Starting phenix.real_space_refine on Thu Mar 5 13:31:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7min_23857/03_2026/7min_23857.cif Found real_map, /net/cci-nas-00/data/ceres_data/7min_23857/03_2026/7min_23857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7min_23857/03_2026/7min_23857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7min_23857/03_2026/7min_23857.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7min_23857/03_2026/7min_23857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7min_23857/03_2026/7min_23857.map" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 36 5.49 5 S 124 5.16 5 Na 4 4.78 5 C 15064 2.51 5 N 3476 2.21 5 O 4024 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22728 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5213 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "B" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5213 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "C" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5213 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "D" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5213 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "A" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 472 Unusual residues: {' NA': 4, 'POV': 9} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Time building chain proxies: 5.08, per 1000 atoms: 0.22 Number of scatterers: 22728 At special positions: 0 Unit cell: (134.977, 134.977, 131.494, 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 124 16.00 P 36 15.00 Na 4 11.00 O 4024 8.00 N 3476 7.00 C 15064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 1.0 seconds 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4904 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 8 sheets defined 64.7% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 118 through 130 removed outlier: 3.799A pdb=" N ARG A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 148 removed outlier: 3.832A pdb=" N ARG A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 162 removed outlier: 3.604A pdb=" N MET A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.831A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.888A pdb=" N ILE A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 218 through 225 removed outlier: 3.966A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.692A pdb=" N THR A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.523A pdb=" N ALA A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.640A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.659A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.719A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.503A pdb=" N ALA A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.601A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.708A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.550A pdb=" N MET A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 4.135A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 removed outlier: 3.906A pdb=" N VAL A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 508 removed outlier: 3.522A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 520 removed outlier: 3.849A pdb=" N ILE A 516 " --> pdb=" O ASP A 512 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 542 removed outlier: 3.571A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.886A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 568 removed outlier: 3.680A pdb=" N THR A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 removed outlier: 3.592A pdb=" N TYR A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 607 removed outlier: 3.625A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 removed outlier: 3.527A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 666 Processing helix chain 'A' and resid 668 through 685 removed outlier: 4.000A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.720A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 removed outlier: 3.583A pdb=" N ARG A 714 " --> pdb=" O TRP A 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 130 Processing helix chain 'B' and resid 131 through 148 removed outlier: 3.832A pdb=" N ARG B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 162 removed outlier: 3.603A pdb=" N MET B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.832A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.889A pdb=" N ILE B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 218 through 225 removed outlier: 3.965A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 removed outlier: 3.691A pdb=" N THR B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.523A pdb=" N ALA B 269 " --> pdb=" O PRO B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.640A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.659A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.719A pdb=" N ARG B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.503A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.601A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.708A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.550A pdb=" N MET B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 4.135A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 removed outlier: 3.906A pdb=" N VAL B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 508 removed outlier: 3.522A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 520 removed outlier: 3.849A pdb=" N ILE B 516 " --> pdb=" O ASP B 512 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER B 518 " --> pdb=" O GLN B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 542 removed outlier: 3.570A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN B 529 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.886A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 568 removed outlier: 3.680A pdb=" N THR B 566 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 removed outlier: 3.591A pdb=" N TYR B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 607 removed outlier: 3.625A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 removed outlier: 3.525A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 666 Processing helix chain 'B' and resid 668 through 685 removed outlier: 4.000A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 682 " --> pdb=" O GLY B 678 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.721A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 715 removed outlier: 3.584A pdb=" N ARG B 714 " --> pdb=" O TRP B 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 130 Processing helix chain 'C' and resid 131 through 148 removed outlier: 3.833A pdb=" N ARG C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG C 148 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 162 removed outlier: 3.604A pdb=" N MET C 159 " --> pdb=" O PRO C 155 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.832A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.889A pdb=" N ILE C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 218 through 225 removed outlier: 3.966A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 removed outlier: 3.692A pdb=" N THR C 231 " --> pdb=" O GLN C 227 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 removed outlier: 3.523A pdb=" N ALA C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.640A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.659A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.719A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.502A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.601A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.708A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.550A pdb=" N MET C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 4.135A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 removed outlier: 3.906A pdb=" N VAL C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 508 removed outlier: 3.522A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 520 removed outlier: 3.848A pdb=" N ILE C 516 " --> pdb=" O ASP C 512 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 517 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER C 518 " --> pdb=" O GLN C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 542 removed outlier: 3.570A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.886A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 568 removed outlier: 3.680A pdb=" N THR C 566 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 586 removed outlier: 3.591A pdb=" N TYR C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 607 removed outlier: 3.624A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 removed outlier: 3.526A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 666 Processing helix chain 'C' and resid 668 through 685 removed outlier: 3.999A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C 682 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 707 removed outlier: 3.720A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS C 705 " --> pdb=" O LEU C 701 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 715 removed outlier: 3.584A pdb=" N ARG C 714 " --> pdb=" O TRP C 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 Processing helix chain 'D' and resid 131 through 148 removed outlier: 3.832A pdb=" N ARG D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG D 148 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 162 removed outlier: 3.604A pdb=" N MET D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.831A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.889A pdb=" N ILE D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 218 through 225 removed outlier: 3.965A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 removed outlier: 3.691A pdb=" N THR D 231 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 removed outlier: 3.523A pdb=" N ALA D 269 " --> pdb=" O PRO D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.640A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.658A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.719A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 removed outlier: 3.503A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.601A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.708A pdb=" N LEU D 373 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 removed outlier: 3.500A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.550A pdb=" N MET D 419 " --> pdb=" O ASN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 4.135A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 429 " --> pdb=" O LEU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 removed outlier: 3.906A pdb=" N VAL D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 508 removed outlier: 3.522A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 508 " --> pdb=" O ALA D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 520 removed outlier: 3.848A pdb=" N ILE D 516 " --> pdb=" O ASP D 512 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU D 517 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER D 518 " --> pdb=" O GLN D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 542 removed outlier: 3.571A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.886A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 552 " --> pdb=" O LEU D 548 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 568 removed outlier: 3.679A pdb=" N THR D 566 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 586 removed outlier: 3.591A pdb=" N TYR D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL D 577 " --> pdb=" O GLY D 573 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 584 " --> pdb=" O GLN D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 607 removed outlier: 3.625A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 removed outlier: 3.525A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 666 Processing helix chain 'D' and resid 668 through 685 removed outlier: 3.999A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU D 682 " --> pdb=" O GLY D 678 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN D 683 " --> pdb=" O GLU D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 707 removed outlier: 3.721A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 715 removed outlier: 3.584A pdb=" N ARG D 714 " --> pdb=" O TRP D 710 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 6.789A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 722 through 724 removed outlier: 6.913A pdb=" N ASP A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 376 through 382 removed outlier: 6.788A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 722 through 724 removed outlier: 6.913A pdb=" N ASP B 727 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 376 through 382 removed outlier: 6.788A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 722 through 724 removed outlier: 6.913A pdb=" N ASP C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 376 through 382 removed outlier: 6.788A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 722 through 724 removed outlier: 6.913A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 923 hydrogen bonds defined for protein. 2745 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: 3.56 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3432 1.31 - 1.43: 6004 1.43 - 1.56: 13412 1.56 - 1.69: 92 1.69 - 1.81: 204 Bond restraints: 23144 Sorted by residual: bond pdb=" C21 POV B 906 " pdb=" O21 POV B 906 " ideal model delta sigma weight residual 1.330 1.422 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C21 POV D 908 " pdb=" O21 POV D 908 " ideal model delta sigma weight residual 1.330 1.421 -0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C21 POV C 906 " pdb=" O21 POV C 906 " ideal model delta sigma weight residual 1.330 1.421 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C21 POV B 902 " pdb=" O21 POV B 902 " ideal model delta sigma weight residual 1.330 1.421 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C21 POV A 903 " pdb=" O21 POV A 903 " ideal model delta sigma weight residual 1.330 1.421 -0.091 2.00e-02 2.50e+03 2.06e+01 ... (remaining 23139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 29585 2.73 - 5.45: 886 5.45 - 8.18: 285 8.18 - 10.91: 127 10.91 - 13.63: 85 Bond angle restraints: 30968 Sorted by residual: angle pdb=" C LEU C 473 " pdb=" N ALA C 474 " pdb=" CA ALA C 474 " ideal model delta sigma weight residual 121.54 131.07 -9.53 1.91e+00 2.74e-01 2.49e+01 angle pdb=" C GLN D 313 " pdb=" N ASN D 314 " pdb=" CA ASN D 314 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.48e+01 angle pdb=" C GLN B 313 " pdb=" N ASN B 314 " pdb=" CA ASN B 314 " ideal model delta sigma weight residual 121.54 131.03 -9.49 1.91e+00 2.74e-01 2.47e+01 angle pdb=" C LEU D 473 " pdb=" N ALA D 474 " pdb=" CA ALA D 474 " ideal model delta sigma weight residual 121.54 131.03 -9.49 1.91e+00 2.74e-01 2.47e+01 angle pdb=" C GLN A 313 " pdb=" N ASN A 314 " pdb=" CA ASN A 314 " ideal model delta sigma weight residual 121.54 131.03 -9.49 1.91e+00 2.74e-01 2.47e+01 ... (remaining 30963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.35: 13517 34.35 - 68.71: 638 68.71 - 103.06: 88 103.06 - 137.41: 41 137.41 - 171.77: 16 Dihedral angle restraints: 14300 sinusoidal: 6744 harmonic: 7556 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 -153.10 67.10 1 1.00e+01 1.00e-02 5.86e+01 dihedral pdb=" CB CYS A 612 " pdb=" SG CYS A 612 " pdb=" SG CYS A 619 " pdb=" CB CYS A 619 " ideal model delta sinusoidal sigma weight residual -86.00 -153.10 67.10 1 1.00e+01 1.00e-02 5.86e+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 -153.08 67.08 1 1.00e+01 1.00e-02 5.86e+01 ... (remaining 14297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2620 0.058 - 0.117: 578 0.117 - 0.175: 90 0.175 - 0.233: 28 0.233 - 0.291: 12 Chirality restraints: 3328 Sorted by residual: chirality pdb=" CG LEU C 469 " pdb=" CB LEU C 469 " pdb=" CD1 LEU C 469 " pdb=" CD2 LEU C 469 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CG LEU D 469 " pdb=" CB LEU D 469 " pdb=" CD1 LEU D 469 " pdb=" CD2 LEU D 469 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CG LEU A 469 " pdb=" CB LEU A 469 " pdb=" CD1 LEU A 469 " pdb=" CD2 LEU A 469 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 3325 not shown) Planarity restraints: 3712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 509 " 0.049 5.00e-02 4.00e+02 7.47e-02 8.93e+00 pdb=" N PRO C 510 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO C 510 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 510 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 509 " 0.049 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO B 510 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 510 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 510 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 509 " 0.049 5.00e-02 4.00e+02 7.44e-02 8.86e+00 pdb=" N PRO A 510 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 510 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 510 " 0.041 5.00e-02 4.00e+02 ... (remaining 3709 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6462 2.82 - 3.34: 18697 3.34 - 3.86: 33266 3.86 - 4.38: 40934 4.38 - 4.90: 71505 Nonbonded interactions: 170864 Sorted by model distance: nonbonded pdb="NA NA A 910 " pdb="NA NA A 911 " model vdw 2.303 1.900 nonbonded pdb=" OG SER C 444 " pdb=" O14 POV C 905 " model vdw 2.330 3.040 nonbonded pdb=" OG SER B 444 " pdb=" O14 POV B 905 " model vdw 2.331 3.040 nonbonded pdb=" OG SER D 444 " pdb=" O14 POV D 907 " model vdw 2.332 3.040 nonbonded pdb=" OG SER A 444 " pdb=" O14 POV A 902 " model vdw 2.335 3.040 ... (remaining 170859 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 118 through 909) selection = chain 'B' 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.970 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 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 : 0.011 0.092 23148 Z= 0.517 Angle : 1.464 13.634 30976 Z= 0.661 Chirality : 0.053 0.291 3328 Planarity : 0.007 0.075 3712 Dihedral : 20.415 171.766 9384 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.58 % Favored : 95.26 % Rotamer: Outliers : 0.18 % Allowed : 5.60 % Favored : 94.22 % 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: -6.07 (0.10), residues: 2552 helix: -4.60 (0.04), residues: 1564 sheet: -0.94 (0.54), residues: 76 loop : -2.78 (0.16), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 149 TYR 0.015 0.003 TYR D 451 PHE 0.034 0.003 PHE D 526 TRP 0.013 0.002 TRP C 692 HIS 0.010 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.01119 (23144) covalent geometry : angle 1.46372 (30968) SS BOND : bond 0.00525 ( 4) SS BOND : angle 1.24895 ( 8) hydrogen bonds : bond 0.35909 ( 923) hydrogen bonds : angle 9.19791 ( 2745) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 356 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 ASN cc_start: 0.8200 (p0) cc_final: 0.7695 (p0) REVERT: A 185 GLU cc_start: 0.7336 (mp0) cc_final: 0.7066 (mp0) REVERT: A 257 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8027 (mm-30) REVERT: A 434 LYS cc_start: 0.8628 (mtpt) cc_final: 0.8346 (mmtt) REVERT: A 440 MET cc_start: 0.9020 (mtp) cc_final: 0.8677 (mtp) REVERT: A 645 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7707 (tp40) REVERT: B 182 ASN cc_start: 0.8209 (p0) cc_final: 0.7716 (p0) REVERT: B 185 GLU cc_start: 0.7213 (mp0) cc_final: 0.7005 (mp0) REVERT: B 440 MET cc_start: 0.9007 (mtp) cc_final: 0.8715 (mtp) REVERT: B 645 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7625 (tp40) REVERT: C 182 ASN cc_start: 0.8173 (p0) cc_final: 0.7648 (p0) REVERT: C 185 GLU cc_start: 0.7328 (mp0) cc_final: 0.7094 (mp0) REVERT: C 257 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7999 (mm-30) REVERT: C 434 LYS cc_start: 0.8639 (mtpt) cc_final: 0.8383 (mmtt) REVERT: C 440 MET cc_start: 0.9041 (mtp) cc_final: 0.8732 (mtp) REVERT: C 645 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7707 (tp40) REVERT: D 182 ASN cc_start: 0.8213 (p0) cc_final: 0.7713 (p0) REVERT: D 440 MET cc_start: 0.9008 (mtp) cc_final: 0.8723 (mtp) REVERT: D 645 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7656 (tp40) outliers start: 4 outliers final: 0 residues processed: 360 average time/residue: 0.1861 time to fit residues: 98.2932 Evaluate side-chains 243 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 220 ASN A 477 HIS ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN B 178 ASN B 220 ASN B 314 ASN B 477 HIS ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 ASN C 178 ASN C 220 ASN C 314 ASN C 477 HIS ** C 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 178 ASN D 220 ASN D 314 ASN D 477 HIS ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 643 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.128816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.085559 restraints weight = 32467.223| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.41 r_work: 0.2775 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 23148 Z= 0.129 Angle : 0.586 7.417 30976 Z= 0.305 Chirality : 0.040 0.155 3328 Planarity : 0.005 0.061 3712 Dihedral : 23.065 165.104 4336 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.83 % Allowed : 7.92 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.23 (0.13), residues: 2552 helix: -1.91 (0.10), residues: 1572 sheet: -0.08 (0.53), residues: 76 loop : -2.51 (0.17), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 714 TYR 0.015 0.001 TYR A 321 PHE 0.013 0.001 PHE A 316 TRP 0.010 0.001 TRP C 710 HIS 0.004 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00283 (23144) covalent geometry : angle 0.58607 (30968) SS BOND : bond 0.00156 ( 4) SS BOND : angle 0.60686 ( 8) hydrogen bonds : bond 0.05810 ( 923) hydrogen bonds : angle 4.00200 ( 2745) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 271 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8221 (mm-30) REVERT: A 434 LYS cc_start: 0.8409 (mtpt) cc_final: 0.8067 (mmtt) REVERT: A 524 PHE cc_start: 0.7955 (t80) cc_final: 0.7729 (t80) REVERT: A 545 LYS cc_start: 0.8421 (mtmp) cc_final: 0.8188 (tttm) REVERT: A 645 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7990 (tp40) REVERT: B 320 MET cc_start: 0.9376 (mmt) cc_final: 0.9119 (mmt) REVERT: B 524 PHE cc_start: 0.7869 (t80) cc_final: 0.7658 (t80) REVERT: B 545 LYS cc_start: 0.8421 (mtmp) cc_final: 0.8175 (tttm) REVERT: B 645 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7980 (tp40) REVERT: C 257 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8205 (mm-30) REVERT: C 320 MET cc_start: 0.9374 (mmt) cc_final: 0.9110 (mmt) REVERT: C 434 LYS cc_start: 0.8405 (mtpt) cc_final: 0.8059 (mmtt) REVERT: C 545 LYS cc_start: 0.8447 (mtmp) cc_final: 0.8171 (tttm) REVERT: C 645 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7980 (tp40) REVERT: D 320 MET cc_start: 0.9375 (mmt) cc_final: 0.9111 (mmt) REVERT: D 645 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7981 (tp40) outliers start: 19 outliers final: 6 residues processed: 283 average time/residue: 0.1798 time to fit residues: 77.6785 Evaluate side-chains 223 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 217 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 241 optimal weight: 0.0980 chunk 189 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 114 optimal weight: 8.9990 chunk 233 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 4 optimal weight: 0.0170 overall best weight: 2.6022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 GLN A 523 HIS B 313 GLN B 523 HIS C 313 GLN C 523 HIS D 313 GLN D 523 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.125222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.082216 restraints weight = 32581.455| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.39 r_work: 0.2743 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23148 Z= 0.161 Angle : 0.581 7.817 30976 Z= 0.297 Chirality : 0.041 0.212 3328 Planarity : 0.004 0.053 3712 Dihedral : 21.460 165.666 4336 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.40 % Allowed : 9.54 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.15), residues: 2552 helix: -0.36 (0.13), residues: 1560 sheet: 0.23 (0.54), residues: 76 loop : -2.35 (0.17), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 714 TYR 0.020 0.002 TYR B 540 PHE 0.018 0.002 PHE A 316 TRP 0.007 0.001 TRP A 559 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00382 (23144) covalent geometry : angle 0.58097 (30968) SS BOND : bond 0.00208 ( 4) SS BOND : angle 0.59024 ( 8) hydrogen bonds : bond 0.05933 ( 923) hydrogen bonds : angle 3.69775 ( 2745) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 0.747 Fit side-chains REVERT: A 257 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8350 (mm-30) REVERT: A 545 LYS cc_start: 0.8585 (mtmp) cc_final: 0.8249 (tttm) REVERT: A 645 GLN cc_start: 0.8338 (mm-40) cc_final: 0.8083 (tp40) REVERT: B 320 MET cc_start: 0.9452 (mmt) cc_final: 0.9189 (mmt) REVERT: B 545 LYS cc_start: 0.8575 (mtmp) cc_final: 0.8239 (tttm) REVERT: B 645 GLN cc_start: 0.8322 (mm-40) cc_final: 0.8026 (tp40) REVERT: C 257 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8325 (mm-30) REVERT: C 320 MET cc_start: 0.9450 (mmt) cc_final: 0.9177 (mmt) REVERT: C 545 LYS cc_start: 0.8623 (mtmp) cc_final: 0.8232 (tttm) REVERT: C 645 GLN cc_start: 0.8335 (mm-40) cc_final: 0.8049 (tp40) REVERT: D 320 MET cc_start: 0.9453 (mmt) cc_final: 0.9191 (mmt) REVERT: D 545 LYS cc_start: 0.8613 (mtmp) cc_final: 0.8231 (tttm) REVERT: D 645 GLN cc_start: 0.8339 (mm-40) cc_final: 0.8050 (tp40) outliers start: 32 outliers final: 6 residues processed: 257 average time/residue: 0.1708 time to fit residues: 68.2365 Evaluate side-chains 219 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 213 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 109 optimal weight: 6.9990 chunk 241 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 195 optimal weight: 20.0000 chunk 219 optimal weight: 5.9990 chunk 242 optimal weight: 9.9990 chunk 251 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN B 647 ASN C 647 ASN D 647 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.124232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.081010 restraints weight = 32696.726| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.39 r_work: 0.2709 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23148 Z= 0.181 Angle : 0.593 10.363 30976 Z= 0.300 Chirality : 0.042 0.220 3328 Planarity : 0.004 0.046 3712 Dihedral : 20.770 166.037 4336 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.80 % Allowed : 10.20 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.16), residues: 2552 helix: 0.30 (0.13), residues: 1556 sheet: 0.35 (0.55), residues: 76 loop : -2.16 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 712 TYR 0.020 0.002 TYR A 540 PHE 0.017 0.002 PHE B 316 TRP 0.007 0.001 TRP A 380 HIS 0.006 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00441 (23144) covalent geometry : angle 0.59265 (30968) SS BOND : bond 0.00186 ( 4) SS BOND : angle 0.41783 ( 8) hydrogen bonds : bond 0.05907 ( 923) hydrogen bonds : angle 3.66832 ( 2745) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 231 time to evaluate : 0.837 Fit side-chains REVERT: A 159 MET cc_start: 0.7901 (mmm) cc_final: 0.7467 (tpt) REVERT: A 257 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8350 (mm-30) REVERT: A 509 ARG cc_start: 0.5793 (OUTLIER) cc_final: 0.5545 (ppt170) REVERT: A 545 LYS cc_start: 0.8635 (mtmp) cc_final: 0.8216 (tttm) REVERT: A 645 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8072 (tp40) REVERT: B 509 ARG cc_start: 0.5757 (OUTLIER) cc_final: 0.5490 (ppt170) REVERT: B 545 LYS cc_start: 0.8627 (mtmp) cc_final: 0.8183 (tttm) REVERT: B 645 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8045 (tp40) REVERT: C 509 ARG cc_start: 0.5750 (OUTLIER) cc_final: 0.5485 (ppt170) REVERT: C 545 LYS cc_start: 0.8646 (mtmp) cc_final: 0.8239 (tttm) REVERT: C 627 ASP cc_start: 0.8713 (m-30) cc_final: 0.8273 (m-30) REVERT: C 645 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8054 (tp40) REVERT: D 509 ARG cc_start: 0.5735 (OUTLIER) cc_final: 0.5478 (ppt170) REVERT: D 545 LYS cc_start: 0.8650 (mtmp) cc_final: 0.8266 (tttm) REVERT: D 627 ASP cc_start: 0.8709 (m-30) cc_final: 0.8270 (m-30) REVERT: D 645 GLN cc_start: 0.8371 (mm-40) cc_final: 0.8051 (tp40) outliers start: 41 outliers final: 7 residues processed: 267 average time/residue: 0.1677 time to fit residues: 69.4339 Evaluate side-chains 228 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 217 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 97 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 208 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 193 optimal weight: 6.9990 chunk 230 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.124722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.081763 restraints weight = 32702.690| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.36 r_work: 0.2714 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 23148 Z= 0.167 Angle : 0.583 9.966 30976 Z= 0.292 Chirality : 0.042 0.152 3328 Planarity : 0.004 0.043 3712 Dihedral : 20.384 168.411 4336 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.05 % Allowed : 10.51 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.16), residues: 2552 helix: 0.66 (0.13), residues: 1560 sheet: 0.51 (0.53), residues: 76 loop : -2.13 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 712 TYR 0.024 0.002 TYR B 540 PHE 0.015 0.001 PHE A 316 TRP 0.007 0.001 TRP A 380 HIS 0.005 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00404 (23144) covalent geometry : angle 0.58281 (30968) SS BOND : bond 0.00167 ( 4) SS BOND : angle 0.30479 ( 8) hydrogen bonds : bond 0.05624 ( 923) hydrogen bonds : angle 3.62065 ( 2745) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 0.891 Fit side-chains REVERT: A 159 MET cc_start: 0.7959 (mmm) cc_final: 0.7531 (tpt) REVERT: A 257 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8348 (mm-30) REVERT: A 509 ARG cc_start: 0.5731 (OUTLIER) cc_final: 0.5527 (ppt170) REVERT: A 545 LYS cc_start: 0.8644 (mtmp) cc_final: 0.8265 (tttm) REVERT: A 645 GLN cc_start: 0.8375 (mm-40) cc_final: 0.8056 (tp40) REVERT: B 509 ARG cc_start: 0.5744 (OUTLIER) cc_final: 0.5502 (ppt170) REVERT: B 542 PHE cc_start: 0.7410 (m-10) cc_final: 0.7102 (m-80) REVERT: B 545 LYS cc_start: 0.8636 (mtmp) cc_final: 0.8221 (tttm) REVERT: B 645 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8049 (tp40) REVERT: C 509 ARG cc_start: 0.5751 (OUTLIER) cc_final: 0.5487 (ppt170) REVERT: C 545 LYS cc_start: 0.8678 (mtmp) cc_final: 0.8280 (tttm) REVERT: C 627 ASP cc_start: 0.8667 (m-30) cc_final: 0.8239 (m-30) REVERT: C 645 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8073 (tp40) REVERT: D 509 ARG cc_start: 0.5730 (OUTLIER) cc_final: 0.5459 (ppt170) REVERT: D 545 LYS cc_start: 0.8675 (mtmp) cc_final: 0.8273 (tttm) REVERT: D 627 ASP cc_start: 0.8661 (m-30) cc_final: 0.8233 (m-30) REVERT: D 645 GLN cc_start: 0.8392 (mm-40) cc_final: 0.8066 (tp40) outliers start: 24 outliers final: 12 residues processed: 243 average time/residue: 0.1738 time to fit residues: 66.0205 Evaluate side-chains 227 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 647 ASN Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 647 ASN Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 79 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 140 optimal weight: 0.0980 chunk 167 optimal weight: 6.9990 chunk 164 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 186 optimal weight: 0.5980 chunk 85 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 99 optimal weight: 0.0980 chunk 127 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.130562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.088050 restraints weight = 32694.824| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.38 r_work: 0.2830 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23148 Z= 0.090 Angle : 0.486 9.755 30976 Z= 0.241 Chirality : 0.037 0.137 3328 Planarity : 0.003 0.037 3712 Dihedral : 19.105 170.978 4336 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.66 % Allowed : 10.95 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.17), residues: 2552 helix: 1.20 (0.13), residues: 1592 sheet: 0.80 (0.55), residues: 76 loop : -2.30 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 509 TYR 0.022 0.001 TYR C 540 PHE 0.017 0.001 PHE A 506 TRP 0.007 0.001 TRP D 692 HIS 0.002 0.000 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00189 (23144) covalent geometry : angle 0.48594 (30968) SS BOND : bond 0.00178 ( 4) SS BOND : angle 0.23491 ( 8) hydrogen bonds : bond 0.03502 ( 923) hydrogen bonds : angle 3.22191 ( 2745) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 233 time to evaluate : 0.864 Fit side-chains REVERT: A 159 MET cc_start: 0.7909 (mmm) cc_final: 0.7421 (tpt) REVERT: A 257 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8412 (mm-30) REVERT: A 524 PHE cc_start: 0.7774 (t80) cc_final: 0.7533 (m-80) REVERT: A 542 PHE cc_start: 0.7237 (m-10) cc_final: 0.6913 (m-80) REVERT: A 545 LYS cc_start: 0.8567 (mtmp) cc_final: 0.8275 (tttm) REVERT: A 645 GLN cc_start: 0.8321 (mm-40) cc_final: 0.8001 (tp40) REVERT: B 509 ARG cc_start: 0.5736 (OUTLIER) cc_final: 0.5469 (ppt170) REVERT: B 524 PHE cc_start: 0.8057 (t80) cc_final: 0.7628 (m-80) REVERT: B 542 PHE cc_start: 0.7266 (m-10) cc_final: 0.6934 (m-80) REVERT: B 545 LYS cc_start: 0.8569 (mtmp) cc_final: 0.8233 (tttm) REVERT: B 645 GLN cc_start: 0.8320 (mm-40) cc_final: 0.7995 (tp40) REVERT: C 509 ARG cc_start: 0.5744 (OUTLIER) cc_final: 0.5455 (ppt170) REVERT: C 542 PHE cc_start: 0.7247 (m-10) cc_final: 0.6920 (m-80) REVERT: C 545 LYS cc_start: 0.8631 (mtmp) cc_final: 0.8314 (tttm) REVERT: C 627 ASP cc_start: 0.8568 (m-30) cc_final: 0.8194 (m-30) REVERT: C 645 GLN cc_start: 0.8344 (mm-40) cc_final: 0.8026 (tp40) REVERT: D 278 VAL cc_start: 0.9041 (t) cc_final: 0.8838 (t) REVERT: D 508 LEU cc_start: 0.7615 (pp) cc_final: 0.7407 (pp) REVERT: D 542 PHE cc_start: 0.7241 (m-10) cc_final: 0.6919 (m-80) REVERT: D 545 LYS cc_start: 0.8636 (mtmp) cc_final: 0.8313 (tttm) REVERT: D 627 ASP cc_start: 0.8558 (m-30) cc_final: 0.8183 (m-30) REVERT: D 645 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8004 (tp40) outliers start: 15 outliers final: 9 residues processed: 247 average time/residue: 0.1695 time to fit residues: 65.2765 Evaluate side-chains 224 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 213 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 548 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 9 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 254 optimal weight: 8.9990 chunk 225 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 214 optimal weight: 0.4980 chunk 87 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.129255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.086361 restraints weight = 32586.907| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.38 r_work: 0.2790 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23148 Z= 0.097 Angle : 0.499 9.814 30976 Z= 0.246 Chirality : 0.038 0.141 3328 Planarity : 0.003 0.039 3712 Dihedral : 18.642 169.927 4336 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.92 % Allowed : 11.25 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.17), residues: 2552 helix: 1.58 (0.13), residues: 1560 sheet: 0.73 (0.55), residues: 76 loop : -2.02 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 714 TYR 0.025 0.001 TYR B 540 PHE 0.018 0.001 PHE B 506 TRP 0.005 0.001 TRP B 559 HIS 0.003 0.000 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00217 (23144) covalent geometry : angle 0.49891 (30968) SS BOND : bond 0.00163 ( 4) SS BOND : angle 0.27699 ( 8) hydrogen bonds : bond 0.04022 ( 923) hydrogen bonds : angle 3.25473 ( 2745) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 240 time to evaluate : 0.858 Fit side-chains REVERT: A 159 MET cc_start: 0.7873 (mmm) cc_final: 0.7387 (tpt) REVERT: A 336 MET cc_start: 0.9195 (ttp) cc_final: 0.8990 (ttm) REVERT: A 524 PHE cc_start: 0.7643 (t80) cc_final: 0.7435 (m-80) REVERT: A 542 PHE cc_start: 0.7209 (m-10) cc_final: 0.6884 (m-80) REVERT: A 545 LYS cc_start: 0.8476 (mtmp) cc_final: 0.8224 (tttm) REVERT: A 645 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7950 (tp40) REVERT: B 524 PHE cc_start: 0.7894 (t80) cc_final: 0.7555 (m-80) REVERT: B 542 PHE cc_start: 0.7233 (m-10) cc_final: 0.6880 (m-80) REVERT: B 545 LYS cc_start: 0.8484 (mtmp) cc_final: 0.8217 (tttm) REVERT: B 645 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7947 (tp40) REVERT: C 336 MET cc_start: 0.9204 (ttp) cc_final: 0.8990 (ttm) REVERT: C 542 PHE cc_start: 0.7232 (m-10) cc_final: 0.6880 (m-80) REVERT: C 545 LYS cc_start: 0.8521 (mtmp) cc_final: 0.8257 (tttm) REVERT: C 627 ASP cc_start: 0.8412 (m-30) cc_final: 0.7990 (m-30) REVERT: C 645 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7955 (tp40) REVERT: D 336 MET cc_start: 0.9185 (ttp) cc_final: 0.8985 (ttm) REVERT: D 542 PHE cc_start: 0.7232 (m-10) cc_final: 0.6881 (m-80) REVERT: D 545 LYS cc_start: 0.8535 (mtmp) cc_final: 0.8262 (tttm) REVERT: D 627 ASP cc_start: 0.8422 (m-30) cc_final: 0.8000 (m-30) REVERT: D 645 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7955 (tp40) outliers start: 21 outliers final: 17 residues processed: 257 average time/residue: 0.1747 time to fit residues: 69.9471 Evaluate side-chains 233 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 216 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 159 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 chunk 252 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 208 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.128254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.085444 restraints weight = 32526.219| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.36 r_work: 0.2771 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23148 Z= 0.111 Angle : 0.515 8.890 30976 Z= 0.257 Chirality : 0.039 0.143 3328 Planarity : 0.003 0.042 3712 Dihedral : 18.415 170.286 4336 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.09 % Allowed : 11.60 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.17), residues: 2552 helix: 1.65 (0.13), residues: 1560 sheet: 0.77 (0.55), residues: 76 loop : -1.89 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 712 TYR 0.031 0.001 TYR B 540 PHE 0.018 0.001 PHE A 506 TRP 0.005 0.001 TRP C 692 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00258 (23144) covalent geometry : angle 0.51536 (30968) SS BOND : bond 0.00128 ( 4) SS BOND : angle 0.22495 ( 8) hydrogen bonds : bond 0.04320 ( 923) hydrogen bonds : angle 3.32969 ( 2745) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 0.892 Fit side-chains REVERT: A 159 MET cc_start: 0.7856 (mmm) cc_final: 0.7369 (tpt) REVERT: A 336 MET cc_start: 0.9211 (ttp) cc_final: 0.8987 (ttm) REVERT: A 524 PHE cc_start: 0.7686 (t80) cc_final: 0.7431 (m-80) REVERT: A 542 PHE cc_start: 0.7246 (m-10) cc_final: 0.6907 (m-80) REVERT: A 545 LYS cc_start: 0.8467 (mtmp) cc_final: 0.8203 (tttm) REVERT: A 645 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7958 (tp40) REVERT: B 524 PHE cc_start: 0.7955 (t80) cc_final: 0.7572 (m-80) REVERT: B 542 PHE cc_start: 0.7298 (m-10) cc_final: 0.6922 (m-80) REVERT: B 545 LYS cc_start: 0.8454 (mtmp) cc_final: 0.8206 (tttm) REVERT: B 645 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7954 (tp40) REVERT: C 336 MET cc_start: 0.9208 (ttp) cc_final: 0.8988 (ttm) REVERT: C 542 PHE cc_start: 0.7251 (m-10) cc_final: 0.6906 (m-80) REVERT: C 545 LYS cc_start: 0.8499 (mtmp) cc_final: 0.8234 (tttm) REVERT: C 627 ASP cc_start: 0.8423 (m-30) cc_final: 0.7994 (m-30) REVERT: C 645 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7949 (tp40) REVERT: D 336 MET cc_start: 0.9198 (ttp) cc_final: 0.8977 (ttm) REVERT: D 542 PHE cc_start: 0.7247 (m-10) cc_final: 0.6907 (m-80) REVERT: D 545 LYS cc_start: 0.8498 (mtmp) cc_final: 0.8261 (tttm) REVERT: D 627 ASP cc_start: 0.8421 (m-30) cc_final: 0.7993 (m-30) REVERT: D 645 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7943 (tp40) outliers start: 25 outliers final: 18 residues processed: 238 average time/residue: 0.1642 time to fit residues: 62.3927 Evaluate side-chains 229 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 647 ASN Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 18 optimal weight: 0.6980 chunk 246 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 70 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 205 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.128850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.086095 restraints weight = 32636.071| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.36 r_work: 0.2782 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23148 Z= 0.103 Angle : 0.509 8.505 30976 Z= 0.254 Chirality : 0.038 0.156 3328 Planarity : 0.003 0.039 3712 Dihedral : 18.059 170.519 4336 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.09 % Allowed : 11.47 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.17), residues: 2552 helix: 1.68 (0.13), residues: 1584 sheet: 0.83 (0.55), residues: 76 loop : -2.06 (0.18), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 714 TYR 0.024 0.001 TYR A 540 PHE 0.023 0.001 PHE D 193 TRP 0.005 0.001 TRP C 692 HIS 0.003 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00236 (23144) covalent geometry : angle 0.50870 (30968) SS BOND : bond 0.00153 ( 4) SS BOND : angle 0.26654 ( 8) hydrogen bonds : bond 0.04075 ( 923) hydrogen bonds : angle 3.32148 ( 2745) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 0.816 Fit side-chains REVERT: A 159 MET cc_start: 0.7820 (mmm) cc_final: 0.7328 (tpt) REVERT: A 336 MET cc_start: 0.9196 (ttp) cc_final: 0.8979 (ttm) REVERT: A 524 PHE cc_start: 0.7632 (t80) cc_final: 0.7407 (m-80) REVERT: A 542 PHE cc_start: 0.7248 (m-10) cc_final: 0.6920 (m-80) REVERT: A 545 LYS cc_start: 0.8450 (mtmp) cc_final: 0.8201 (tttm) REVERT: A 645 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7929 (tp40) REVERT: B 524 PHE cc_start: 0.7900 (t80) cc_final: 0.7563 (m-80) REVERT: B 542 PHE cc_start: 0.7203 (m-10) cc_final: 0.6828 (m-80) REVERT: B 545 LYS cc_start: 0.8435 (mtmp) cc_final: 0.8200 (tttm) REVERT: B 645 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7945 (tp40) REVERT: C 336 MET cc_start: 0.9193 (ttp) cc_final: 0.8978 (ttm) REVERT: C 542 PHE cc_start: 0.7250 (m-10) cc_final: 0.6908 (m-80) REVERT: C 545 LYS cc_start: 0.8503 (mtmp) cc_final: 0.8253 (tttm) REVERT: C 627 ASP cc_start: 0.8407 (m-30) cc_final: 0.7977 (m-30) REVERT: C 645 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7954 (tp40) REVERT: D 336 MET cc_start: 0.9180 (ttp) cc_final: 0.8962 (ttm) REVERT: D 542 PHE cc_start: 0.7240 (m-10) cc_final: 0.6897 (m-80) REVERT: D 545 LYS cc_start: 0.8496 (mtmp) cc_final: 0.8277 (tttm) REVERT: D 627 ASP cc_start: 0.8407 (m-30) cc_final: 0.7979 (m-30) REVERT: D 645 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7954 (tp40) outliers start: 25 outliers final: 21 residues processed: 241 average time/residue: 0.1640 time to fit residues: 62.1400 Evaluate side-chains 234 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 213 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 647 ASN Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 174 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 123 optimal weight: 0.0070 chunk 32 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 overall best weight: 0.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.131025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.088422 restraints weight = 32634.450| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.36 r_work: 0.2821 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23148 Z= 0.092 Angle : 0.504 10.135 30976 Z= 0.251 Chirality : 0.038 0.214 3328 Planarity : 0.003 0.039 3712 Dihedral : 17.468 170.718 4336 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.92 % Allowed : 11.78 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.17), residues: 2552 helix: 1.85 (0.13), residues: 1580 sheet: 0.89 (0.56), residues: 76 loop : -2.00 (0.18), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 188 TYR 0.025 0.001 TYR D 540 PHE 0.010 0.001 PHE C 193 TRP 0.008 0.001 TRP B 739 HIS 0.002 0.000 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00200 (23144) covalent geometry : angle 0.50382 (30968) SS BOND : bond 0.00110 ( 4) SS BOND : angle 0.28615 ( 8) hydrogen bonds : bond 0.03547 ( 923) hydrogen bonds : angle 3.27886 ( 2745) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 0.836 Fit side-chains REVERT: A 159 MET cc_start: 0.7804 (mmm) cc_final: 0.7299 (tpt) REVERT: A 336 MET cc_start: 0.9191 (ttp) cc_final: 0.8974 (ttm) REVERT: A 645 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7940 (tp40) REVERT: B 524 PHE cc_start: 0.7891 (t80) cc_final: 0.7602 (m-80) REVERT: B 542 PHE cc_start: 0.7163 (m-10) cc_final: 0.6792 (m-80) REVERT: B 645 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7922 (tp40) REVERT: C 336 MET cc_start: 0.9189 (ttp) cc_final: 0.8980 (ttm) REVERT: C 627 ASP cc_start: 0.8373 (m-30) cc_final: 0.7945 (m-30) REVERT: C 645 GLN cc_start: 0.8274 (mm-40) cc_final: 0.7957 (tp40) REVERT: D 336 MET cc_start: 0.9187 (ttp) cc_final: 0.8981 (ttm) REVERT: D 627 ASP cc_start: 0.8379 (m-30) cc_final: 0.7950 (m-30) REVERT: D 645 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7919 (tp40) outliers start: 21 outliers final: 16 residues processed: 242 average time/residue: 0.1669 time to fit residues: 63.8419 Evaluate side-chains 229 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 213 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 647 ASN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 647 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 66 optimal weight: 3.9990 chunk 209 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 162 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 234 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 chunk 212 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.126862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.083817 restraints weight = 32391.018| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.35 r_work: 0.2741 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23148 Z= 0.139 Angle : 0.555 7.893 30976 Z= 0.278 Chirality : 0.041 0.247 3328 Planarity : 0.003 0.039 3712 Dihedral : 17.677 169.615 4336 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.74 % Allowed : 12.04 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.17), residues: 2552 helix: 1.69 (0.13), residues: 1584 sheet: 0.68 (0.55), residues: 76 loop : -1.91 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 188 TYR 0.025 0.002 TYR A 540 PHE 0.020 0.001 PHE D 193 TRP 0.006 0.001 TRP C 739 HIS 0.005 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00331 (23144) covalent geometry : angle 0.55493 (30968) SS BOND : bond 0.00116 ( 4) SS BOND : angle 0.36934 ( 8) hydrogen bonds : bond 0.04923 ( 923) hydrogen bonds : angle 3.52481 ( 2745) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5564.23 seconds wall clock time: 96 minutes 1.15 seconds (5761.15 seconds total)