A 650 " pdb=" O LYS D 545 " model vdw 2.246 3.040 nonbonded pdb=" O LYS C 545 " pdb=" OH TYR D 650 " model vdw 2.252 3.040 nonbonded pdb=" O LYS A 545 " pdb=" OH TYR B 650 " model vdw 2.269 3.040 nonbonded pdb=" OH TYR C 260 " pdb=" OD2 ASP C 293 " model vdw 2.284 3.040 nonbonded pdb=" OH TYR B 260 " pdb=" OD2 ASP B 293 " model vdw 2.284 3.040 ... (remaining 170197 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 60 through 1107) selection = (chain 'B' and resid 60 through 1107) selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.800 Find NCS groups from input model: 0.550 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: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 : 0.010 0.097 22368 Z= 0.451 Angle : 1.150 12.064 29972 Z= 0.579 Chirality : 0.061 0.353 3264 Planarity : 0.006 0.057 3600 Dihedral : 18.698 176.651 8872 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.60 % Favored : 91.92 % Rotamer: Outliers : 0.98 % Allowed : 4.81 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.27 (0.11), residues: 2488 helix: -4.73 (0.05), residues: 1444 sheet: -3.20 (0.41), residues: 92 loop : -2.94 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 567 TYR 0.016 0.003 TYR D 390 PHE 0.027 0.003 PHE D 259 TRP 0.034 0.003 TRP A 521 HIS 0.007 0.002 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.01044 / 0.45 (22360) covalent geometry : angle 1.15040 / 0.58 (29956) SS BOND : bond 0.00384 / 0.22 ( 8) SS BOND : angle 0.64514 / 0.43 ( 16) hydrogen bonds : bond 0.35429 / 22.69 ( 774) hydrogen bonds : angle 11.02515 / 7.51 ( 2274) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 420 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8011 (ttmm) cc_final: 0.7686 (ptmt) REVERT: A 122 ARG cc_start: 0.7911 (mmm160) cc_final: 0.7395 (ptt90) REVERT: A 131 CYS cc_start: 0.7097 (m) cc_final: 0.6650 (t) REVERT: A 184 LYS cc_start: 0.8370 (mttt) cc_final: 0.7995 (mttp) REVERT: A 409 TYR cc_start: 0.8662 (m-10) cc_final: 0.8433 (m-10) REVERT: A 489 PHE cc_start: 0.8145 (t80) cc_final: 0.7942 (t80) REVERT: A 546 GLU cc_start: 0.6668 (mt-10) cc_final: 0.5926 (mp0) REVERT: A 647 ASN cc_start: 0.7137 (m110) cc_final: 0.6874 (m110) REVERT: A 664 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8074 (tt) REVERT: A 702 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7320 (pt0) REVERT: A 741 GLU cc_start: 0.7192 (tt0) cc_final: 0.6842 (tp30) REVERT: B 351 MET cc_start: 0.8442 (mtt) cc_final: 0.8137 (mtp) REVERT: B 492 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7740 (pt) REVERT: B 627 ASP cc_start: 0.7771 (m-30) cc_final: 0.7423 (m-30) REVERT: B 647 ASN cc_start: 0.6737 (m110) cc_final: 0.6217 (p0) REVERT: B 690 ARG cc_start: 0.7554 (mtt90) cc_final: 0.7024 (mtm110) REVERT: B 702 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7126 (pt0) REVERT: C 159 MET cc_start: 0.5901 (mmm) cc_final: 0.5668 (mmm) REVERT: C 323 MET cc_start: 0.8410 (ttt) cc_final: 0.8143 (ttm) REVERT: C 340 ASP cc_start: 0.8782 (t0) cc_final: 0.8582 (t0) REVERT: C 546 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6563 (mp0) REVERT: C 627 ASP cc_start: 0.7719 (m-30) cc_final: 0.7421 (m-30) REVERT: C 647 ASN cc_start: 0.6748 (m110) cc_final: 0.6351 (p0) REVERT: C 690 ARG cc_start: 0.7542 (mtt90) cc_final: 0.6993 (mtm110) REVERT: C 702 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7361 (pt0) REVERT: D 285 GLU cc_start: 0.6948 (pp20) cc_final: 0.6664 (pp20) REVERT: D 546 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6639 (mp0) REVERT: D 627 ASP cc_start: 0.7761 (m-30) cc_final: 0.7424 (m-30) REVERT: D 664 LEU cc_start: 0.8761 (tt) cc_final: 0.8491 (tp) REVERT: D 690 ARG cc_start: 0.7536 (mtt90) cc_final: 0.6939 (mtm110) REVERT: D 702 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7417 (pt0) outliers start: 22 outliers final: 4 residues processed: 437 average time/residue: 0.1721 time to fit residues: 114.2174 Evaluate side-chains 305 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 299 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain D residue 669 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 HIS A 339 ASN A 430 HIS A 671 ASN A 735 ASN A 750 ASN B 297 ASN B 430 HIS B 580 GLN B 671 ASN B 745 HIS B 750 ASN C 297 ASN C 430 HIS C 671 ASN C 745 HIS C 750 ASN D 671 ASN D 735 ASN D 745 HIS D 750 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.177938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.129941 restraints weight = 25823.076| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.44 r_work: 0.3409 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22368 Z= 0.141 Angle : 0.606 8.532 29972 Z= 0.311 Chirality : 0.039 0.154 3264 Planarity : 0.005 0.050 3600 Dihedral : 21.252 176.969 3940 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.35 % Favored : 94.49 % Rotamer: Outliers : 1.65 % Allowed : 10.47 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.41 (0.14), residues: 2488 helix: -2.84 (0.10), residues: 1472 sheet: -2.52 (0.48), residues: 92 loop : -2.84 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 690 TYR 0.016 0.001 TYR D 540 PHE 0.014 0.001 PHE A 526 TRP 0.018 0.002 TRP A 521 HIS 0.004 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (22360) covalent geometry : angle 0.60621 / 0.31 (29956) SS BOND : bond 0.00265 / 0.16 ( 8) SS BOND : angle 0.48746 / 0.33 ( 16) hydrogen bonds : bond 0.04067 / 2.58 ( 774) hydrogen bonds : angle 5.03985 / 3.41 ( 2274) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 330 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.7012 (m) cc_final: 0.6805 (t) REVERT: A 184 LYS cc_start: 0.8421 (mttt) cc_final: 0.8150 (mttp) REVERT: A 276 GLU cc_start: 0.8039 (mp0) cc_final: 0.7776 (pm20) REVERT: A 315 ASP cc_start: 0.6411 (p0) cc_final: 0.6207 (p0) REVERT: A 355 GLU cc_start: 0.8426 (tp30) cc_final: 0.8105 (tp30) REVERT: A 431 MET cc_start: 0.8133 (mmp) cc_final: 0.7753 (mtp) REVERT: A 546 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6583 (mp0) REVERT: A 664 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8624 (tt) REVERT: A 702 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7591 (pt0) REVERT: B 409 TYR cc_start: 0.8675 (m-10) cc_final: 0.8202 (m-10) REVERT: B 415 ASN cc_start: 0.7257 (t0) cc_final: 0.6865 (t0) REVERT: B 664 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8632 (tp) REVERT: B 690 ARG cc_start: 0.8080 (mtt90) cc_final: 0.7603 (mtm110) REVERT: B 702 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7786 (pt0) REVERT: C 323 MET cc_start: 0.8642 (ttt) cc_final: 0.8301 (ttm) REVERT: C 409 TYR cc_start: 0.8614 (m-10) cc_final: 0.8267 (m-10) REVERT: C 546 GLU cc_start: 0.7665 (mt-10) cc_final: 0.6921 (mp0) REVERT: C 664 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8602 (tp) REVERT: C 702 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7796 (pt0) REVERT: D 159 MET cc_start: 0.6070 (mmm) cc_final: 0.5796 (mmm) REVERT: D 322 ASP cc_start: 0.8224 (t0) cc_final: 0.8019 (t0) REVERT: D 409 TYR cc_start: 0.8622 (m-10) cc_final: 0.8353 (m-10) REVERT: D 546 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7099 (mp0) REVERT: D 578 MET cc_start: 0.8190 (mtt) cc_final: 0.7985 (mtp) REVERT: D 664 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8638 (tp) REVERT: D 690 ARG cc_start: 0.8095 (mtt90) cc_final: 0.7663 (mtm110) REVERT: D 702 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7819 (pt0) outliers start: 37 outliers final: 10 residues processed: 354 average time/residue: 0.1611 time to fit residues: 88.7491 Evaluate side-chains 298 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 284 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 750 ASN Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 207 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 HIS B 585 HIS B 735 ASN B 750 ASN C 585 HIS C 735 ASN D 585 HIS D 750 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.165261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116041 restraints weight = 25733.002| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.56 r_work: 0.3207 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 22368 Z= 0.246 Angle : 0.667 7.909 29972 Z= 0.337 Chirality : 0.043 0.183 3264 Planarity : 0.004 0.055 3600 Dihedral : 20.131 163.176 3930 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.71 % Favored : 93.17 % Rotamer: Outliers : 3.21 % Allowed : 12.57 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.32 (0.16), residues: 2488 helix: -1.84 (0.12), residues: 1504 sheet: -3.16 (0.43), residues: 108 loop : -2.45 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 327 TYR 0.019 0.002 TYR A 451 PHE 0.015 0.002 PHE A 316 TRP 0.035 0.002 TRP A 521 HIS 0.007 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.25 (22360) covalent geometry : angle 0.66736 / 0.34 (29956) SS BOND : bond 0.00147 / 0.08 ( 8) SS BOND : angle 0.59067 / 0.39 ( 16) hydrogen bonds : bond 0.04793 / 3.03 ( 774) hydrogen bonds : angle 4.63919 / 3.11 ( 2274) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 302 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.8030 (mmm160) cc_final: 0.7424 (ptt90) REVERT: A 131 CYS cc_start: 0.7234 (m) cc_final: 0.6875 (t) REVERT: A 184 LYS cc_start: 0.8518 (mttt) cc_final: 0.8131 (ttmm) REVERT: A 340 ASP cc_start: 0.8835 (t0) cc_final: 0.8576 (t0) REVERT: A 430 HIS cc_start: 0.7484 (OUTLIER) cc_final: 0.7188 (t-90) REVERT: A 431 MET cc_start: 0.8099 (mmp) cc_final: 0.7629 (mtp) REVERT: A 546 GLU cc_start: 0.7507 (mt-10) cc_final: 0.6702 (mp0) REVERT: A 664 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8541 (tt) REVERT: A 702 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7856 (tt0) REVERT: B 66 LYS cc_start: 0.8019 (ttmm) cc_final: 0.7770 (ttpt) REVERT: B 154 VAL cc_start: 0.5415 (OUTLIER) cc_final: 0.5215 (p) REVERT: B 315 ASP cc_start: 0.7256 (p0) cc_final: 0.7032 (p0) REVERT: B 409 TYR cc_start: 0.8687 (m-10) cc_final: 0.8373 (m-80) REVERT: B 430 HIS cc_start: 0.7427 (OUTLIER) cc_final: 0.7088 (t-90) REVERT: B 664 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8648 (tp) REVERT: B 690 ARG cc_start: 0.8137 (mtt90) cc_final: 0.7498 (mtm110) REVERT: B 702 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7809 (tt0) REVERT: C 184 LYS cc_start: 0.8165 (mtpp) cc_final: 0.7875 (mtpp) REVERT: C 286 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7827 (mm-40) REVERT: C 409 TYR cc_start: 0.8644 (m-10) cc_final: 0.8323 (m-10) REVERT: C 430 HIS cc_start: 0.7480 (OUTLIER) cc_final: 0.7152 (t-90) REVERT: C 546 GLU cc_start: 0.7713 (mt-10) cc_final: 0.6888 (mp0) REVERT: C 664 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8683 (tp) REVERT: C 690 ARG cc_start: 0.8140 (mtt90) cc_final: 0.7545 (mtm110) REVERT: D 154 VAL cc_start: 0.5218 (OUTLIER) cc_final: 0.5006 (p) REVERT: D 159 MET cc_start: 0.6206 (mmm) cc_final: 0.5843 (mmm) REVERT: D 286 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7740 (mm-40) REVERT: D 366 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8199 (mmtt) REVERT: D 409 TYR cc_start: 0.8641 (m-10) cc_final: 0.8315 (m-10) REVERT: D 430 HIS cc_start: 0.7452 (OUTLIER) cc_final: 0.7137 (t-90) REVERT: D 546 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7173 (mp0) REVERT: D 664 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8639 (tp) REVERT: D 690 ARG cc_start: 0.8139 (mtt90) cc_final: 0.7535 (mtm110) outliers start: 72 outliers final: 42 residues processed: 349 average time/residue: 0.1700 time to fit residues: 90.6268 Evaluate side-chains 336 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 281 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 750 ASN Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 286 GLN Chi-restraints excluded: chain D residue 366 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 555 MET Chi-restraints excluded: chain D residue 572 MET Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 750 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 219 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 182 optimal weight: 7.9990 chunk 153 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 246 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 750 ASN C 286 GLN D 182 ASN D 415 ASN D 750 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.171542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121045 restraints weight = 24861.005| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.59 r_work: 0.3223 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22368 Z= 0.108 Angle : 0.506 6.933 29972 Z= 0.261 Chirality : 0.038 0.137 3264 Planarity : 0.003 0.041 3600 Dihedral : 18.833 152.688 3930 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.98 % Favored : 94.90 % Rotamer: Outliers : 2.50 % Allowed : 14.26 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.16), residues: 2488 helix: -1.04 (0.13), residues: 1512 sheet: -2.63 (0.45), residues: 92 loop : -2.37 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 327 TYR 0.011 0.001 TYR C 547 PHE 0.009 0.001 PHE A 316 TRP 0.015 0.001 TRP B 521 HIS 0.003 0.001 HIS D 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (22360) covalent geometry : angle 0.50635 / 0.26 (29956) SS BOND : bond 0.00135 / 0.08 ( 8) SS BOND : angle 0.48577 / 0.32 ( 16) hydrogen bonds : bond 0.03282 / 2.07 ( 774) hydrogen bonds : angle 4.16836 / 2.79 ( 2274) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 301 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.8159 (mmm160) cc_final: 0.7336 (ptt90) REVERT: A 131 CYS cc_start: 0.7245 (m) cc_final: 0.6731 (t) REVERT: A 182 ASN cc_start: 0.8069 (t0) cc_final: 0.7644 (t0) REVERT: A 184 LYS cc_start: 0.8305 (mttt) cc_final: 0.7995 (ttmm) REVERT: A 340 ASP cc_start: 0.8676 (t0) cc_final: 0.8450 (t0) REVERT: A 415 ASN cc_start: 0.7634 (t0) cc_final: 0.7302 (t0) REVERT: A 430 HIS cc_start: 0.6993 (OUTLIER) cc_final: 0.6749 (t-90) REVERT: A 431 MET cc_start: 0.7581 (mmp) cc_final: 0.7008 (mtp) REVERT: A 440 MET cc_start: 0.7847 (mtm) cc_final: 0.7549 (mtp) REVERT: A 546 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6241 (mp0) REVERT: A 664 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8005 (tt) REVERT: A 702 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7330 (tt0) REVERT: B 66 LYS cc_start: 0.7845 (ttmm) cc_final: 0.7550 (ttpt) REVERT: B 154 VAL cc_start: 0.5366 (OUTLIER) cc_final: 0.5114 (p) REVERT: B 409 TYR cc_start: 0.8264 (m-10) cc_final: 0.8007 (m-80) REVERT: B 430 HIS cc_start: 0.7042 (OUTLIER) cc_final: 0.6779 (t-90) REVERT: B 542 PHE cc_start: 0.7457 (m-80) cc_final: 0.7088 (m-80) REVERT: B 690 ARG cc_start: 0.7901 (mtt90) cc_final: 0.7073 (mtm110) REVERT: B 702 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7358 (tt0) REVERT: C 66 LYS cc_start: 0.8350 (mtpt) cc_final: 0.7965 (ttpt) REVERT: C 415 ASN cc_start: 0.7472 (t0) cc_final: 0.7095 (t0) REVERT: C 430 HIS cc_start: 0.7033 (OUTLIER) cc_final: 0.6783 (t-90) REVERT: C 546 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6354 (mp0) REVERT: C 690 ARG cc_start: 0.7949 (mtt90) cc_final: 0.7117 (mtm110) REVERT: C 702 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7465 (tt0) REVERT: D 159 MET cc_start: 0.6186 (mmm) cc_final: 0.5829 (mmm) REVERT: D 288 ASP cc_start: 0.7680 (m-30) cc_final: 0.7412 (m-30) REVERT: D 340 ASP cc_start: 0.8774 (t0) cc_final: 0.8494 (t0) REVERT: D 409 TYR cc_start: 0.8186 (m-10) cc_final: 0.7971 (m-10) REVERT: D 430 HIS cc_start: 0.7073 (OUTLIER) cc_final: 0.6800 (t-90) REVERT: D 546 GLU cc_start: 0.7529 (mt-10) cc_final: 0.6678 (mp0) REVERT: D 690 ARG cc_start: 0.7905 (mtt90) cc_final: 0.7272 (ttp-110) REVERT: D 702 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7481 (tt0) outliers start: 56 outliers final: 28 residues processed: 335 average time/residue: 0.1729 time to fit residues: 88.8871 Evaluate side-chains 326 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 292 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 572 MET Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 204 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 221 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 514 GLN B 514 GLN B 750 ASN D 514 GLN D 750 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.167205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.116654 restraints weight = 24913.970| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.58 r_work: 0.3166 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22368 Z= 0.191 Angle : 0.568 8.666 29972 Z= 0.288 Chirality : 0.041 0.189 3264 Planarity : 0.003 0.041 3600 Dihedral : 18.788 137.086 3930 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.75 % Favored : 94.17 % Rotamer: Outliers : 3.48 % Allowed : 13.95 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.17), residues: 2488 helix: -0.94 (0.13), residues: 1532 sheet: -3.18 (0.42), residues: 108 loop : -2.23 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 363 TYR 0.015 0.002 TYR A 451 PHE 0.012 0.001 PHE D 316 TRP 0.021 0.001 TRP D 521 HIS 0.006 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.19 (22360) covalent geometry : angle 0.56823 / 0.29 (29956) SS BOND : bond 0.00107 / 0.06 ( 8) SS BOND : angle 0.57153 / 0.38 ( 16) hydrogen bonds : bond 0.03852 / 2.44 ( 774) hydrogen bonds : angle 4.20268 / 2.82 ( 2274) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 306 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.8121 (mmm160) cc_final: 0.7273 (ptt90) REVERT: A 131 CYS cc_start: 0.7253 (m) cc_final: 0.6749 (t) REVERT: A 182 ASN cc_start: 0.8088 (t0) cc_final: 0.7681 (t0) REVERT: A 340 ASP cc_start: 0.8723 (t0) cc_final: 0.8350 (t0) REVERT: A 430 HIS cc_start: 0.7056 (OUTLIER) cc_final: 0.6807 (t-90) REVERT: A 431 MET cc_start: 0.7622 (mmp) cc_final: 0.7035 (mtp) REVERT: A 546 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6382 (mp0) REVERT: A 664 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8145 (tt) REVERT: A 702 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7449 (tt0) REVERT: B 280 LEU cc_start: 0.8088 (mp) cc_final: 0.7874 (tp) REVERT: B 409 TYR cc_start: 0.8327 (m-10) cc_final: 0.8068 (m-80) REVERT: B 430 HIS cc_start: 0.7081 (OUTLIER) cc_final: 0.6820 (t-90) REVERT: B 538 PHE cc_start: 0.7583 (m-10) cc_final: 0.7367 (m-10) REVERT: B 542 PHE cc_start: 0.7417 (m-80) cc_final: 0.6945 (m-80) REVERT: B 664 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8422 (tp) REVERT: B 690 ARG cc_start: 0.7890 (mtt90) cc_final: 0.7067 (mtm110) REVERT: B 702 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7500 (tt0) REVERT: C 430 HIS cc_start: 0.7093 (OUTLIER) cc_final: 0.6835 (t-90) REVERT: C 514 GLN cc_start: 0.7864 (mt0) cc_final: 0.7635 (mt0) REVERT: C 546 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6426 (mp0) REVERT: C 649 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7611 (ptpt) REVERT: C 664 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8406 (tp) REVERT: C 690 ARG cc_start: 0.7919 (mtt90) cc_final: 0.7116 (mtm110) REVERT: C 702 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7510 (tt0) REVERT: D 159 MET cc_start: 0.6300 (mmm) cc_final: 0.5949 (mmm) REVERT: D 409 TYR cc_start: 0.8325 (m-10) cc_final: 0.8046 (m-10) REVERT: D 430 HIS cc_start: 0.7127 (OUTLIER) cc_final: 0.6819 (t-90) REVERT: D 431 MET cc_start: 0.7635 (mmp) cc_final: 0.7041 (mtp) REVERT: D 514 GLN cc_start: 0.7806 (mt0) cc_final: 0.7505 (mt0) REVERT: D 546 GLU cc_start: 0.7608 (mt-10) cc_final: 0.6723 (mp0) REVERT: D 664 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8409 (tp) REVERT: D 690 ARG cc_start: 0.7874 (mtt90) cc_final: 0.7102 (mtm110) REVERT: D 696 ARG cc_start: 0.7855 (ttm170) cc_final: 0.7605 (ttm-80) outliers start: 78 outliers final: 47 residues processed: 362 average time/residue: 0.1716 time to fit residues: 94.5472 Evaluate side-chains 352 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 296 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 572 MET Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 750 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 73 optimal weight: 0.0970 chunk 173 optimal weight: 0.7980 chunk 205 optimal weight: 0.9980 chunk 13 optimal weight: 20.0000 chunk 163 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 237 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN B 514 GLN B 750 ASN D 284 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.173159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.123172 restraints weight = 24697.899| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.55 r_work: 0.3248 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 22368 Z= 0.083 Angle : 0.467 9.138 29972 Z= 0.239 Chirality : 0.037 0.132 3264 Planarity : 0.003 0.040 3600 Dihedral : 17.795 132.754 3930 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.32 % Allowed : 14.53 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.73 (0.17), residues: 2488 helix: -0.39 (0.14), residues: 1544 sheet: -2.20 (0.46), residues: 88 loop : -2.31 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 122 TYR 0.011 0.001 TYR C 547 PHE 0.012 0.001 PHE C 193 TRP 0.010 0.001 TRP B 521 HIS 0.003 0.001 HIS D 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00184 / 0.08 (22360) covalent geometry : angle 0.46700 / 0.24 (29956) SS BOND : bond 0.00199 / 0.12 ( 8) SS BOND : angle 0.42709 / 0.28 ( 16) hydrogen bonds : bond 0.02815 / 1.77 ( 774) hydrogen bonds : angle 3.86358 / 2.59 ( 2274) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 317 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8483 (mtpt) cc_final: 0.7851 (ptmt) REVERT: A 68 MET cc_start: 0.7577 (mtp) cc_final: 0.7224 (mtm) REVERT: A 122 ARG cc_start: 0.8008 (mmm160) cc_final: 0.7211 (ptt90) REVERT: A 131 CYS cc_start: 0.7203 (m) cc_final: 0.6737 (t) REVERT: A 182 ASN cc_start: 0.7954 (t0) cc_final: 0.6954 (t0) REVERT: A 340 ASP cc_start: 0.8686 (t0) cc_final: 0.8419 (t0) REVERT: A 415 ASN cc_start: 0.7623 (t0) cc_final: 0.7050 (p0) REVERT: A 430 HIS cc_start: 0.6937 (OUTLIER) cc_final: 0.6729 (t-90) REVERT: A 431 MET cc_start: 0.7447 (mmp) cc_final: 0.6851 (mtp) REVERT: A 546 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6195 (mp0) REVERT: A 664 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8047 (tt) REVERT: A 696 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7486 (ttm-80) REVERT: A 717 MET cc_start: 0.7166 (mtm) cc_final: 0.6948 (mtm) REVERT: B 66 LYS cc_start: 0.8251 (mtpt) cc_final: 0.7842 (ttpt) REVERT: B 308 GLU cc_start: 0.7265 (tp30) cc_final: 0.6947 (pp20) REVERT: B 340 ASP cc_start: 0.8721 (t0) cc_final: 0.8304 (t0) REVERT: B 415 ASN cc_start: 0.7433 (t0) cc_final: 0.7137 (t0) REVERT: B 430 HIS cc_start: 0.6990 (OUTLIER) cc_final: 0.6758 (t-90) REVERT: B 431 MET cc_start: 0.7473 (mmp) cc_final: 0.6898 (mtp) REVERT: B 492 ILE cc_start: 0.7311 (OUTLIER) cc_final: 0.6982 (pt) REVERT: B 514 GLN cc_start: 0.7763 (mt0) cc_final: 0.7558 (mt0) REVERT: B 538 PHE cc_start: 0.7374 (m-10) cc_final: 0.7156 (m-10) REVERT: B 542 PHE cc_start: 0.7451 (m-80) cc_final: 0.7019 (m-80) REVERT: B 664 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8222 (tp) REVERT: B 690 ARG cc_start: 0.7832 (mtt90) cc_final: 0.6936 (ttp80) REVERT: B 702 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7373 (tt0) REVERT: C 131 CYS cc_start: 0.7520 (m) cc_final: 0.6200 (t) REVERT: C 340 ASP cc_start: 0.8717 (t0) cc_final: 0.8327 (t0) REVERT: C 415 ASN cc_start: 0.7462 (t0) cc_final: 0.7116 (t0) REVERT: C 430 HIS cc_start: 0.7016 (OUTLIER) cc_final: 0.6764 (t-90) REVERT: C 431 MET cc_start: 0.7453 (mmp) cc_final: 0.6862 (mtp) REVERT: C 546 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6466 (mp0) REVERT: C 664 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8230 (tp) REVERT: C 690 ARG cc_start: 0.7861 (mtt90) cc_final: 0.6982 (ttp80) REVERT: C 696 ARG cc_start: 0.7780 (ttm-80) cc_final: 0.7532 (ttm-80) REVERT: C 702 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7424 (tt0) REVERT: D 159 MET cc_start: 0.6283 (mmm) cc_final: 0.5932 (mmm) REVERT: D 284 HIS cc_start: 0.7041 (t70) cc_final: 0.6828 (t70) REVERT: D 340 ASP cc_start: 0.8758 (t0) cc_final: 0.8383 (t0) REVERT: D 409 TYR cc_start: 0.8144 (m-10) cc_final: 0.7942 (m-10) REVERT: D 415 ASN cc_start: 0.7426 (t0) cc_final: 0.7032 (t0) REVERT: D 430 HIS cc_start: 0.7043 (OUTLIER) cc_final: 0.6782 (t-90) REVERT: D 431 MET cc_start: 0.7409 (mmp) cc_final: 0.6858 (mtp) REVERT: D 514 GLN cc_start: 0.7744 (mt0) cc_final: 0.7440 (mt0) REVERT: D 546 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6640 (mp0) REVERT: D 547 TYR cc_start: 0.8297 (p90) cc_final: 0.8046 (p90) REVERT: D 664 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8222 (tp) REVERT: D 690 ARG cc_start: 0.7876 (mtt90) cc_final: 0.7036 (mtm110) REVERT: D 702 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7473 (tt0) outliers start: 52 outliers final: 31 residues processed: 351 average time/residue: 0.1714 time to fit residues: 91.9636 Evaluate side-chains 335 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 295 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 612 CYS Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 750 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 612 CYS Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 612 CYS Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 203 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 13 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 205 optimal weight: 0.7980 chunk 134 optimal weight: 6.9990 chunk 218 optimal weight: 0.3980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 750 ASN C 284 HIS D 284 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.169579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119151 restraints weight = 24730.089| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.56 r_work: 0.3196 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22368 Z= 0.132 Angle : 0.522 10.543 29972 Z= 0.261 Chirality : 0.039 0.142 3264 Planarity : 0.003 0.038 3600 Dihedral : 17.688 134.203 3930 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.85 % Allowed : 14.39 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.51 (0.17), residues: 2488 helix: -0.22 (0.14), residues: 1544 sheet: -3.02 (0.41), residues: 108 loop : -2.06 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 696 TYR 0.013 0.001 TYR B 451 PHE 0.010 0.001 PHE B 316 TRP 0.015 0.001 TRP D 521 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (22360) covalent geometry : angle 0.52205 / 0.26 (29956) SS BOND : bond 0.00104 / 0.06 ( 8) SS BOND : angle 0.50320 / 0.34 ( 16) hydrogen bonds : bond 0.03246 / 2.04 ( 774) hydrogen bonds : angle 3.87605 / 2.59 ( 2274) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 313 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8436 (mtpt) cc_final: 0.7775 (ptmt) REVERT: A 74 GLN cc_start: 0.7051 (mm-40) cc_final: 0.6323 (mm-40) REVERT: A 122 ARG cc_start: 0.8015 (mmm160) cc_final: 0.7201 (ptt90) REVERT: A 131 CYS cc_start: 0.7233 (m) cc_final: 0.6743 (t) REVERT: A 182 ASN cc_start: 0.7950 (t0) cc_final: 0.7074 (t0) REVERT: A 340 ASP cc_start: 0.8666 (t0) cc_final: 0.8354 (t0) REVERT: A 415 ASN cc_start: 0.7637 (t0) cc_final: 0.7227 (t0) REVERT: A 430 HIS cc_start: 0.7011 (OUTLIER) cc_final: 0.6761 (t-90) REVERT: A 431 MET cc_start: 0.7583 (mmp) cc_final: 0.7009 (mtp) REVERT: A 546 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6361 (mp0) REVERT: A 631 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7500 (tp30) REVERT: A 664 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8043 (tt) REVERT: B 66 LYS cc_start: 0.8316 (mtpt) cc_final: 0.8107 (ttpt) REVERT: B 415 ASN cc_start: 0.7450 (t0) cc_final: 0.7124 (t0) REVERT: B 430 HIS cc_start: 0.7050 (OUTLIER) cc_final: 0.6783 (t-90) REVERT: B 431 MET cc_start: 0.7564 (mmp) cc_final: 0.6990 (mtp) REVERT: B 538 PHE cc_start: 0.7397 (m-10) cc_final: 0.7175 (m-10) REVERT: B 542 PHE cc_start: 0.7549 (m-80) cc_final: 0.7060 (m-80) REVERT: B 690 ARG cc_start: 0.7860 (mtt90) cc_final: 0.6956 (ttp80) REVERT: B 702 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7413 (tt0) REVERT: C 66 LYS cc_start: 0.8295 (mtpt) cc_final: 0.7625 (ptmt) REVERT: C 131 CYS cc_start: 0.7468 (m) cc_final: 0.6193 (t) REVERT: C 202 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.8008 (mtm-85) REVERT: C 415 ASN cc_start: 0.7482 (t0) cc_final: 0.7077 (t0) REVERT: C 430 HIS cc_start: 0.7055 (OUTLIER) cc_final: 0.6790 (t-90) REVERT: C 431 MET cc_start: 0.7537 (mmp) cc_final: 0.6954 (mtp) REVERT: C 546 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6491 (mp0) REVERT: C 690 ARG cc_start: 0.7871 (mtt90) cc_final: 0.7054 (mtm110) REVERT: C 696 ARG cc_start: 0.7859 (ttm-80) cc_final: 0.7596 (ttm-80) REVERT: D 66 LYS cc_start: 0.8437 (mtpt) cc_final: 0.7988 (ttpt) REVERT: D 159 MET cc_start: 0.6203 (mmm) cc_final: 0.5859 (mmm) REVERT: D 188 ARG cc_start: 0.8108 (mpp80) cc_final: 0.7873 (mpp80) REVERT: D 332 GLU cc_start: 0.7215 (pt0) cc_final: 0.7011 (tp30) REVERT: D 340 ASP cc_start: 0.8744 (t0) cc_final: 0.8539 (t0) REVERT: D 409 TYR cc_start: 0.8181 (m-10) cc_final: 0.7956 (m-10) REVERT: D 430 HIS cc_start: 0.7093 (OUTLIER) cc_final: 0.6808 (t-90) REVERT: D 431 MET cc_start: 0.7499 (mmp) cc_final: 0.6977 (mtp) REVERT: D 546 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6686 (mp0) REVERT: D 547 TYR cc_start: 0.8331 (p90) cc_final: 0.8039 (p90) REVERT: D 690 ARG cc_start: 0.7862 (mtt90) cc_final: 0.6942 (ttp80) REVERT: D 702 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7520 (tt0) outliers start: 64 outliers final: 47 residues processed: 350 average time/residue: 0.1633 time to fit residues: 88.2249 Evaluate side-chains 348 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 296 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 612 CYS Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 750 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 612 CYS Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 572 MET Chi-restraints excluded: chain D residue 612 CYS Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 33 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 248 optimal weight: 0.0030 chunk 128 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 overall best weight: 3.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 750 ASN D 514 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.164897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.114334 restraints weight = 24899.257| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.57 r_work: 0.3134 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 22368 Z= 0.249 Angle : 0.649 11.486 29972 Z= 0.319 Chirality : 0.043 0.191 3264 Planarity : 0.004 0.047 3600 Dihedral : 18.457 138.785 3930 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.59 % Favored : 94.37 % Rotamer: Outliers : 3.07 % Allowed : 14.66 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.76 (0.17), residues: 2488 helix: -0.46 (0.14), residues: 1520 sheet: -2.25 (0.45), residues: 88 loop : -2.18 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 696 TYR 0.016 0.002 TYR C 451 PHE 0.014 0.002 PHE B 316 TRP 0.021 0.002 TRP C 521 HIS 0.008 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.25 (22360) covalent geometry : angle 0.64898 / 0.32 (29956) SS BOND : bond 0.00129 / 0.07 ( 8) SS BOND : angle 0.61014 / 0.40 ( 16) hydrogen bonds : bond 0.04060 / 2.57 ( 774) hydrogen bonds : angle 4.20624 / 2.81 ( 2274) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 301 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7977 (mmm160) cc_final: 0.7165 (mtm180) REVERT: A 131 CYS cc_start: 0.7205 (m) cc_final: 0.6704 (t) REVERT: A 182 ASN cc_start: 0.8034 (t0) cc_final: 0.7666 (t0) REVERT: A 189 ILE cc_start: 0.8090 (tp) cc_final: 0.7804 (pt) REVERT: A 430 HIS cc_start: 0.7078 (OUTLIER) cc_final: 0.6823 (t-90) REVERT: A 431 MET cc_start: 0.7644 (mmp) cc_final: 0.7070 (mtp) REVERT: A 546 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6477 (mp0) REVERT: A 664 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8190 (tt) REVERT: B 286 GLN cc_start: 0.8304 (mm-40) cc_final: 0.8057 (mm-40) REVERT: B 430 HIS cc_start: 0.7114 (OUTLIER) cc_final: 0.6819 (t-90) REVERT: B 431 MET cc_start: 0.7605 (mmp) cc_final: 0.7015 (mtp) REVERT: B 690 ARG cc_start: 0.7902 (mtt90) cc_final: 0.7104 (mtm110) REVERT: C 131 CYS cc_start: 0.7407 (m) cc_final: 0.6164 (t) REVERT: C 202 ARG cc_start: 0.8321 (mtm-85) cc_final: 0.7992 (mtm-85) REVERT: C 415 ASN cc_start: 0.7484 (t0) cc_final: 0.6959 (t0) REVERT: C 430 HIS cc_start: 0.7146 (OUTLIER) cc_final: 0.6850 (t-90) REVERT: C 431 MET cc_start: 0.7655 (mmp) cc_final: 0.7045 (mtp) REVERT: C 546 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6567 (mp0) REVERT: C 690 ARG cc_start: 0.7933 (mtt90) cc_final: 0.7160 (mtm110) REVERT: D 159 MET cc_start: 0.6265 (mmm) cc_final: 0.5875 (mmm) REVERT: D 188 ARG cc_start: 0.8121 (mpp80) cc_final: 0.7877 (mpp80) REVERT: D 315 ASP cc_start: 0.6857 (p0) cc_final: 0.6627 (p0) REVERT: D 361 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7577 (mp) REVERT: D 409 TYR cc_start: 0.8346 (m-10) cc_final: 0.8127 (m-10) REVERT: D 415 ASN cc_start: 0.7367 (t0) cc_final: 0.6931 (t0) REVERT: D 430 HIS cc_start: 0.7143 (OUTLIER) cc_final: 0.6825 (t-90) REVERT: D 431 MET cc_start: 0.7597 (mmp) cc_final: 0.7000 (mtp) REVERT: D 514 GLN cc_start: 0.7752 (mt0) cc_final: 0.7438 (mt0) REVERT: D 546 GLU cc_start: 0.7539 (mt-10) cc_final: 0.6605 (mp0) REVERT: D 547 TYR cc_start: 0.8498 (p90) cc_final: 0.8181 (p90) REVERT: D 690 ARG cc_start: 0.7922 (mtt90) cc_final: 0.7089 (mtm110) outliers start: 69 outliers final: 48 residues processed: 345 average time/residue: 0.1640 time to fit residues: 86.7658 Evaluate side-chains 346 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 292 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 612 CYS Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 750 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 612 CYS Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 572 MET Chi-restraints excluded: chain D residue 612 CYS Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 45 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 240 optimal weight: 0.7980 chunk 228 optimal weight: 0.7980 chunk 137 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 HIS B 523 HIS B 750 ASN C 523 HIS D 523 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.165686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.116143 restraints weight = 24950.561| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.60 r_work: 0.3182 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22368 Z= 0.157 Angle : 0.562 12.018 29972 Z= 0.279 Chirality : 0.040 0.324 3264 Planarity : 0.003 0.047 3600 Dihedral : 18.067 136.396 3930 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.67 % Allowed : 15.73 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.61 (0.17), residues: 2488 helix: -0.31 (0.14), residues: 1536 sheet: -3.08 (0.41), residues: 108 loop : -2.06 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 696 TYR 0.012 0.001 TYR C 451 PHE 0.027 0.001 PHE D 193 TRP 0.015 0.001 TRP D 521 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (22360) covalent geometry : angle 0.56209 / 0.28 (29956) SS BOND : bond 0.00109 / 0.07 ( 8) SS BOND : angle 0.51487 / 0.34 ( 16) hydrogen bonds : bond 0.03412 / 2.15 ( 774) hydrogen bonds : angle 4.02279 / 2.69 ( 2274) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 296 time to evaluate : 0.491 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 122 ARG cc_start: 0.7978 (mmm160) cc_final: 0.7211 (mtm180) REVERT: A 131 CYS cc_start: 0.7218 (m) cc_final: 0.6772 (t) REVERT: A 182 ASN cc_start: 0.8108 (t0) cc_final: 0.7730 (t0) REVERT: A 340 ASP cc_start: 0.8773 (t0) cc_final: 0.8425 (t0) REVERT: A 430 HIS cc_start: 0.7227 (OUTLIER) cc_final: 0.6985 (t-90) REVERT: A 431 MET cc_start: 0.7899 (mmp) cc_final: 0.7359 (mtp) REVERT: A 546 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6664 (mp0) REVERT: A 664 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8322 (tt) REVERT: A 690 ARG cc_start: 0.7953 (ttp-110) cc_final: 0.7720 (ttm110) REVERT: B 415 ASN cc_start: 0.7668 (t0) cc_final: 0.7410 (t0) REVERT: B 430 HIS cc_start: 0.7312 (OUTLIER) cc_final: 0.7056 (t-90) REVERT: B 431 MET cc_start: 0.7878 (mmp) cc_final: 0.7343 (mtp) REVERT: B 514 GLN cc_start: 0.7996 (mt0) cc_final: 0.7697 (mt0) REVERT: B 690 ARG cc_start: 0.7986 (mtt90) cc_final: 0.7278 (mtm110) REVERT: B 702 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7474 (tp30) REVERT: B 750 ASN cc_start: 0.6898 (OUTLIER) cc_final: 0.6630 (t0) REVERT: C 131 CYS cc_start: 0.7347 (m) cc_final: 0.6302 (t) REVERT: C 202 ARG cc_start: 0.8335 (mtm-85) cc_final: 0.8001 (mtm-85) REVERT: C 308 GLU cc_start: 0.7774 (tp30) cc_final: 0.7469 (tp30) REVERT: C 415 ASN cc_start: 0.7501 (t0) cc_final: 0.7081 (t0) REVERT: C 430 HIS cc_start: 0.7291 (OUTLIER) cc_final: 0.7030 (t-90) REVERT: C 431 MET cc_start: 0.7869 (mmp) cc_final: 0.7309 (mtp) REVERT: C 546 GLU cc_start: 0.7461 (mt-10) cc_final: 0.6723 (mp0) REVERT: C 690 ARG cc_start: 0.8012 (mtt90) cc_final: 0.7319 (mtm110) REVERT: C 702 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7728 (tt0) REVERT: D 159 MET cc_start: 0.6262 (mmm) cc_final: 0.5866 (mmm) REVERT: D 188 ARG cc_start: 0.8114 (mpp80) cc_final: 0.7847 (mpp80) REVERT: D 202 ARG cc_start: 0.8410 (mtm-85) cc_final: 0.7989 (mtm-85) REVERT: D 409 TYR cc_start: 0.8420 (m-10) cc_final: 0.8177 (m-10) REVERT: D 415 ASN cc_start: 0.7431 (t0) cc_final: 0.7126 (t0) REVERT: D 430 HIS cc_start: 0.7351 (OUTLIER) cc_final: 0.7044 (t-90) REVERT: D 431 MET cc_start: 0.7850 (mmp) cc_final: 0.7363 (mtp) REVERT: D 546 GLU cc_start: 0.7606 (mt-10) cc_final: 0.6925 (mp0) REVERT: D 690 ARG cc_start: 0.8006 (mtt90) cc_final: 0.7280 (mtm110) REVERT: D 702 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7772 (tt0) outliers start: 60 outliers final: 46 residues processed: 334 average time/residue: 0.1390 time to fit residues: 71.4024 Evaluate side-chains 342 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 290 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 612 CYS Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 750 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 612 CYS Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 572 MET Chi-restraints excluded: chain D residue 612 CYS Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 132 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 202 optimal weight: 30.0000 chunk 232 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 162 optimal weight: 9.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS B 750 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.169235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.119576 restraints weight = 24855.971| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.61 r_work: 0.3209 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22368 Z= 0.119 Angle : 0.528 12.422 29972 Z= 0.263 Chirality : 0.038 0.238 3264 Planarity : 0.003 0.042 3600 Dihedral : 17.560 134.121 3930 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.50 % Allowed : 15.95 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.30 (0.17), residues: 2488 helix: -0.09 (0.14), residues: 1556 sheet: -2.14 (0.45), residues: 88 loop : -2.08 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 696 TYR 0.011 0.001 TYR C 451 PHE 0.024 0.001 PHE D 193 TRP 0.013 0.001 TRP D 521 HIS 0.004 0.001 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (22360) covalent geometry : angle 0.52805 / 0.26 (29956) SS BOND : bond 0.00154 / 0.10 ( 8) SS BOND : angle 0.51294 / 0.33 ( 16) hydrogen bonds : bond 0.03089 / 1.94 ( 774) hydrogen bonds : angle 3.87390 / 2.59 ( 2274) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 296 time to evaluate : 0.868 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 66 LYS cc_start: 0.8519 (mtpt) cc_final: 0.7926 (ptmt) REVERT: A 122 ARG cc_start: 0.7919 (mmm160) cc_final: 0.7104 (ptt90) REVERT: A 182 ASN cc_start: 0.8064 (t0) cc_final: 0.7604 (t0) REVERT: A 340 ASP cc_start: 0.8725 (t0) cc_final: 0.8426 (t0) REVERT: A 430 HIS cc_start: 0.7212 (OUTLIER) cc_final: 0.6962 (t-90) REVERT: A 431 MET cc_start: 0.7874 (mmp) cc_final: 0.7346 (mtp) REVERT: A 546 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6567 (mp0) REVERT: A 664 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8293 (tt) REVERT: A 690 ARG cc_start: 0.7975 (ttp-110) cc_final: 0.7753 (ttm110) REVERT: B 66 LYS cc_start: 0.8350 (mtpt) cc_final: 0.7754 (ptmt) REVERT: B 202 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.8179 (mtm-85) REVERT: B 430 HIS cc_start: 0.7292 (OUTLIER) cc_final: 0.7037 (t-90) REVERT: B 431 MET cc_start: 0.7859 (mmp) cc_final: 0.7342 (mtp) REVERT: B 514 GLN cc_start: 0.7998 (mt0) cc_final: 0.7700 (mt0) REVERT: B 690 ARG cc_start: 0.7948 (mtt90) cc_final: 0.7200 (ttp80) REVERT: B 702 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7483 (tp30) REVERT: C 66 LYS cc_start: 0.8406 (mtpt) cc_final: 0.7837 (ptmt) REVERT: C 131 CYS cc_start: 0.7260 (m) cc_final: 0.6332 (t) REVERT: C 202 ARG cc_start: 0.8302 (mtm-85) cc_final: 0.7962 (mtm-85) REVERT: C 308 GLU cc_start: 0.7767 (tp30) cc_final: 0.7464 (tp30) REVERT: C 415 ASN cc_start: 0.7521 (t0) cc_final: 0.7242 (t0) REVERT: C 430 HIS cc_start: 0.7272 (OUTLIER) cc_final: 0.7015 (t-90) REVERT: C 431 MET cc_start: 0.7839 (mmp) cc_final: 0.7310 (mtp) REVERT: C 546 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6633 (mp0) REVERT: C 690 ARG cc_start: 0.7971 (mtt90) cc_final: 0.7293 (mtm110) REVERT: C 702 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7721 (tp30) REVERT: D 66 LYS cc_start: 0.8453 (mtpt) cc_final: 0.7917 (ptmt) REVERT: D 159 MET cc_start: 0.6284 (mmm) cc_final: 0.5916 (mmm) REVERT: D 188 ARG cc_start: 0.8089 (mpp80) cc_final: 0.7799 (mpp80) REVERT: D 202 ARG cc_start: 0.8322 (mtm-85) cc_final: 0.7904 (mtm-85) REVERT: D 320 MET cc_start: 0.8933 (mmm) cc_final: 0.8667 (mmm) REVERT: D 409 TYR cc_start: 0.8344 (m-10) cc_final: 0.8144 (m-10) REVERT: D 430 HIS cc_start: 0.7314 (OUTLIER) cc_final: 0.7031 (t-90) REVERT: D 431 MET cc_start: 0.7824 (mmp) cc_final: 0.7350 (mtp) REVERT: D 440 MET cc_start: 0.8158 (mtm) cc_final: 0.7903 (mtp) REVERT: D 546 GLU cc_start: 0.7570 (mt-10) cc_final: 0.6953 (mp0) REVERT: D 547 TYR cc_start: 0.8572 (p90) cc_final: 0.8290 (p90) REVERT: D 690 ARG cc_start: 0.7997 (mtt90) cc_final: 0.7206 (ttp80) REVERT: D 702 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7697 (tt0) outliers start: 56 outliers final: 48 residues processed: 326 average time/residue: 0.1661 time to fit residues: 83.0883 Evaluate side-chains 343 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 290 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 612 CYS Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 612 CYS Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 572 MET Chi-restraints excluded: chain D residue 612 CYS Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 48 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 225 optimal weight: 9.9990 chunk 176 optimal weight: 0.9980 chunk 194 optimal weight: 20.0000 chunk 153 optimal weight: 7.9990 chunk 250 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 GLN B 750 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.165099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115648 restraints weight = 24940.300| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.58 r_work: 0.3160 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22368 Z= 0.215 Angle : 0.614 12.647 29972 Z= 0.303 Chirality : 0.042 0.192 3264 Planarity : 0.004 0.049 3600 Dihedral : 18.025 137.823 3930 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.51 % Favored : 94.45 % Rotamer: Outliers : 2.63 % Allowed : 15.95 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.39 (0.17), residues: 2488 helix: -0.21 (0.14), residues: 1516 sheet: -2.19 (0.45), residues: 88 loop : -1.92 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 567 TYR 0.016 0.002 TYR C 451 PHE 0.021 0.001 PHE D 193 TRP 0.018 0.001 TRP D 521 HIS 0.007 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.22 (22360) covalent geometry : angle 0.61354 / 0.30 (29956) SS BOND : bond 0.00101 / 0.06 ( 8) SS BOND : angle 0.54461 / 0.37 ( 16) hydrogen bonds : bond 0.03791 / 2.39 ( 774) hydrogen bonds : angle 4.09554 / 2.73 ( 2274) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5307.73 seconds wall clock time: 91 minutes 50.99 seconds (5510.99 seconds total)