Starting phenix.real_space_refine on Sat Jul 4 18:35:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7min_23857/07_2026/7min_23857.cif Found real_map, /net/cci-nas-00/data/ceres_data/7min_23857/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7min_23857/07_2026/7min_23857.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7min_23857/07_2026/7min_23857.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7min_23857/07_2026/7min_23857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7min_23857/07_2026/7min_23857.map" model { file = "/net/cci-nas-00/data/ceres_data/7min_23857/07_2026/7min_23857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7min_23857/07_2026/7min_23857.cif" } 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-6108/lib/python3.11/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: 5.02, 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: 1.88 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: 0.59 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: 3.97 Time building geometry restraints manager: 2.59 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: 13409 34.35 - 68.71: 534 68.71 - 103.06: 84 103.06 - 137.41: 41 137.41 - 171.77: 16 Dihedral angle restraints: 14084 sinusoidal: 6528 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 14081 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: 1.480 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.940 Find NCS groups from input model: 0.580 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 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 : 19.814 171.766 9168 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/Z covalent geometry : bond 0.01119 / 0.52 (23144) covalent geometry : angle 1.46372 / 0.66 (30968) SS BOND : bond 0.00525 / 0.26 ( 4) SS BOND : angle 1.24895 / 0.72 ( 8) hydrogen bonds : bond 0.35909 / 23.10 ( 923) hydrogen bonds : angle 9.19791 / 6.34 ( 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 : 0.854 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: 0.1899 time to fit residues: 100.6737 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 : 0.793 ------------------------------------------------------------------------------- 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... 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 = 0.3562 r_free = 0.3562 target = 0.128382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.084984 restraints weight = 32456.472| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.41 r_work: 0.2766 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- 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 = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23148 Z= 0.130 Angle : 0.593 7.358 30976 Z= 0.309 Chirality : 0.040 0.156 3328 Planarity : 0.005 0.060 3712 Dihedral : 22.808 165.183 4120 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.74 % Allowed : 8.14 % Favored : 91.11 % 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: -3.12 (0.13), residues: 2552 helix: -1.80 (0.11), residues: 1572 sheet: -0.05 (0.53), residues: 76 loop : -2.51 (0.17), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 714 TYR 0.015 0.001 TYR A 321 PHE 0.014 0.001 PHE A 625 TRP 0.010 0.001 TRP A 710 HIS 0.004 0.001 HIS B 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (23144) covalent geometry : angle 0.59292 / 0.31 (30968) SS BOND : bond 0.00155 / 0.08 ( 4) SS BOND : angle 0.57272 / 0.33 ( 8) hydrogen bonds : bond 0.06023 / 3.88 ( 923) hydrogen bonds : angle 4.00611 / 2.74 ( 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 281 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 264 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8233 (mm-30) REVERT: A 434 LYS cc_start: 0.8426 (mtpt) cc_final: 0.8083 (mmtt) REVERT: A 524 PHE cc_start: 0.7997 (t80) cc_final: 0.7781 (t80) REVERT: A 545 LYS cc_start: 0.8431 (mtmp) cc_final: 0.8151 (tttm) REVERT: A 645 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7983 (tp40) REVERT: B 320 MET cc_start: 0.9380 (mmt) cc_final: 0.9119 (mmt) REVERT: B 524 PHE cc_start: 0.7950 (t80) cc_final: 0.7735 (t80) REVERT: B 545 LYS cc_start: 0.8442 (mtmp) cc_final: 0.8150 (tttm) REVERT: B 645 GLN cc_start: 0.8255 (mm-40) cc_final: 0.7985 (tp40) REVERT: C 257 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8206 (mm-30) REVERT: C 320 MET cc_start: 0.9379 (mmt) cc_final: 0.9117 (mmt) REVERT: C 434 LYS cc_start: 0.8440 (mtpt) cc_final: 0.8086 (mmtt) REVERT: C 645 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7992 (tp40) REVERT: D 320 MET cc_start: 0.9381 (mmt) cc_final: 0.9119 (mmt) REVERT: D 645 GLN cc_start: 0.8255 (mm-40) cc_final: 0.7981 (tp40) outliers start: 17 outliers final: 9 residues processed: 276 average time/residue: 0.1700 time to fit residues: 71.3840 Evaluate side-chains 223 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 214 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 123 ILE 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: 8.9990 chunk 189 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 233 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.124564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.081387 restraints weight = 32606.134| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.40 r_work: 0.2729 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 23148 Z= 0.180 Angle : 0.598 7.269 30976 Z= 0.306 Chirality : 0.042 0.181 3328 Planarity : 0.004 0.054 3712 Dihedral : 21.176 165.928 4120 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.45 % Favored : 96.39 % Rotamer: Outliers : 1.53 % Allowed : 9.76 % Favored : 88.70 % 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: -1.55 (0.15), residues: 2552 helix: -0.35 (0.13), residues: 1556 sheet: 0.16 (0.54), residues: 76 loop : -2.25 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 714 TYR 0.016 0.002 TYR A 321 PHE 0.019 0.002 PHE A 316 TRP 0.006 0.001 TRP A 559 HIS 0.006 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (23144) covalent geometry : angle 0.59805 / 0.31 (30968) SS BOND : bond 0.00205 / 0.10 ( 4) SS BOND : angle 0.60662 / 0.35 ( 8) hydrogen bonds : bond 0.06245 / 4.02 ( 923) hydrogen bonds : angle 3.77486 / 2.59 ( 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 269 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 234 time to evaluate : 0.834 Fit side-chains REVERT: A 257 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8350 (mm-30) REVERT: A 545 LYS cc_start: 0.8618 (mtmp) cc_final: 0.8211 (tttm) REVERT: A 645 GLN cc_start: 0.8344 (mm-40) cc_final: 0.8090 (tp40) REVERT: B 320 MET cc_start: 0.9469 (mmt) cc_final: 0.9194 (mmt) REVERT: B 545 LYS cc_start: 0.8588 (mtmp) cc_final: 0.8184 (tttm) REVERT: B 645 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8035 (tp40) REVERT: C 320 MET cc_start: 0.9471 (mmt) cc_final: 0.9187 (mmt) REVERT: C 545 LYS cc_start: 0.8629 (mtmp) cc_final: 0.8217 (tttm) REVERT: C 645 GLN cc_start: 0.8353 (mm-40) cc_final: 0.8066 (tp40) REVERT: D 320 MET cc_start: 0.9467 (mmt) cc_final: 0.9186 (mmt) REVERT: D 545 LYS cc_start: 0.8618 (mtmp) cc_final: 0.8208 (tttm) REVERT: D 611 LYS cc_start: 0.7033 (tptt) cc_final: 0.6832 (tptt) REVERT: D 645 GLN cc_start: 0.8353 (mm-40) cc_final: 0.8063 (tp40) outliers start: 35 outliers final: 6 residues processed: 261 average time/residue: 0.1576 time to fit residues: 64.3279 Evaluate side-chains 217 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 211 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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: 5.9990 chunk 241 optimal weight: 0.5980 chunk 216 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 195 optimal weight: 20.0000 chunk 219 optimal weight: 5.9990 chunk 242 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3502 r_free = 0.3502 target = 0.123937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.080906 restraints weight = 32792.418| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.37 r_work: 0.2699 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2552 r_free = 0.2552 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2552 r_free = 0.2552 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 23148 Z= 0.188 Angle : 0.597 10.136 30976 Z= 0.303 Chirality : 0.042 0.218 3328 Planarity : 0.004 0.046 3712 Dihedral : 20.542 165.289 4120 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.72 % Favored : 96.12 % Rotamer: Outliers : 1.66 % Allowed : 10.77 % Favored : 87.57 % 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: -0.91 (0.16), residues: 2552 helix: 0.26 (0.13), residues: 1556 sheet: 0.37 (0.54), residues: 76 loop : -2.18 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 712 TYR 0.015 0.002 TYR A 321 PHE 0.017 0.002 PHE A 316 TRP 0.007 0.001 TRP A 380 HIS 0.006 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (23144) covalent geometry : angle 0.59725 / 0.30 (30968) SS BOND : bond 0.00186 / 0.09 ( 4) SS BOND : angle 0.47192 / 0.28 ( 8) hydrogen bonds : bond 0.06040 / 3.88 ( 923) hydrogen bonds : angle 3.71098 / 2.55 ( 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 262 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 224 time to evaluate : 0.802 Fit side-chains REVERT: A 159 MET cc_start: 0.8018 (tpp) cc_final: 0.7804 (tpt) REVERT: A 257 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8345 (mm-30) REVERT: A 509 ARG cc_start: 0.5847 (OUTLIER) cc_final: 0.5579 (ppt170) REVERT: A 545 LYS cc_start: 0.8646 (mtmp) cc_final: 0.8257 (tttm) REVERT: A 645 GLN cc_start: 0.8364 (mm-40) cc_final: 0.8051 (tp40) REVERT: B 509 ARG cc_start: 0.5798 (OUTLIER) cc_final: 0.5498 (ppt170) REVERT: B 545 LYS cc_start: 0.8640 (mtmp) cc_final: 0.8176 (tttm) REVERT: B 645 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8047 (tp40) REVERT: C 320 MET cc_start: 0.9470 (mmt) cc_final: 0.9185 (mmt) REVERT: C 509 ARG cc_start: 0.5761 (OUTLIER) cc_final: 0.5489 (ppt170) REVERT: C 545 LYS cc_start: 0.8655 (mtmp) cc_final: 0.8263 (tttm) REVERT: C 627 ASP cc_start: 0.8676 (m-30) cc_final: 0.8238 (m-30) REVERT: C 645 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8045 (tp40) REVERT: D 320 MET cc_start: 0.9466 (mmt) cc_final: 0.9181 (mmt) REVERT: D 509 ARG cc_start: 0.5753 (OUTLIER) cc_final: 0.5463 (ppt170) REVERT: D 545 LYS cc_start: 0.8657 (mtmp) cc_final: 0.8261 (tttm) REVERT: D 627 ASP cc_start: 0.8676 (m-30) cc_final: 0.8239 (m-30) REVERT: D 645 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8051 (tp40) outliers start: 38 outliers final: 7 residues processed: 259 average time/residue: 0.1606 time to fit residues: 64.7841 Evaluate side-chains 223 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 212 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 MET 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 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: 6.9990 chunk 7 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 64 optimal weight: 20.0000 chunk 208 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 230 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.121614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.078466 restraints weight = 32674.278| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.38 r_work: 0.2674 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2515 r_free = 0.2515 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2514 r_free = 0.2514 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 23148 Z= 0.269 Angle : 0.689 10.332 30976 Z= 0.345 Chirality : 0.046 0.298 3328 Planarity : 0.004 0.043 3712 Dihedral : 20.768 165.290 4120 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.15 % Favored : 95.69 % Rotamer: Outliers : 1.49 % Allowed : 10.81 % Favored : 87.70 % 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: -0.88 (0.16), residues: 2552 helix: 0.37 (0.13), residues: 1556 sheet: -0.80 (0.45), residues: 108 loop : -2.26 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 712 TYR 0.030 0.003 TYR C 390 PHE 0.020 0.002 PHE A 316 TRP 0.009 0.001 TRP A 380 HIS 0.009 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00664 / 0.27 (23144) covalent geometry : angle 0.68899 / 0.35 (30968) SS BOND : bond 0.00215 / 0.11 ( 4) SS BOND : angle 0.38599 / 0.23 ( 8) hydrogen bonds : bond 0.06981 / 4.49 ( 923) hydrogen bonds : angle 3.90566 / 2.68 ( 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 250 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 0.957 Fit side-chains REVERT: A 509 ARG cc_start: 0.5798 (OUTLIER) cc_final: 0.5515 (ppt170) REVERT: A 545 LYS cc_start: 0.8620 (mtmp) cc_final: 0.8132 (tttm) REVERT: A 645 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8055 (tp40) REVERT: B 509 ARG cc_start: 0.5818 (OUTLIER) cc_final: 0.5482 (ppt170) REVERT: B 645 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8076 (tp40) REVERT: C 509 ARG cc_start: 0.5768 (OUTLIER) cc_final: 0.5491 (ppt170) REVERT: C 545 LYS cc_start: 0.8641 (mtmp) cc_final: 0.8164 (tttm) REVERT: C 627 ASP cc_start: 0.8740 (m-30) cc_final: 0.8304 (m-30) REVERT: C 645 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8079 (tp40) REVERT: D 509 ARG cc_start: 0.5817 (OUTLIER) cc_final: 0.5469 (ppt170) REVERT: D 545 LYS cc_start: 0.8650 (mtmp) cc_final: 0.8161 (tttm) REVERT: D 580 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8617 (tt0) REVERT: D 627 ASP cc_start: 0.8744 (m-30) cc_final: 0.8309 (m-30) REVERT: D 645 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8090 (tp40) outliers start: 34 outliers final: 10 residues processed: 244 average time/residue: 0.1662 time to fit residues: 63.2960 Evaluate side-chains 227 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 212 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 MET 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 C residue 509 ARG Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 580 GLN 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: 1.9990 chunk 104 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 164 optimal weight: 0.3980 chunk 201 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 85 optimal weight: 0.0980 chunk 132 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.127979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.085360 restraints weight = 32593.948| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.35 r_work: 0.2771 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23148 Z= 0.104 Angle : 0.520 9.631 30976 Z= 0.259 Chirality : 0.038 0.208 3328 Planarity : 0.003 0.037 3712 Dihedral : 19.377 168.604 4120 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.31 % Allowed : 10.99 % Favored : 87.70 % 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: -0.14 (0.16), residues: 2552 helix: 1.09 (0.13), residues: 1564 sheet: 0.69 (0.53), residues: 76 loop : -2.33 (0.17), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 714 TYR 0.009 0.001 TYR A 321 PHE 0.010 0.001 PHE C 524 TRP 0.007 0.001 TRP C 710 HIS 0.002 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (23144) covalent geometry : angle 0.52046 / 0.26 (30968) SS BOND : bond 0.00169 / 0.08 ( 4) SS BOND : angle 0.27529 / 0.17 ( 8) hydrogen bonds : bond 0.04110 / 2.63 ( 923) hydrogen bonds : angle 3.35824 / 2.30 ( 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 261 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 0.866 Fit side-chains REVERT: A 159 MET cc_start: 0.8095 (tpp) cc_final: 0.7885 (tpt) REVERT: A 509 ARG cc_start: 0.5801 (OUTLIER) cc_final: 0.5594 (ppt170) REVERT: A 524 PHE cc_start: 0.7961 (t80) cc_final: 0.7578 (m-80) REVERT: A 541 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6945 (mt) REVERT: A 542 PHE cc_start: 0.7361 (m-10) cc_final: 0.7027 (m-80) REVERT: A 545 LYS cc_start: 0.8587 (mtmp) cc_final: 0.8242 (tttm) REVERT: A 627 ASP cc_start: 0.8613 (m-30) cc_final: 0.8254 (m-30) REVERT: A 645 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8031 (tp40) REVERT: B 509 ARG cc_start: 0.5810 (OUTLIER) cc_final: 0.5548 (ppt170) REVERT: B 524 PHE cc_start: 0.7880 (t80) cc_final: 0.7499 (m-80) REVERT: B 542 PHE cc_start: 0.7321 (m-10) cc_final: 0.6985 (m-80) REVERT: B 545 LYS cc_start: 0.8598 (mtmp) cc_final: 0.8237 (tttm) REVERT: B 645 GLN cc_start: 0.8357 (mm-40) cc_final: 0.8024 (tp40) REVERT: C 509 ARG cc_start: 0.5861 (OUTLIER) cc_final: 0.5471 (ppt170) REVERT: C 542 PHE cc_start: 0.7309 (m-10) cc_final: 0.6973 (m-80) REVERT: C 545 LYS cc_start: 0.8634 (mtmp) cc_final: 0.8239 (tttm) REVERT: C 627 ASP cc_start: 0.8633 (m-30) cc_final: 0.8232 (m-30) REVERT: C 645 GLN cc_start: 0.8364 (mm-40) cc_final: 0.8032 (tp40) REVERT: D 509 ARG cc_start: 0.5852 (OUTLIER) cc_final: 0.5468 (ppt170) REVERT: D 542 PHE cc_start: 0.7304 (m-10) cc_final: 0.6970 (m-80) REVERT: D 545 LYS cc_start: 0.8619 (mtmp) cc_final: 0.8255 (tttm) REVERT: D 627 ASP cc_start: 0.8635 (m-30) cc_final: 0.8235 (m-30) REVERT: D 645 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8036 (tp40) outliers start: 30 outliers final: 19 residues processed: 257 average time/residue: 0.1658 time to fit residues: 66.7004 Evaluate side-chains 235 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 509 ARG 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 154 VAL Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain D residue 541 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 9 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 254 optimal weight: 8.9990 chunk 225 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 214 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.124174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.081188 restraints weight = 32660.853| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.35 r_work: 0.2699 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 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 = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 23148 Z= 0.182 Angle : 0.599 9.923 30976 Z= 0.298 Chirality : 0.042 0.232 3328 Planarity : 0.004 0.033 3712 Dihedral : 19.510 166.003 4120 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.58 % Allowed : 11.69 % Favored : 86.73 % 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: -0.07 (0.16), residues: 2552 helix: 1.12 (0.13), residues: 1560 sheet: 0.59 (0.53), residues: 76 loop : -2.22 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 712 TYR 0.016 0.002 TYR A 390 PHE 0.020 0.001 PHE A 506 TRP 0.007 0.001 TRP D 380 HIS 0.006 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.18 (23144) covalent geometry : angle 0.59954 / 0.30 (30968) SS BOND : bond 0.00172 / 0.09 ( 4) SS BOND : angle 0.38985 / 0.22 ( 8) hydrogen bonds : bond 0.05719 / 3.68 ( 923) hydrogen bonds : angle 3.61372 / 2.48 ( 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 266 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 0.847 Fit side-chains REVERT: A 159 MET cc_start: 0.8076 (tpp) cc_final: 0.7854 (tpt) REVERT: A 509 ARG cc_start: 0.5869 (OUTLIER) cc_final: 0.5463 (ppt170) REVERT: A 542 PHE cc_start: 0.7351 (m-10) cc_final: 0.7020 (m-80) REVERT: A 545 LYS cc_start: 0.8617 (mtmp) cc_final: 0.8222 (tttm) REVERT: A 580 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8742 (tt0) REVERT: A 627 ASP cc_start: 0.8733 (m-30) cc_final: 0.8328 (m-30) REVERT: A 645 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8043 (tp40) REVERT: B 509 ARG cc_start: 0.5773 (OUTLIER) cc_final: 0.5396 (ppt170) REVERT: B 542 PHE cc_start: 0.7326 (m-10) cc_final: 0.6990 (m-80) REVERT: B 545 LYS cc_start: 0.8579 (mtmp) cc_final: 0.8197 (tttm) REVERT: B 580 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8736 (tt0) REVERT: B 627 ASP cc_start: 0.8742 (m-30) cc_final: 0.8335 (m-30) REVERT: B 645 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8041 (tp40) REVERT: C 509 ARG cc_start: 0.5743 (OUTLIER) cc_final: 0.5460 (ppt170) REVERT: C 542 PHE cc_start: 0.7302 (m-10) cc_final: 0.6965 (m-80) REVERT: C 545 LYS cc_start: 0.8670 (mtmp) cc_final: 0.8275 (tttm) REVERT: C 580 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8737 (tt0) REVERT: C 627 ASP cc_start: 0.8709 (m-30) cc_final: 0.8275 (m-30) REVERT: C 645 GLN cc_start: 0.8388 (mm-40) cc_final: 0.8062 (tp40) REVERT: D 509 ARG cc_start: 0.5691 (OUTLIER) cc_final: 0.5409 (ppt170) REVERT: D 542 PHE cc_start: 0.7318 (m-10) cc_final: 0.6984 (m-80) REVERT: D 545 LYS cc_start: 0.8663 (mtmp) cc_final: 0.8269 (tttm) REVERT: D 627 ASP cc_start: 0.8701 (m-30) cc_final: 0.8266 (m-30) REVERT: D 645 GLN cc_start: 0.8394 (mm-40) cc_final: 0.8067 (tp40) outliers start: 36 outliers final: 21 residues processed: 261 average time/residue: 0.1664 time to fit residues: 67.9558 Evaluate side-chains 254 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 509 ARG Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 647 ASN Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 647 ASN 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: 2.9990 chunk 158 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 133 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 252 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 208 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 417 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.123235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.079967 restraints weight = 32377.540| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.38 r_work: 0.2689 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 23148 Z= 0.189 Angle : 0.598 9.082 30976 Z= 0.299 Chirality : 0.042 0.221 3328 Planarity : 0.004 0.031 3712 Dihedral : 19.421 165.350 4120 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.27 % Allowed : 11.38 % Favored : 87.35 % 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: -0.06 (0.16), residues: 2552 helix: 1.11 (0.13), residues: 1560 sheet: 0.64 (0.53), residues: 76 loop : -2.19 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 712 TYR 0.016 0.002 TYR A 390 PHE 0.020 0.001 PHE D 193 TRP 0.007 0.001 TRP D 380 HIS 0.005 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 (23144) covalent geometry : angle 0.59799 / 0.30 (30968) SS BOND : bond 0.00154 / 0.08 ( 4) SS BOND : angle 0.25787 / 0.16 ( 8) hydrogen bonds : bond 0.05849 / 3.76 ( 923) hydrogen bonds : angle 3.65336 / 2.51 ( 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 255 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 0.860 Fit side-chains REVERT: A 159 MET cc_start: 0.8074 (tpp) cc_final: 0.7828 (tpt) REVERT: A 509 ARG cc_start: 0.5754 (OUTLIER) cc_final: 0.5432 (ptm160) REVERT: A 542 PHE cc_start: 0.7337 (m-10) cc_final: 0.7008 (m-80) REVERT: A 545 LYS cc_start: 0.8615 (mtmp) cc_final: 0.8147 (tttm) REVERT: A 580 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8755 (tt0) REVERT: A 627 ASP cc_start: 0.8773 (m-30) cc_final: 0.8373 (m-30) REVERT: A 645 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8062 (tp40) REVERT: B 336 MET cc_start: 0.9206 (ttp) cc_final: 0.9000 (ttm) REVERT: B 509 ARG cc_start: 0.5829 (OUTLIER) cc_final: 0.5500 (ppt170) REVERT: B 542 PHE cc_start: 0.7343 (m-10) cc_final: 0.7010 (m-80) REVERT: B 580 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8754 (tt0) REVERT: B 627 ASP cc_start: 0.8778 (m-30) cc_final: 0.8378 (m-30) REVERT: B 645 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8013 (tp40) REVERT: C 336 MET cc_start: 0.9221 (ttp) cc_final: 0.9014 (ttm) REVERT: C 509 ARG cc_start: 0.5708 (OUTLIER) cc_final: 0.5399 (ppt170) REVERT: C 542 PHE cc_start: 0.7265 (m-10) cc_final: 0.6935 (m-80) REVERT: C 545 LYS cc_start: 0.8683 (mtmp) cc_final: 0.8254 (tttm) REVERT: C 580 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8759 (tt0) REVERT: C 627 ASP cc_start: 0.8761 (m-30) cc_final: 0.8324 (m-30) REVERT: C 645 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8028 (tp40) REVERT: D 336 MET cc_start: 0.9210 (ttp) cc_final: 0.9008 (ttm) REVERT: D 509 ARG cc_start: 0.5701 (OUTLIER) cc_final: 0.5406 (ppt170) REVERT: D 542 PHE cc_start: 0.7322 (m-10) cc_final: 0.6993 (m-80) REVERT: D 545 LYS cc_start: 0.8681 (mtmp) cc_final: 0.8257 (tttm) REVERT: D 627 ASP cc_start: 0.8802 (m-30) cc_final: 0.8367 (m-30) REVERT: D 645 GLN cc_start: 0.8403 (mm-40) cc_final: 0.8035 (tp40) outliers start: 29 outliers final: 19 residues processed: 251 average time/residue: 0.1685 time to fit residues: 66.2559 Evaluate side-chains 253 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 509 ARG Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 647 ASN Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 647 ASN 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: 1.9990 chunk 194 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 251 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.127073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.084204 restraints weight = 32541.608| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.36 r_work: 0.2747 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.3412 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 : 0.517 8.399 30976 Z= 0.258 Chirality : 0.039 0.179 3328 Planarity : 0.003 0.030 3712 Dihedral : 18.488 167.713 4120 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.01 % Allowed : 11.95 % Favored : 87.04 % 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: 0.36 (0.17), residues: 2552 helix: 1.49 (0.13), residues: 1552 sheet: 0.72 (0.54), residues: 76 loop : -2.07 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 712 TYR 0.026 0.001 TYR C 540 PHE 0.020 0.001 PHE D 193 TRP 0.007 0.001 TRP A 710 HIS 0.003 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (23144) covalent geometry : angle 0.51736 / 0.26 (30968) SS BOND : bond 0.00158 / 0.08 ( 4) SS BOND : angle 0.23957 / 0.13 ( 8) hydrogen bonds : bond 0.04329 / 2.77 ( 923) hydrogen bonds : angle 3.36076 / 2.30 ( 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 235 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 0.852 Fit side-chains REVERT: A 159 MET cc_start: 0.8037 (tpp) cc_final: 0.7718 (tpt) REVERT: A 509 ARG cc_start: 0.5769 (OUTLIER) cc_final: 0.5364 (ptm160) REVERT: A 524 PHE cc_start: 0.8138 (t80) cc_final: 0.7645 (m-80) REVERT: A 542 PHE cc_start: 0.7291 (m-10) cc_final: 0.6939 (m-80) REVERT: A 545 LYS cc_start: 0.8562 (mtmp) cc_final: 0.8193 (tttm) REVERT: A 580 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8737 (tt0) REVERT: A 627 ASP cc_start: 0.8645 (m-30) cc_final: 0.8270 (m-30) REVERT: A 645 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8024 (tp40) REVERT: B 336 MET cc_start: 0.9204 (ttp) cc_final: 0.8992 (ttm) REVERT: B 509 ARG cc_start: 0.5767 (OUTLIER) cc_final: 0.5470 (ppt170) REVERT: B 524 PHE cc_start: 0.7965 (t80) cc_final: 0.7526 (m-80) REVERT: B 542 PHE cc_start: 0.7261 (m-10) cc_final: 0.6905 (m-80) REVERT: B 545 LYS cc_start: 0.8591 (mtmp) cc_final: 0.8207 (tttm) REVERT: B 580 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8732 (tt0) REVERT: B 627 ASP cc_start: 0.8639 (m-30) cc_final: 0.8258 (m-30) REVERT: B 645 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8005 (tp40) REVERT: C 336 MET cc_start: 0.9219 (ttp) cc_final: 0.8999 (ttm) REVERT: C 509 ARG cc_start: 0.5741 (OUTLIER) cc_final: 0.5392 (ppt170) REVERT: C 542 PHE cc_start: 0.7243 (m-10) cc_final: 0.6890 (m-80) REVERT: C 545 LYS cc_start: 0.8611 (mtmp) cc_final: 0.8254 (tttm) REVERT: C 580 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8744 (tt0) REVERT: C 627 ASP cc_start: 0.8663 (m-30) cc_final: 0.8251 (m-30) REVERT: C 645 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8006 (tp40) REVERT: D 159 MET cc_start: 0.8067 (tpp) cc_final: 0.7818 (tpt) REVERT: D 336 MET cc_start: 0.9209 (ttp) cc_final: 0.8999 (ttm) REVERT: D 509 ARG cc_start: 0.5719 (OUTLIER) cc_final: 0.5304 (ptm160) REVERT: D 542 PHE cc_start: 0.7254 (m-10) cc_final: 0.6899 (m-80) REVERT: D 545 LYS cc_start: 0.8618 (mtmp) cc_final: 0.8259 (tttm) REVERT: D 627 ASP cc_start: 0.8660 (m-30) cc_final: 0.8245 (m-30) REVERT: D 645 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8011 (tp40) outliers start: 23 outliers final: 15 residues processed: 234 average time/residue: 0.1704 time to fit residues: 61.7739 Evaluate side-chains 232 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 580 GLN 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 154 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 82 optimal weight: 0.6980 chunk 34 optimal weight: 0.0570 chunk 174 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 123 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.130709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.087981 restraints weight = 32383.688| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.43 r_work: 0.2817 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- 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: 16 | |-----------------------------------------------------------------------------| |-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: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23148 Z= 0.086 Angle : 0.488 10.043 30976 Z= 0.240 Chirality : 0.037 0.159 3328 Planarity : 0.003 0.031 3712 Dihedral : 17.359 168.844 4120 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.01 % Allowed : 12.26 % Favored : 86.73 % 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: 0.69 (0.17), residues: 2552 helix: 1.78 (0.13), residues: 1576 sheet: 0.85 (0.56), residues: 76 loop : -2.11 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 714 TYR 0.036 0.001 TYR C 540 PHE 0.010 0.001 PHE A 193 TRP 0.007 0.001 TRP C 710 HIS 0.002 0.000 HIS C 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.09 (23144) covalent geometry : angle 0.48764 / 0.24 (30968) SS BOND : bond 0.00169 / 0.08 ( 4) SS BOND : angle 0.35190 / 0.20 ( 8) hydrogen bonds : bond 0.03266 / 2.09 ( 923) hydrogen bonds : angle 3.15617 / 2.16 ( 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 273 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 250 time to evaluate : 0.870 Fit side-chains REVERT: A 509 ARG cc_start: 0.5654 (OUTLIER) cc_final: 0.5323 (ptm160) REVERT: A 524 PHE cc_start: 0.7878 (t80) cc_final: 0.7606 (m-80) REVERT: A 542 PHE cc_start: 0.7268 (m-10) cc_final: 0.6916 (m-80) REVERT: A 545 LYS cc_start: 0.8431 (mtmp) cc_final: 0.8181 (tttm) REVERT: A 645 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7937 (tp40) REVERT: B 159 MET cc_start: 0.8062 (tpp) cc_final: 0.7804 (tpt) REVERT: B 336 MET cc_start: 0.9184 (ttp) cc_final: 0.8975 (ttm) REVERT: B 509 ARG cc_start: 0.5713 (OUTLIER) cc_final: 0.5346 (ptm160) REVERT: B 542 PHE cc_start: 0.7276 (m-10) cc_final: 0.6916 (m-80) REVERT: B 545 LYS cc_start: 0.8422 (mtmp) cc_final: 0.8175 (tttm) REVERT: B 611 LYS cc_start: 0.6980 (tptt) cc_final: 0.6662 (tptt) REVERT: B 645 GLN cc_start: 0.8285 (mm-40) cc_final: 0.7895 (tp40) REVERT: C 336 MET cc_start: 0.9188 (ttp) cc_final: 0.8966 (ttm) REVERT: C 509 ARG cc_start: 0.5635 (OUTLIER) cc_final: 0.5356 (ppt170) REVERT: C 542 PHE cc_start: 0.7161 (m-10) cc_final: 0.6793 (m-80) REVERT: C 545 LYS cc_start: 0.8486 (mtmp) cc_final: 0.8261 (tttm) REVERT: C 580 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8579 (tt0) REVERT: C 627 ASP cc_start: 0.8375 (m-30) cc_final: 0.7955 (m-30) REVERT: C 645 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7903 (tp40) REVERT: D 159 MET cc_start: 0.8061 (tpp) cc_final: 0.7793 (tpt) REVERT: D 336 MET cc_start: 0.9188 (ttp) cc_final: 0.8980 (ttm) REVERT: D 509 ARG cc_start: 0.5595 (OUTLIER) cc_final: 0.5245 (ptm160) REVERT: D 542 PHE cc_start: 0.7254 (m-10) cc_final: 0.6899 (m-80) REVERT: D 545 LYS cc_start: 0.8486 (mtmp) cc_final: 0.8258 (tttm) REVERT: D 611 LYS cc_start: 0.6965 (tptt) cc_final: 0.6652 (tptt) REVERT: D 627 ASP cc_start: 0.8372 (m-30) cc_final: 0.7949 (m-30) REVERT: D 645 GLN cc_start: 0.8295 (mm-40) cc_final: 0.7908 (tp40) outliers start: 23 outliers final: 16 residues processed: 273 average time/residue: 0.1728 time to fit residues: 73.4004 Evaluate side-chains 238 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 509 ARG Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 647 ASN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 603 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 66 optimal weight: 4.9990 chunk 209 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 162 optimal weight: 7.9990 chunk 250 optimal weight: 1.9990 chunk 234 optimal weight: 0.0980 chunk 217 optimal weight: 8.9990 chunk 212 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.128876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.086292 restraints weight = 32530.134| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.35 r_work: 0.2781 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.3666 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= 0.104 Angle : 0.512 9.382 30976 Z= 0.253 Chirality : 0.038 0.174 3328 Planarity : 0.003 0.029 3712 Dihedral : 17.259 168.515 4120 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.01 % Allowed : 12.30 % Favored : 86.69 % 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: 0.87 (0.17), residues: 2552 helix: 1.91 (0.13), residues: 1548 sheet: 0.76 (0.55), residues: 76 loop : -1.86 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 712 TYR 0.010 0.001 TYR A 321 PHE 0.021 0.001 PHE D 193 TRP 0.008 0.001 TRP A 331 HIS 0.003 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (23144) covalent geometry : angle 0.51192 / 0.25 (30968) SS BOND : bond 0.00120 / 0.06 ( 4) SS BOND : angle 0.41114 / 0.24 ( 8) hydrogen bonds : bond 0.03962 / 2.54 ( 923) hydrogen bonds : angle 3.25142 / 2.23 ( 2745) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5788.88 seconds wall clock time: 99 minutes 57.52 seconds (5997.52 seconds total)