Starting phenix.real_space_refine on Fri Aug 7 16:34:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13ll_77136/08_2026/13ll_77136.cif Found real_map, /net/cci-nas-00/data/ceres_data/13ll_77136/08_2026/13ll_77136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/13ll_77136/08_2026/13ll_77136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13ll_77136/08_2026/13ll_77136.map" model { file = "/net/cci-nas-00/data/ceres_data/13ll_77136/08_2026/13ll_77136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13ll_77136/08_2026/13ll_77136.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 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 128 5.16 5 Na 3 4.78 5 C 14788 2.51 5 N 3404 2.21 5 O 4053 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22412 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5103 Classifications: {'peptide': 627} Link IDs: {'PTRANS': 16, 'TRANS': 610} Chain breaks: 1 Chain: "B" Number of atoms: 5103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5103 Classifications: {'peptide': 627} Link IDs: {'PTRANS': 16, 'TRANS': 610} Chain breaks: 1 Chain: "C" Number of atoms: 5103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5103 Classifications: {'peptide': 627} Link IDs: {'PTRANS': 16, 'TRANS': 610} Chain breaks: 1 Chain: "D" Number of atoms: 5103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5103 Classifications: {'peptide': 627} Link IDs: {'PTRANS': 16, 'TRANS': 610} Chain breaks: 1 Chain: "A" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 470 Unusual residues: {' NA': 2, 'POV': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "B" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 521 Unusual residues: {' NA': 1, 'POV': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} 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: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 416 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Time building chain proxies: 4.86, per 1000 atoms: 0.22 Number of scatterers: 22412 At special positions: 0 Unit cell: (151.081, 151.081, 131.883, 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 128 16.00 P 36 15.00 Na 3 11.00 O 4053 8.00 N 3404 7.00 C 14788 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: 1.66 Conformation dependent library (CDL) restraints added in 903.0 milliseconds 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4792 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 4 sheets defined 64.2% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 118 through 130 removed outlier: 3.708A pdb=" N ARG A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 148 removed outlier: 3.535A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.743A pdb=" N MET A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.696A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 4.070A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.760A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.747A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.532A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.548A pdb=" N GLN A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.605A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 345 through 352 removed outlier: 3.676A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.589A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.602A pdb=" N MET A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 434 removed outlier: 3.534A pdb=" N LYS A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 460 removed outlier: 3.540A pdb=" N SER A 444 " --> pdb=" O MET A 440 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR A 454 " --> pdb=" O PHE A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 507 removed outlier: 3.533A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 519 removed outlier: 3.825A pdb=" N LEU A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 519' Processing helix chain 'A' and resid 520 through 541 removed outlier: 3.884A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 530 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.972A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 554 " --> pdb=" O CYS A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 568 removed outlier: 3.875A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 576 Processing helix chain 'A' and resid 579 through 584 Processing helix chain 'A' and resid 586 through 607 removed outlier: 3.675A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 removed outlier: 3.571A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 666 removed outlier: 3.623A pdb=" N VAL A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 685 removed outlier: 3.557A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 707 removed outlier: 3.793A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN A 695 " --> pdb=" O ILE A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 removed outlier: 3.869A pdb=" N SER A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 130 removed outlier: 3.734A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 148 removed outlier: 3.534A pdb=" N VAL B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 153 through 159 removed outlier: 3.742A pdb=" N MET B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.695A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 4.070A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.760A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.747A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 removed outlier: 3.531A pdb=" N ALA B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.548A pdb=" N GLN B 279 " --> pdb=" O PRO B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.605A pdb=" N ARG B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 345 through 352 removed outlier: 3.677A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.588A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.602A pdb=" N MET B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 434 removed outlier: 3.534A pdb=" N LYS B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 460 removed outlier: 3.540A pdb=" N SER B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR B 454 " --> pdb=" O PHE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 507 removed outlier: 3.532A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 500 " --> pdb=" O CYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 519 removed outlier: 3.825A pdb=" N LEU B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER B 518 " --> pdb=" O GLN B 514 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 513 through 519' Processing helix chain 'B' and resid 520 through 541 removed outlier: 3.884A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 530 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.973A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 554 " --> pdb=" O CYS B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 568 removed outlier: 3.875A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 576 Processing helix chain 'B' and resid 579 through 584 Processing helix chain 'B' and resid 586 through 607 removed outlier: 3.675A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 595 " --> pdb=" O LEU B 591 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 removed outlier: 3.570A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 666 removed outlier: 3.623A pdb=" N VAL B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 685 removed outlier: 3.557A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 707 removed outlier: 3.793A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN B 695 " --> pdb=" O ILE B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 removed outlier: 3.870A pdb=" N SER B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 130 removed outlier: 3.735A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 148 removed outlier: 3.535A pdb=" N VAL C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 153 through 159 removed outlier: 3.743A pdb=" N MET C 159 " --> pdb=" O PRO C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.695A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 4.070A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.760A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.747A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 removed outlier: 3.531A pdb=" N ALA C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.549A pdb=" N GLN C 279 " --> pdb=" O PRO C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.605A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 336 Processing helix chain 'C' and resid 345 through 352 removed outlier: 3.677A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.588A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.602A pdb=" N MET C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 434 removed outlier: 3.534A pdb=" N LYS C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 460 removed outlier: 3.539A pdb=" N SER C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 453 " --> pdb=" O PHE C 449 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR C 454 " --> pdb=" O PHE C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 507 removed outlier: 3.532A pdb=" N VAL C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 519 removed outlier: 3.825A pdb=" N LEU C 517 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER C 518 " --> pdb=" O GLN C 514 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP C 519 " --> pdb=" O SER C 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 513 through 519' Processing helix chain 'C' and resid 520 through 541 removed outlier: 3.884A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE C 526 " --> pdb=" O PHE C 522 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C 530 " --> pdb=" O PHE C 526 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 541 " --> pdb=" O VAL C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.972A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 554 " --> pdb=" O CYS C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 568 removed outlier: 3.875A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 576 Processing helix chain 'C' and resid 579 through 584 Processing helix chain 'C' and resid 586 through 607 removed outlier: 3.675A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C 595 " --> pdb=" O LEU C 591 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 removed outlier: 3.570A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 666 removed outlier: 3.623A pdb=" N VAL C 662 " --> pdb=" O LEU C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 685 removed outlier: 3.557A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 707 removed outlier: 3.793A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN C 695 " --> pdb=" O ILE C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 removed outlier: 3.870A pdb=" N SER C 713 " --> pdb=" O GLU C 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.735A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 148 removed outlier: 3.534A pdb=" N VAL D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 153 through 159 removed outlier: 3.743A pdb=" N MET D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.695A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 4.070A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 removed outlier: 3.760A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.747A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 removed outlier: 3.531A pdb=" N ALA D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.549A pdb=" N GLN D 279 " --> pdb=" O PRO D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.605A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 345 through 352 removed outlier: 3.678A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.588A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.602A pdb=" N MET D 419 " --> pdb=" O ASN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 434 removed outlier: 3.535A pdb=" N LYS D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 460 removed outlier: 3.539A pdb=" N SER D 444 " --> pdb=" O MET D 440 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 453 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR D 454 " --> pdb=" O PHE D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 507 removed outlier: 3.533A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA D 494 " --> pdb=" O VAL D 490 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS D 500 " --> pdb=" O CYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 519 removed outlier: 3.825A pdb=" N LEU D 517 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER D 518 " --> pdb=" O GLN D 514 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP D 519 " --> pdb=" O SER D 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 513 through 519' Processing helix chain 'D' and resid 520 through 541 removed outlier: 3.884A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE D 526 " --> pdb=" O PHE D 522 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA D 530 " --> pdb=" O PHE D 526 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU D 541 " --> pdb=" O VAL D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.972A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 554 " --> pdb=" O CYS D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 568 removed outlier: 3.875A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 576 Processing helix chain 'D' and resid 579 through 584 Processing helix chain 'D' and resid 586 through 607 removed outlier: 3.675A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE D 595 " --> pdb=" O LEU D 591 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE D 597 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 removed outlier: 3.570A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 666 removed outlier: 3.623A pdb=" N VAL D 662 " --> pdb=" O LEU D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 685 removed outlier: 3.558A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 707 removed outlier: 3.792A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN D 695 " --> pdb=" O ILE D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 removed outlier: 3.869A pdb=" N SER D 713 " --> pdb=" O GLU D 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 6.855A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASP A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 382 removed outlier: 6.855A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASP B 727 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 382 removed outlier: 6.856A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASP C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 382 removed outlier: 6.856A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 896 hydrogen bonds defined for protein. 2640 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: 3.68 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3651 1.32 - 1.44: 5570 1.44 - 1.57: 13191 1.57 - 1.69: 72 1.69 - 1.81: 212 Bond restraints: 22696 Sorted by residual: bond pdb=" O12 POV B1107 " pdb=" P POV B1107 " ideal model delta sigma weight residual 1.657 1.590 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" O12 POV D1106 " pdb=" P POV D1106 " ideal model delta sigma weight residual 1.657 1.590 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" O12 POV A1104 " pdb=" P POV A1104 " ideal model delta sigma weight residual 1.657 1.591 0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" O12 POV C1105 " pdb=" P POV C1105 " ideal model delta sigma weight residual 1.657 1.591 0.066 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O12 POV B1101 " pdb=" P POV B1101 " ideal model delta sigma weight residual 1.657 1.594 0.063 2.00e-02 2.50e+03 1.01e+01 ... (remaining 22691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 28704 2.11 - 4.22: 1441 4.22 - 6.33: 153 6.33 - 8.44: 30 8.44 - 10.55: 16 Bond angle restraints: 30344 Sorted by residual: angle pdb=" CG ARG D 696 " pdb=" CD ARG D 696 " pdb=" NE ARG D 696 " ideal model delta sigma weight residual 112.00 119.69 -7.69 2.20e+00 2.07e-01 1.22e+01 angle pdb=" CG ARG B 696 " pdb=" CD ARG B 696 " pdb=" NE ARG B 696 " ideal model delta sigma weight residual 112.00 119.67 -7.67 2.20e+00 2.07e-01 1.21e+01 angle pdb=" CG ARG C 696 " pdb=" CD ARG C 696 " pdb=" NE ARG C 696 " ideal model delta sigma weight residual 112.00 119.64 -7.64 2.20e+00 2.07e-01 1.21e+01 angle pdb=" CG ARG A 696 " pdb=" CD ARG A 696 " pdb=" NE ARG A 696 " ideal model delta sigma weight residual 112.00 119.64 -7.64 2.20e+00 2.07e-01 1.21e+01 angle pdb=" N GLU A 423 " pdb=" CA GLU A 423 " pdb=" C GLU A 423 " ideal model delta sigma weight residual 109.81 117.14 -7.33 2.21e+00 2.05e-01 1.10e+01 ... (remaining 30339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 13534 35.35 - 70.70: 347 70.70 - 106.06: 62 106.06 - 141.41: 34 141.41 - 176.76: 27 Dihedral angle restraints: 14004 sinusoidal: 6620 harmonic: 7384 Sorted by residual: 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 93.00 177.58 -84.58 1 1.00e+01 1.00e-02 8.69e+01 dihedral pdb=" CB CYS D 612 " pdb=" SG CYS D 612 " pdb=" SG CYS D 619 " pdb=" CB CYS D 619 " ideal model delta sinusoidal sigma weight residual 93.00 177.56 -84.56 1 1.00e+01 1.00e-02 8.69e+01 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 93.00 177.54 -84.54 1 1.00e+01 1.00e-02 8.69e+01 ... (remaining 14001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2696 0.072 - 0.144: 457 0.144 - 0.215: 85 0.215 - 0.287: 2 0.287 - 0.359: 4 Chirality restraints: 3244 Sorted by residual: chirality pdb=" CG LEU D 429 " pdb=" CB LEU D 429 " pdb=" CD1 LEU D 429 " pdb=" CD2 LEU D 429 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CG LEU B 429 " pdb=" CB LEU B 429 " pdb=" CD1 LEU B 429 " pdb=" CD2 LEU B 429 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CG LEU A 429 " pdb=" CB LEU A 429 " pdb=" CD1 LEU A 429 " pdb=" CD2 LEU A 429 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 3241 not shown) Planarity restraints: 3632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 526 " 0.013 2.00e-02 2.50e+03 1.51e-02 3.97e+00 pdb=" CG PHE A 526 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 526 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 526 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 526 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 526 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 526 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 526 " 0.013 2.00e-02 2.50e+03 1.50e-02 3.93e+00 pdb=" CG PHE C 526 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 526 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE C 526 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 526 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE C 526 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 526 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 526 " 0.013 2.00e-02 2.50e+03 1.50e-02 3.92e+00 pdb=" CG PHE D 526 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE D 526 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE D 526 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE D 526 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE D 526 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE D 526 " 0.007 2.00e-02 2.50e+03 ... (remaining 3629 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 268 2.60 - 3.18: 17975 3.18 - 3.75: 31587 3.75 - 4.33: 48492 4.33 - 4.90: 81572 Nonbonded interactions: 179894 Sorted by model distance: nonbonded pdb=" OH TYR C 260 " pdb=" OD2 ASP C 293 " model vdw 2.030 3.040 nonbonded pdb=" OH TYR B 260 " pdb=" OD2 ASP B 293 " model vdw 2.030 3.040 nonbonded pdb=" OH TYR A 260 " pdb=" OD2 ASP A 293 " model vdw 2.031 3.040 nonbonded pdb=" OH TYR D 260 " pdb=" OD2 ASP D 293 " model vdw 2.031 3.040 nonbonded pdb=" O PRO C 753 " pdb=" OH TYR D 213 " model vdw 2.043 3.040 ... (remaining 179889 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 1108) selection = (chain 'B' and resid 118 through 1108) selection = (chain 'C' and resid 118 through 1108) 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: 1.670 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: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.990 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:9.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 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 : 0.013 0.104 22700 Z= 0.532 Angle : 1.042 10.548 30352 Z= 0.505 Chirality : 0.058 0.359 3244 Planarity : 0.005 0.048 3632 Dihedral : 19.178 176.760 9200 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.48 (0.12), residues: 2492 helix: -4.17 (0.07), residues: 1500 sheet: -0.82 (0.50), residues: 112 loop : -2.60 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG D 363 TYR 0.022 0.003 TYR A 451 PHE 0.033 0.003 PHE A 526 TRP 0.008 0.002 TRP D 742 HIS 0.005 0.002 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.01305 / 0.53 (22696) covalent geometry : angle 1.04150 / 0.50 (30344) SS BOND : bond 0.00073 / 0.04 ( 4) SS BOND : angle 1.32844 / 0.90 ( 8) hydrogen bonds : bond 0.33209 / 21.85 ( 896) hydrogen bonds : angle 10.50622 / 7.28 ( 2640) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 475 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 LEU cc_start: 0.8372 (tp) cc_final: 0.8160 (mp) REVERT: A 293 ASP cc_start: 0.7018 (p0) cc_final: 0.6727 (p0) REVERT: A 401 ASN cc_start: 0.7324 (p0) cc_final: 0.6603 (t0) REVERT: A 431 MET cc_start: 0.7567 (mtp) cc_final: 0.7338 (mtm) REVERT: A 545 LYS cc_start: 0.7609 (pttm) cc_final: 0.7372 (mtpt) REVERT: A 574 MET cc_start: 0.8818 (mtp) cc_final: 0.8559 (mtm) REVERT: A 683 ASN cc_start: 0.8039 (m110) cc_final: 0.7687 (m110) REVERT: A 687 GLU cc_start: 0.7578 (pp20) cc_final: 0.7377 (tp30) REVERT: A 698 ARG cc_start: 0.7286 (mtp85) cc_final: 0.6623 (mtt90) REVERT: A 714 ARG cc_start: 0.7983 (ttm-80) cc_final: 0.7648 (ttt-90) REVERT: B 401 ASN cc_start: 0.7329 (p0) cc_final: 0.6553 (m-40) REVERT: B 431 MET cc_start: 0.7566 (mtp) cc_final: 0.7318 (mtm) REVERT: B 479 MET cc_start: 0.2109 (ttt) cc_final: 0.0741 (tpt) REVERT: B 545 LYS cc_start: 0.7565 (pttm) cc_final: 0.7302 (mtpt) REVERT: B 574 MET cc_start: 0.8783 (mtp) cc_final: 0.8575 (mtm) REVERT: B 683 ASN cc_start: 0.7904 (m110) cc_final: 0.7638 (m110) REVERT: B 687 GLU cc_start: 0.7562 (pp20) cc_final: 0.7352 (tp30) REVERT: B 698 ARG cc_start: 0.7178 (mtp85) cc_final: 0.6454 (mtt90) REVERT: B 714 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.7573 (ttt-90) REVERT: C 173 MET cc_start: 0.8197 (mtp) cc_final: 0.7944 (mtp) REVERT: C 233 LEU cc_start: 0.8381 (tp) cc_final: 0.8166 (mp) REVERT: C 401 ASN cc_start: 0.7347 (p0) cc_final: 0.6566 (t0) REVERT: C 431 MET cc_start: 0.7564 (mtp) cc_final: 0.7338 (mtm) REVERT: C 479 MET cc_start: 0.2126 (ttt) cc_final: 0.0777 (tpt) REVERT: C 545 LYS cc_start: 0.7632 (pttm) cc_final: 0.7360 (mtpt) REVERT: C 574 MET cc_start: 0.8753 (mtp) cc_final: 0.8491 (mtm) REVERT: C 683 ASN cc_start: 0.8061 (m110) cc_final: 0.7726 (m110) REVERT: C 698 ARG cc_start: 0.7296 (mtp85) cc_final: 0.6645 (mtt90) REVERT: C 714 ARG cc_start: 0.7956 (ttm-80) cc_final: 0.7623 (ttt-90) REVERT: D 233 LEU cc_start: 0.8348 (tp) cc_final: 0.8099 (mp) REVERT: D 401 ASN cc_start: 0.7341 (p0) cc_final: 0.6562 (m-40) REVERT: D 479 MET cc_start: 0.2144 (ttt) cc_final: 0.0790 (tpt) REVERT: D 538 PHE cc_start: 0.6878 (t80) cc_final: 0.6678 (t80) REVERT: D 545 LYS cc_start: 0.7589 (pttm) cc_final: 0.7294 (mtpt) REVERT: D 574 MET cc_start: 0.8770 (mtp) cc_final: 0.8523 (mtm) REVERT: D 683 ASN cc_start: 0.8012 (m110) cc_final: 0.7742 (m110) REVERT: D 698 ARG cc_start: 0.7254 (mtp85) cc_final: 0.6630 (mtt90) REVERT: D 714 ARG cc_start: 0.8030 (ttm-80) cc_final: 0.7705 (ttt-90) outliers start: 0 outliers final: 4 residues processed: 475 average time/residue: 0.6082 time to fit residues: 326.2311 Evaluate side-chains 327 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 323 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 330 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN A 314 ASN A 338 ASN A 410 ASN A 415 ASN A 426 HIS A 585 HIS A 616 ASN B 314 ASN B 338 ASN B 410 ASN B 415 ASN B 426 HIS B 585 HIS B 616 ASN C 216 GLN C 227 GLN C 314 ASN C 338 ASN C 410 ASN C 415 ASN C 426 HIS C 585 HIS C 616 ASN D 178 ASN D 216 GLN D 279 GLN D 314 ASN D 338 ASN D 410 ASN D 415 ASN D 426 HIS D 585 HIS D 616 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.169911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.120729 restraints weight = 22912.663| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.13 r_work: 0.3030 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22700 Z= 0.166 Angle : 0.658 7.564 30352 Z= 0.329 Chirality : 0.040 0.187 3244 Planarity : 0.005 0.046 3632 Dihedral : 23.411 179.196 4280 Min Nonbonded Distance : 1.639 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.15 % Allowed : 7.91 % Favored : 88.94 % 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: -3.38 (0.15), residues: 2492 helix: -2.13 (0.11), residues: 1548 sheet: -0.49 (0.52), residues: 112 loop : -2.38 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 690 TYR 0.018 0.002 TYR A 540 PHE 0.018 0.002 PHE D 526 TRP 0.016 0.002 TRP A 481 HIS 0.008 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (22696) covalent geometry : angle 0.65775 / 0.33 (30344) SS BOND : bond 0.00013 / 0.01 ( 4) SS BOND : angle 0.84371 / 0.55 ( 8) hydrogen bonds : bond 0.05341 / 3.54 ( 896) hydrogen bonds : angle 4.50015 / 3.10 ( 2640) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 352 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7426 (mp0) cc_final: 0.7077 (mp0) REVERT: A 233 LEU cc_start: 0.8133 (tp) cc_final: 0.7886 (mp) REVERT: A 323 MET cc_start: 0.8704 (ttp) cc_final: 0.8501 (ttm) REVERT: A 401 ASN cc_start: 0.7553 (p0) cc_final: 0.6683 (t0) REVERT: A 431 MET cc_start: 0.8504 (mtp) cc_final: 0.8254 (mtm) REVERT: A 479 MET cc_start: 0.2509 (OUTLIER) cc_final: -0.0010 (tpt) REVERT: A 538 PHE cc_start: 0.7468 (t80) cc_final: 0.6302 (m-10) REVERT: A 545 LYS cc_start: 0.7741 (pttm) cc_final: 0.7306 (mtpt) REVERT: A 574 MET cc_start: 0.9062 (mtp) cc_final: 0.8800 (mtm) REVERT: A 687 GLU cc_start: 0.7776 (pp20) cc_final: 0.7161 (tp30) REVERT: A 698 ARG cc_start: 0.7790 (mtp85) cc_final: 0.6803 (mtt90) REVERT: A 714 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7476 (ttt-90) REVERT: A 716 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.7037 (tpm170) REVERT: A 750 ASN cc_start: 0.8009 (m-40) cc_final: 0.7789 (m110) REVERT: B 320 MET cc_start: 0.8571 (mmt) cc_final: 0.8362 (mmt) REVERT: B 323 MET cc_start: 0.8811 (ttp) cc_final: 0.8589 (ttm) REVERT: B 401 ASN cc_start: 0.7548 (p0) cc_final: 0.6670 (t0) REVERT: B 429 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8447 (mt) REVERT: B 431 MET cc_start: 0.8513 (mtp) cc_final: 0.8257 (mtm) REVERT: B 479 MET cc_start: 0.1735 (ttt) cc_final: 0.0051 (tpt) REVERT: B 538 PHE cc_start: 0.7439 (t80) cc_final: 0.6221 (m-10) REVERT: B 545 LYS cc_start: 0.7711 (pttm) cc_final: 0.7238 (mtpt) REVERT: B 574 MET cc_start: 0.9098 (mtp) cc_final: 0.8815 (mtm) REVERT: B 655 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7767 (tp) REVERT: B 698 ARG cc_start: 0.7801 (mtp85) cc_final: 0.6832 (mtt90) REVERT: B 714 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7566 (ttt-90) REVERT: B 716 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6224 (ttm170) REVERT: B 743 LYS cc_start: 0.8342 (mtmm) cc_final: 0.7982 (pttm) REVERT: B 750 ASN cc_start: 0.7990 (m-40) cc_final: 0.7743 (m110) REVERT: C 185 GLU cc_start: 0.7418 (mp0) cc_final: 0.7061 (mp0) REVERT: C 233 LEU cc_start: 0.8116 (tp) cc_final: 0.7889 (mp) REVERT: C 323 MET cc_start: 0.8697 (ttp) cc_final: 0.8472 (ttm) REVERT: C 401 ASN cc_start: 0.7549 (p0) cc_final: 0.6616 (t0) REVERT: C 431 MET cc_start: 0.8508 (mtp) cc_final: 0.8257 (mtm) REVERT: C 479 MET cc_start: 0.1761 (ttt) cc_final: 0.0195 (tpt) REVERT: C 538 PHE cc_start: 0.7417 (t80) cc_final: 0.6231 (m-10) REVERT: C 545 LYS cc_start: 0.7735 (pttm) cc_final: 0.7269 (mtpt) REVERT: C 574 MET cc_start: 0.9101 (mtp) cc_final: 0.8816 (mtm) REVERT: C 655 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7798 (tp) REVERT: C 698 ARG cc_start: 0.7791 (mtp85) cc_final: 0.6802 (mtt90) REVERT: C 714 ARG cc_start: 0.8192 (ttm-80) cc_final: 0.7565 (ttt-90) REVERT: C 716 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.7034 (tpm170) REVERT: C 750 ASN cc_start: 0.7976 (m-40) cc_final: 0.7751 (m110) REVERT: D 233 LEU cc_start: 0.8158 (tp) cc_final: 0.7872 (mp) REVERT: D 320 MET cc_start: 0.8525 (mmt) cc_final: 0.8284 (mmt) REVERT: D 323 MET cc_start: 0.8720 (ttp) cc_final: 0.8502 (ttm) REVERT: D 401 ASN cc_start: 0.7581 (p0) cc_final: 0.6676 (t0) REVERT: D 479 MET cc_start: 0.1852 (ttt) cc_final: 0.0286 (tpt) REVERT: D 574 MET cc_start: 0.9099 (mtp) cc_final: 0.8818 (mtm) REVERT: D 655 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7767 (tp) REVERT: D 687 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6794 (pt0) REVERT: D 698 ARG cc_start: 0.7819 (mtp85) cc_final: 0.6840 (mtt90) REVERT: D 714 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.7569 (ttt-90) REVERT: D 716 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.7058 (tpm170) REVERT: D 743 LYS cc_start: 0.8483 (mtmm) cc_final: 0.8157 (pttm) REVERT: D 750 ASN cc_start: 0.8020 (m-40) cc_final: 0.7779 (m110) outliers start: 70 outliers final: 20 residues processed: 394 average time/residue: 0.5730 time to fit residues: 257.5888 Evaluate side-chains 357 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 327 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 687 GLU Chi-restraints excluded: chain D residue 716 ARG Chi-restraints excluded: chain D residue 747 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 65 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 245 optimal weight: 0.4980 chunk 239 optimal weight: 0.8980 chunk 184 optimal weight: 7.9990 chunk 189 optimal weight: 0.0010 chunk 67 optimal weight: 0.8980 chunk 218 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 HIS A 279 GLN A 585 HIS B 150 HIS B 279 GLN B 585 HIS C 150 HIS C 279 GLN C 297 ASN C 585 HIS D 150 HIS D 279 GLN D 585 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.172675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.124726 restraints weight = 23059.193| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.11 r_work: 0.3068 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22700 Z= 0.103 Angle : 0.512 6.265 30352 Z= 0.262 Chirality : 0.036 0.128 3244 Planarity : 0.004 0.041 3632 Dihedral : 21.624 173.371 4280 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.07 % Allowed : 10.66 % Favored : 87.28 % 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: -1.76 (0.16), residues: 2492 helix: -0.66 (0.13), residues: 1564 sheet: -0.21 (0.50), residues: 112 loop : -2.13 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 122 TYR 0.011 0.001 TYR B 208 PHE 0.011 0.001 PHE B 193 TRP 0.009 0.001 TRP A 481 HIS 0.006 0.001 HIS B 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (22696) covalent geometry : angle 0.51227 / 0.26 (30344) SS BOND : bond 0.00083 / 0.04 ( 4) SS BOND : angle 0.32059 / 0.22 ( 8) hydrogen bonds : bond 0.03450 / 2.28 ( 896) hydrogen bonds : angle 3.64887 / 2.51 ( 2640) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 342 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7473 (mp0) cc_final: 0.7218 (mp0) REVERT: A 233 LEU cc_start: 0.8145 (tp) cc_final: 0.7923 (mp) REVERT: A 401 ASN cc_start: 0.7465 (p0) cc_final: 0.6645 (t0) REVERT: A 431 MET cc_start: 0.8467 (mtp) cc_final: 0.8217 (mtm) REVERT: A 479 MET cc_start: 0.2715 (OUTLIER) cc_final: 0.0047 (tpt) REVERT: A 538 PHE cc_start: 0.7494 (t80) cc_final: 0.6289 (m-10) REVERT: A 585 HIS cc_start: 0.7302 (t-90) cc_final: 0.7071 (m90) REVERT: A 687 GLU cc_start: 0.7842 (pp20) cc_final: 0.7218 (tp30) REVERT: A 691 ILE cc_start: 0.7816 (mt) cc_final: 0.7575 (mt) REVERT: A 698 ARG cc_start: 0.7779 (mtp85) cc_final: 0.6813 (mtt90) REVERT: A 714 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.7510 (ttt-90) REVERT: A 716 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.7046 (tpm170) REVERT: B 320 MET cc_start: 0.8596 (mmt) cc_final: 0.8346 (mmt) REVERT: B 324 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8328 (mp) REVERT: B 351 MET cc_start: 0.8922 (mtp) cc_final: 0.8692 (mtp) REVERT: B 401 ASN cc_start: 0.7426 (p0) cc_final: 0.6624 (t0) REVERT: B 431 MET cc_start: 0.8497 (mtp) cc_final: 0.8248 (mtm) REVERT: B 479 MET cc_start: 0.1905 (ttt) cc_final: 0.0130 (tpt) REVERT: B 538 PHE cc_start: 0.7361 (t80) cc_final: 0.6158 (m-10) REVERT: B 574 MET cc_start: 0.9060 (mtp) cc_final: 0.8778 (mtm) REVERT: B 683 ASN cc_start: 0.7262 (OUTLIER) cc_final: 0.6968 (m110) REVERT: B 687 GLU cc_start: 0.7805 (pt0) cc_final: 0.6878 (tp30) REVERT: B 691 ILE cc_start: 0.8029 (mt) cc_final: 0.7705 (mt) REVERT: B 698 ARG cc_start: 0.7776 (mtp85) cc_final: 0.6802 (mtt90) REVERT: B 714 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7528 (ttt-90) REVERT: B 743 LYS cc_start: 0.8267 (mtmm) cc_final: 0.7998 (ptpp) REVERT: B 750 ASN cc_start: 0.7968 (m-40) cc_final: 0.7765 (m110) REVERT: C 185 GLU cc_start: 0.7492 (mp0) cc_final: 0.7235 (mp0) REVERT: C 233 LEU cc_start: 0.8131 (tp) cc_final: 0.7923 (mp) REVERT: C 401 ASN cc_start: 0.7448 (p0) cc_final: 0.6597 (t0) REVERT: C 431 MET cc_start: 0.8489 (mtp) cc_final: 0.8245 (mtm) REVERT: C 479 MET cc_start: 0.1879 (ttt) cc_final: 0.0150 (tpt) REVERT: C 538 PHE cc_start: 0.7502 (t80) cc_final: 0.6312 (m-10) REVERT: C 574 MET cc_start: 0.9055 (mtp) cc_final: 0.8795 (mtm) REVERT: C 585 HIS cc_start: 0.7318 (t-90) cc_final: 0.7076 (m90) REVERT: C 652 ILE cc_start: 0.7856 (mm) cc_final: 0.7628 (mm) REVERT: C 687 GLU cc_start: 0.7342 (tp30) cc_final: 0.6521 (pt0) REVERT: C 691 ILE cc_start: 0.8063 (mt) cc_final: 0.7725 (mt) REVERT: C 698 ARG cc_start: 0.7776 (mtp85) cc_final: 0.6809 (mtt90) REVERT: C 714 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7529 (ttt-90) REVERT: C 750 ASN cc_start: 0.7887 (m-40) cc_final: 0.7679 (m110) REVERT: D 185 GLU cc_start: 0.7449 (mp0) cc_final: 0.7097 (mp0) REVERT: D 233 LEU cc_start: 0.8195 (tp) cc_final: 0.7933 (mp) REVERT: D 351 MET cc_start: 0.8918 (mtp) cc_final: 0.8686 (mtp) REVERT: D 401 ASN cc_start: 0.7455 (p0) cc_final: 0.6591 (t0) REVERT: D 479 MET cc_start: 0.1900 (ttt) cc_final: 0.0216 (tpt) REVERT: D 574 MET cc_start: 0.9070 (mtp) cc_final: 0.8795 (mtm) REVERT: D 683 ASN cc_start: 0.7334 (OUTLIER) cc_final: 0.7053 (m110) REVERT: D 687 GLU cc_start: 0.7383 (tp30) cc_final: 0.6806 (pt0) REVERT: D 698 ARG cc_start: 0.7754 (mtp85) cc_final: 0.6768 (mtt90) REVERT: D 714 ARG cc_start: 0.8255 (ttm-80) cc_final: 0.7587 (ttt-90) REVERT: D 716 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.7043 (tpm170) REVERT: D 743 LYS cc_start: 0.8318 (mtmm) cc_final: 0.8028 (ptpp) REVERT: D 750 ASN cc_start: 0.7934 (m-40) cc_final: 0.7715 (m110) outliers start: 46 outliers final: 2 residues processed: 365 average time/residue: 0.5985 time to fit residues: 248.7662 Evaluate side-chains 321 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 313 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 683 ASN Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain D residue 683 ASN Chi-restraints excluded: chain D residue 716 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 72 optimal weight: 0.9990 chunk 231 optimal weight: 0.0020 chunk 158 optimal weight: 0.0570 chunk 195 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.4112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN B 279 GLN B 297 ASN B 585 HIS C 279 GLN D 279 GLN D 297 ASN D 585 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.165585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.116683 restraints weight = 23202.826| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.10 r_work: 0.3016 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22700 Z= 0.118 Angle : 0.524 6.191 30352 Z= 0.265 Chirality : 0.038 0.127 3244 Planarity : 0.004 0.039 3632 Dihedral : 20.706 170.275 4272 Min Nonbonded Distance : 1.581 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.52 % Allowed : 11.11 % Favored : 86.38 % 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: -1.12 (0.17), residues: 2492 helix: -0.08 (0.13), residues: 1592 sheet: -0.10 (0.49), residues: 112 loop : -2.09 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 122 TYR 0.010 0.001 TYR A 451 PHE 0.015 0.001 PHE A 526 TRP 0.007 0.001 TRP A 481 HIS 0.005 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (22696) covalent geometry : angle 0.52375 / 0.27 (30344) SS BOND : bond 0.00065 / 0.03 ( 4) SS BOND : angle 0.17384 / 0.12 ( 8) hydrogen bonds : bond 0.03461 / 2.28 ( 896) hydrogen bonds : angle 3.54429 / 2.45 ( 2640) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 335 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7534 (mp0) cc_final: 0.7246 (mp0) REVERT: A 233 LEU cc_start: 0.8222 (tp) cc_final: 0.7922 (mp) REVERT: A 401 ASN cc_start: 0.7601 (p0) cc_final: 0.6701 (t0) REVERT: A 431 MET cc_start: 0.8514 (mtp) cc_final: 0.8228 (mtm) REVERT: A 479 MET cc_start: 0.2622 (OUTLIER) cc_final: -0.0034 (tpt) REVERT: A 538 PHE cc_start: 0.7455 (t80) cc_final: 0.6233 (OUTLIER) REVERT: A 687 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7377 (tp30) REVERT: A 698 ARG cc_start: 0.7787 (mtp85) cc_final: 0.6809 (mtt90) REVERT: A 714 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7512 (ttt-90) REVERT: B 320 MET cc_start: 0.8642 (mmt) cc_final: 0.8411 (mmt) REVERT: B 351 MET cc_start: 0.8926 (mtp) cc_final: 0.8695 (mtp) REVERT: B 401 ASN cc_start: 0.7603 (p0) cc_final: 0.6683 (t0) REVERT: B 431 MET cc_start: 0.8497 (mtp) cc_final: 0.8209 (mtm) REVERT: B 538 PHE cc_start: 0.7400 (t80) cc_final: 0.6136 (m-10) REVERT: B 574 MET cc_start: 0.9115 (mtp) cc_final: 0.8833 (mtm) REVERT: B 581 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7256 (mppt) REVERT: B 698 ARG cc_start: 0.7804 (mtp85) cc_final: 0.6823 (mtt90) REVERT: B 714 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7505 (ttt-90) REVERT: B 716 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.7110 (tpm170) REVERT: C 129 GLU cc_start: 0.6513 (mp0) cc_final: 0.6300 (mp0) REVERT: C 185 GLU cc_start: 0.7570 (mp0) cc_final: 0.7262 (mp0) REVERT: C 233 LEU cc_start: 0.8204 (tp) cc_final: 0.7914 (mp) REVERT: C 351 MET cc_start: 0.8951 (mtp) cc_final: 0.8720 (mtp) REVERT: C 401 ASN cc_start: 0.7594 (p0) cc_final: 0.6650 (t0) REVERT: C 431 MET cc_start: 0.8529 (mtp) cc_final: 0.8263 (mtm) REVERT: C 538 PHE cc_start: 0.7537 (t80) cc_final: 0.6307 (m-10) REVERT: C 574 MET cc_start: 0.9101 (mtp) cc_final: 0.8822 (mtm) REVERT: C 698 ARG cc_start: 0.7807 (mtp85) cc_final: 0.6830 (mtt90) REVERT: C 714 ARG cc_start: 0.8193 (ttm-80) cc_final: 0.7531 (ttt-90) REVERT: C 716 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.7109 (tpm170) REVERT: D 185 GLU cc_start: 0.7465 (mp0) cc_final: 0.7141 (mp0) REVERT: D 233 LEU cc_start: 0.8227 (tp) cc_final: 0.7924 (mp) REVERT: D 351 MET cc_start: 0.8932 (mtp) cc_final: 0.8702 (mtp) REVERT: D 401 ASN cc_start: 0.7615 (p0) cc_final: 0.6677 (t0) REVERT: D 574 MET cc_start: 0.9114 (mtp) cc_final: 0.8835 (mtm) REVERT: D 581 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7196 (mppt) REVERT: D 584 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7594 (mp) REVERT: D 585 HIS cc_start: 0.7329 (t-90) cc_final: 0.7030 (m-70) REVERT: D 687 GLU cc_start: 0.7417 (tp30) cc_final: 0.6783 (pt0) REVERT: D 698 ARG cc_start: 0.7784 (mtp85) cc_final: 0.6803 (mtt90) REVERT: D 714 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7513 (ttt-90) REVERT: D 743 LYS cc_start: 0.8302 (mtmm) cc_final: 0.8034 (pttm) outliers start: 56 outliers final: 11 residues processed: 358 average time/residue: 0.5711 time to fit residues: 233.1400 Evaluate side-chains 334 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 317 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 581 LYS Chi-restraints excluded: chain D residue 584 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 124 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 228 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 218 optimal weight: 0.8980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN B 279 GLN B 286 GLN B 585 HIS C 279 GLN D 279 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.162896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.116231 restraints weight = 23085.761| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.91 r_work: 0.3128 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22700 Z= 0.111 Angle : 0.504 6.280 30352 Z= 0.257 Chirality : 0.037 0.128 3244 Planarity : 0.003 0.039 3632 Dihedral : 20.257 170.896 4272 Min Nonbonded Distance : 1.576 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.16 % Allowed : 12.72 % Favored : 85.12 % 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: -0.74 (0.17), residues: 2492 helix: 0.30 (0.13), residues: 1596 sheet: 0.03 (0.49), residues: 112 loop : -2.13 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 147 TYR 0.011 0.001 TYR D 540 PHE 0.015 0.001 PHE B 193 TRP 0.010 0.001 TRP C 481 HIS 0.005 0.001 HIS B 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (22696) covalent geometry : angle 0.50370 / 0.26 (30344) SS BOND : bond 0.00019 / 0.01 ( 4) SS BOND : angle 0.15768 / 0.11 ( 8) hydrogen bonds : bond 0.03167 / 2.08 ( 896) hydrogen bonds : angle 3.45771 / 2.40 ( 2640) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 323 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7421 (mp0) cc_final: 0.7126 (mp0) REVERT: A 233 LEU cc_start: 0.8042 (tp) cc_final: 0.7735 (mp) REVERT: A 367 GLU cc_start: 0.6380 (mp0) cc_final: 0.6171 (mp0) REVERT: A 401 ASN cc_start: 0.7638 (p0) cc_final: 0.6615 (t0) REVERT: A 431 MET cc_start: 0.8479 (mtp) cc_final: 0.8187 (mtm) REVERT: A 479 MET cc_start: 0.2359 (OUTLIER) cc_final: -0.0191 (tpt) REVERT: A 538 PHE cc_start: 0.7369 (t80) cc_final: 0.6049 (OUTLIER) REVERT: A 687 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7277 (tp30) REVERT: A 698 ARG cc_start: 0.7820 (mtp85) cc_final: 0.6720 (mtt90) REVERT: A 714 ARG cc_start: 0.8076 (ttm-80) cc_final: 0.7353 (ttt-90) REVERT: B 251 ASN cc_start: 0.8108 (m110) cc_final: 0.7649 (m-40) REVERT: B 351 MET cc_start: 0.8971 (mtp) cc_final: 0.8750 (mtp) REVERT: B 401 ASN cc_start: 0.7627 (p0) cc_final: 0.6603 (t0) REVERT: B 431 MET cc_start: 0.8522 (mtp) cc_final: 0.8244 (mtm) REVERT: B 479 MET cc_start: 0.2498 (OUTLIER) cc_final: -0.0023 (tpt) REVERT: B 538 PHE cc_start: 0.7298 (t80) cc_final: 0.5979 (m-10) REVERT: B 574 MET cc_start: 0.9088 (mtp) cc_final: 0.8828 (mtm) REVERT: B 683 ASN cc_start: 0.7057 (OUTLIER) cc_final: 0.6777 (m-40) REVERT: B 698 ARG cc_start: 0.7817 (mtp85) cc_final: 0.6710 (mtt90) REVERT: B 714 ARG cc_start: 0.8083 (ttm-80) cc_final: 0.7337 (ttt-90) REVERT: B 716 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.7109 (tpm170) REVERT: C 129 GLU cc_start: 0.6507 (mp0) cc_final: 0.6279 (mp0) REVERT: C 185 GLU cc_start: 0.7427 (mp0) cc_final: 0.7116 (mp0) REVERT: C 233 LEU cc_start: 0.8019 (tp) cc_final: 0.7713 (mp) REVERT: C 351 MET cc_start: 0.9003 (mtp) cc_final: 0.8783 (mtp) REVERT: C 401 ASN cc_start: 0.7609 (p0) cc_final: 0.7276 (p0) REVERT: C 431 MET cc_start: 0.8525 (mtp) cc_final: 0.8251 (mtm) REVERT: C 479 MET cc_start: 0.2311 (OUTLIER) cc_final: -0.0118 (tpt) REVERT: C 538 PHE cc_start: 0.7379 (t80) cc_final: 0.6092 (m-80) REVERT: C 574 MET cc_start: 0.9089 (mtp) cc_final: 0.8822 (mtm) REVERT: C 698 ARG cc_start: 0.7823 (mtp85) cc_final: 0.6709 (mtt90) REVERT: C 714 ARG cc_start: 0.8071 (ttm-80) cc_final: 0.7341 (ttt-90) REVERT: C 716 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.7099 (tpm170) REVERT: D 129 GLU cc_start: 0.6587 (mp0) cc_final: 0.6340 (mp0) REVERT: D 185 GLU cc_start: 0.7372 (mp0) cc_final: 0.7053 (mp0) REVERT: D 233 LEU cc_start: 0.8044 (tp) cc_final: 0.7724 (mp) REVERT: D 351 MET cc_start: 0.8973 (mtp) cc_final: 0.8750 (mtp) REVERT: D 401 ASN cc_start: 0.7627 (p0) cc_final: 0.6585 (t0) REVERT: D 479 MET cc_start: 0.2450 (OUTLIER) cc_final: 0.0132 (tpt) REVERT: D 574 MET cc_start: 0.9081 (mtp) cc_final: 0.8815 (mtm) REVERT: D 584 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7572 (mp) REVERT: D 585 HIS cc_start: 0.7360 (t-90) cc_final: 0.6978 (m90) REVERT: D 683 ASN cc_start: 0.7053 (OUTLIER) cc_final: 0.6795 (m-40) REVERT: D 698 ARG cc_start: 0.7804 (mtp85) cc_final: 0.6693 (mtt90) REVERT: D 714 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7351 (ttt-90) REVERT: D 716 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.7147 (tpm170) outliers start: 48 outliers final: 10 residues processed: 342 average time/residue: 0.5774 time to fit residues: 224.5534 Evaluate side-chains 327 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 307 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 683 ASN Chi-restraints excluded: chain B residue 712 ARG Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 683 ASN Chi-restraints excluded: chain D residue 687 GLU Chi-restraints excluded: chain D residue 716 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 55 optimal weight: 9.9990 chunk 205 optimal weight: 0.0970 chunk 62 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 239 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN B 279 GLN B 297 ASN B 514 GLN B 585 HIS C 279 GLN C 297 ASN D 279 GLN D 297 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.159812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.111690 restraints weight = 23375.415| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.99 r_work: 0.3027 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22700 Z= 0.168 Angle : 0.568 6.453 30352 Z= 0.286 Chirality : 0.040 0.156 3244 Planarity : 0.004 0.040 3632 Dihedral : 20.213 168.715 4272 Min Nonbonded Distance : 1.495 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.65 % Allowed : 12.54 % Favored : 84.80 % 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: -0.65 (0.17), residues: 2492 helix: 0.35 (0.13), residues: 1572 sheet: 0.15 (0.50), residues: 112 loop : -2.00 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 369 TYR 0.013 0.002 TYR B 451 PHE 0.017 0.001 PHE B 193 TRP 0.011 0.001 TRP B 742 HIS 0.006 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 (22696) covalent geometry : angle 0.56796 / 0.29 (30344) SS BOND : bond 0.00035 / 0.02 ( 4) SS BOND : angle 0.10538 / 0.07 ( 8) hydrogen bonds : bond 0.03861 / 2.53 ( 896) hydrogen bonds : angle 3.65335 / 2.54 ( 2640) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 320 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7198 (ttp-110) cc_final: 0.6917 (mtp-110) REVERT: A 185 GLU cc_start: 0.7478 (mp0) cc_final: 0.7142 (mp0) REVERT: A 233 LEU cc_start: 0.8150 (tp) cc_final: 0.7802 (mp) REVERT: A 351 MET cc_start: 0.9026 (mtp) cc_final: 0.8818 (mtp) REVERT: A 431 MET cc_start: 0.8574 (mtp) cc_final: 0.8289 (mtm) REVERT: A 479 MET cc_start: 0.2276 (OUTLIER) cc_final: -0.0093 (tpt) REVERT: A 584 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7659 (mp) REVERT: A 687 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7354 (tp30) REVERT: A 698 ARG cc_start: 0.8026 (mtp85) cc_final: 0.6909 (mtt90) REVERT: A 714 ARG cc_start: 0.8158 (ttm-80) cc_final: 0.7437 (ttt-90) REVERT: A 716 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7120 (tpm170) REVERT: B 351 MET cc_start: 0.9056 (mtp) cc_final: 0.8849 (mtp) REVERT: B 431 MET cc_start: 0.8582 (mtp) cc_final: 0.8305 (mtm) REVERT: B 479 MET cc_start: 0.2470 (OUTLIER) cc_final: -0.0132 (tpt) REVERT: B 538 PHE cc_start: 0.7394 (t80) cc_final: 0.6078 (OUTLIER) REVERT: B 574 MET cc_start: 0.9171 (mtp) cc_final: 0.8908 (mtm) REVERT: B 581 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7345 (mppt) REVERT: B 683 ASN cc_start: 0.7209 (OUTLIER) cc_final: 0.6935 (m-40) REVERT: B 698 ARG cc_start: 0.8029 (mtp85) cc_final: 0.6917 (mtt90) REVERT: B 714 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7402 (ttt-90) REVERT: C 129 GLU cc_start: 0.6769 (mp0) cc_final: 0.6404 (mp0) REVERT: C 185 GLU cc_start: 0.7464 (mp0) cc_final: 0.7123 (mp0) REVERT: C 233 LEU cc_start: 0.8134 (tp) cc_final: 0.7791 (mp) REVERT: C 351 MET cc_start: 0.9089 (mtp) cc_final: 0.8888 (mtp) REVERT: C 366 LYS cc_start: 0.8027 (mttm) cc_final: 0.7639 (mppt) REVERT: C 431 MET cc_start: 0.8590 (mtp) cc_final: 0.8302 (mtm) REVERT: C 479 MET cc_start: 0.2378 (OUTLIER) cc_final: -0.0129 (tpt) REVERT: C 574 MET cc_start: 0.9163 (mtp) cc_final: 0.8908 (mtm) REVERT: C 584 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7660 (mp) REVERT: C 698 ARG cc_start: 0.8033 (mtp85) cc_final: 0.6908 (mtt90) REVERT: C 714 ARG cc_start: 0.8160 (ttm-80) cc_final: 0.7414 (ttt-90) REVERT: D 129 GLU cc_start: 0.6790 (mp0) cc_final: 0.6476 (mp0) REVERT: D 367 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6625 (pm20) REVERT: D 479 MET cc_start: 0.2475 (OUTLIER) cc_final: 0.0008 (tpt) REVERT: D 574 MET cc_start: 0.9168 (mtp) cc_final: 0.8909 (mtm) REVERT: D 581 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7362 (mppt) REVERT: D 584 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7655 (mp) REVERT: D 585 HIS cc_start: 0.7404 (t-90) cc_final: 0.7063 (m90) REVERT: D 683 ASN cc_start: 0.7208 (OUTLIER) cc_final: 0.6933 (m-40) REVERT: D 698 ARG cc_start: 0.8036 (mtp85) cc_final: 0.6922 (mtt90) REVERT: D 714 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7436 (ttt-90) outliers start: 59 outliers final: 22 residues processed: 342 average time/residue: 0.6256 time to fit residues: 243.8378 Evaluate side-chains 342 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 308 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 683 ASN Chi-restraints excluded: chain B residue 712 ARG Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 581 LYS Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 683 ASN Chi-restraints excluded: chain D residue 687 GLU Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 747 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 183 optimal weight: 0.6980 chunk 29 optimal weight: 0.0050 chunk 2 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 191 optimal weight: 0.4980 chunk 179 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN B 279 GLN B 585 HIS C 279 GLN D 279 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.173642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.135167 restraints weight = 22780.603| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.61 r_work: 0.3128 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22700 Z= 0.098 Angle : 0.490 5.965 30352 Z= 0.253 Chirality : 0.036 0.125 3244 Planarity : 0.003 0.038 3632 Dihedral : 19.598 172.361 4272 Min Nonbonded Distance : 1.595 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.89 % Allowed : 13.98 % Favored : 84.13 % 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: -0.31 (0.17), residues: 2492 helix: 0.64 (0.13), residues: 1596 sheet: 0.35 (0.50), residues: 112 loop : -2.02 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 369 TYR 0.015 0.001 TYR B 208 PHE 0.018 0.001 PHE C 193 TRP 0.007 0.001 TRP A 742 HIS 0.006 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (22696) covalent geometry : angle 0.48956 / 0.25 (30344) SS BOND : bond 0.00012 / 0.01 ( 4) SS BOND : angle 0.20013 / 0.14 ( 8) hydrogen bonds : bond 0.02957 / 1.94 ( 896) hydrogen bonds : angle 3.42727 / 2.38 ( 2640) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 312 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7271 (ttp-110) cc_final: 0.6956 (mtp-110) REVERT: A 185 GLU cc_start: 0.7574 (mp0) cc_final: 0.7257 (mp0) REVERT: A 233 LEU cc_start: 0.8266 (tp) cc_final: 0.7919 (mp) REVERT: A 251 ASN cc_start: 0.8191 (m110) cc_final: 0.7731 (m-40) REVERT: A 351 MET cc_start: 0.8987 (mtp) cc_final: 0.8759 (mtp) REVERT: A 401 ASN cc_start: 0.7766 (p0) cc_final: 0.7462 (p0) REVERT: A 431 MET cc_start: 0.8469 (mtp) cc_final: 0.8183 (mtm) REVERT: A 479 MET cc_start: 0.2383 (OUTLIER) cc_final: -0.0147 (tpt) REVERT: A 687 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7443 (tp30) REVERT: A 698 ARG cc_start: 0.7917 (mtp85) cc_final: 0.6891 (mtt90) REVERT: A 714 ARG cc_start: 0.8171 (ttm-80) cc_final: 0.7508 (ttt-90) REVERT: A 716 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7063 (tpm170) REVERT: B 351 MET cc_start: 0.8989 (mtp) cc_final: 0.8773 (mtp) REVERT: B 431 MET cc_start: 0.8477 (mtp) cc_final: 0.8188 (mtm) REVERT: B 479 MET cc_start: 0.2677 (OUTLIER) cc_final: 0.0014 (tpt) REVERT: B 538 PHE cc_start: 0.7475 (t80) cc_final: 0.6195 (m-80) REVERT: B 574 MET cc_start: 0.9157 (mtp) cc_final: 0.8883 (mtm) REVERT: B 581 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7467 (mppt) REVERT: B 683 ASN cc_start: 0.7340 (OUTLIER) cc_final: 0.7092 (m-40) REVERT: B 698 ARG cc_start: 0.7953 (mtp85) cc_final: 0.6911 (mtt90) REVERT: B 714 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7503 (ttt-90) REVERT: C 122 ARG cc_start: 0.7309 (ttp-110) cc_final: 0.7000 (mtp-110) REVERT: C 185 GLU cc_start: 0.7517 (mp0) cc_final: 0.7189 (mp0) REVERT: C 233 LEU cc_start: 0.8256 (tp) cc_final: 0.7912 (mp) REVERT: C 351 MET cc_start: 0.9028 (mtp) cc_final: 0.8802 (mtp) REVERT: C 431 MET cc_start: 0.8468 (mtp) cc_final: 0.8185 (mtm) REVERT: C 479 MET cc_start: 0.2488 (OUTLIER) cc_final: -0.0099 (tpt) REVERT: C 538 PHE cc_start: 0.7502 (t80) cc_final: 0.6201 (m-80) REVERT: C 574 MET cc_start: 0.9169 (mtp) cc_final: 0.8901 (mtm) REVERT: C 698 ARG cc_start: 0.7915 (mtp85) cc_final: 0.6874 (mtt90) REVERT: C 714 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7478 (ttt-90) REVERT: C 717 MET cc_start: 0.8849 (mmt) cc_final: 0.8573 (mmt) REVERT: D 367 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6817 (pm20) REVERT: D 479 MET cc_start: 0.2525 (OUTLIER) cc_final: 0.0012 (tpt) REVERT: D 574 MET cc_start: 0.9168 (mtp) cc_final: 0.8898 (mtm) REVERT: D 584 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7708 (mp) REVERT: D 585 HIS cc_start: 0.7443 (t-90) cc_final: 0.7196 (m90) REVERT: D 683 ASN cc_start: 0.7354 (OUTLIER) cc_final: 0.7116 (m-40) REVERT: D 698 ARG cc_start: 0.7941 (mtp85) cc_final: 0.6900 (mtt90) REVERT: D 714 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7533 (ttt-90) REVERT: D 738 LYS cc_start: 0.8873 (tptt) cc_final: 0.8635 (ptmt) outliers start: 42 outliers final: 9 residues processed: 331 average time/residue: 0.6140 time to fit residues: 232.2852 Evaluate side-chains 323 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 304 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 683 ASN Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 683 ASN Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 99 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 135 optimal weight: 0.6980 chunk 235 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN A 514 GLN B 279 GLN B 585 HIS C 279 GLN D 279 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.173274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.137548 restraints weight = 22769.279| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.51 r_work: 0.3135 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 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 : 0.003 0.043 22700 Z= 0.110 Angle : 0.501 5.943 30352 Z= 0.256 Chirality : 0.037 0.119 3244 Planarity : 0.003 0.038 3632 Dihedral : 19.361 171.336 4272 Min Nonbonded Distance : 1.578 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.02 % Allowed : 14.16 % Favored : 83.81 % 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: -0.22 (0.17), residues: 2492 helix: 0.70 (0.13), residues: 1596 sheet: 0.45 (0.51), residues: 112 loop : -1.99 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 122 TYR 0.015 0.001 TYR B 540 PHE 0.021 0.001 PHE D 193 TRP 0.007 0.001 TRP A 742 HIS 0.006 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (22696) covalent geometry : angle 0.50107 / 0.26 (30344) SS BOND : bond 0.00014 / 0.01 ( 4) SS BOND : angle 0.14024 / 0.10 ( 8) hydrogen bonds : bond 0.03076 / 2.02 ( 896) hydrogen bonds : angle 3.41680 / 2.37 ( 2640) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 302 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7325 (ttp-110) cc_final: 0.7001 (mtp-110) REVERT: A 185 GLU cc_start: 0.7550 (mp0) cc_final: 0.7232 (mp0) REVERT: A 233 LEU cc_start: 0.8322 (tp) cc_final: 0.7971 (mp) REVERT: A 251 ASN cc_start: 0.8214 (m110) cc_final: 0.7757 (m-40) REVERT: A 351 MET cc_start: 0.8996 (mtp) cc_final: 0.8781 (mtp) REVERT: A 401 ASN cc_start: 0.7742 (p0) cc_final: 0.7425 (p0) REVERT: A 431 MET cc_start: 0.8472 (mtp) cc_final: 0.8194 (mtm) REVERT: A 479 MET cc_start: 0.2398 (OUTLIER) cc_final: -0.0081 (tpt) REVERT: A 538 PHE cc_start: 0.7577 (t80) cc_final: 0.7286 (t80) REVERT: A 687 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7304 (tp30) REVERT: A 698 ARG cc_start: 0.7941 (mtp85) cc_final: 0.6919 (mtt90) REVERT: A 714 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7557 (ttt-90) REVERT: A 716 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7036 (tpm170) REVERT: B 188 ARG cc_start: 0.8068 (mtm-85) cc_final: 0.7585 (mtt-85) REVERT: B 351 MET cc_start: 0.8981 (mtp) cc_final: 0.8758 (mtp) REVERT: B 431 MET cc_start: 0.8494 (mtp) cc_final: 0.8207 (mtm) REVERT: B 479 MET cc_start: 0.2668 (OUTLIER) cc_final: 0.0030 (tpt) REVERT: B 538 PHE cc_start: 0.7461 (t80) cc_final: 0.6192 (m-80) REVERT: B 574 MET cc_start: 0.9148 (mtp) cc_final: 0.8870 (mtm) REVERT: B 581 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7507 (mppt) REVERT: B 683 ASN cc_start: 0.7408 (OUTLIER) cc_final: 0.7173 (m-40) REVERT: B 698 ARG cc_start: 0.8000 (mtp85) cc_final: 0.6956 (mtt90) REVERT: B 714 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7540 (ttt-90) REVERT: B 736 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7712 (pt0) REVERT: C 122 ARG cc_start: 0.7368 (ttp-110) cc_final: 0.7059 (mtp-110) REVERT: C 185 GLU cc_start: 0.7527 (mp0) cc_final: 0.7185 (mp0) REVERT: C 233 LEU cc_start: 0.8326 (tp) cc_final: 0.7965 (mp) REVERT: C 351 MET cc_start: 0.9035 (mtp) cc_final: 0.8830 (mtp) REVERT: C 431 MET cc_start: 0.8461 (mtp) cc_final: 0.8171 (mtm) REVERT: C 479 MET cc_start: 0.2434 (OUTLIER) cc_final: -0.0076 (tpt) REVERT: C 538 PHE cc_start: 0.7582 (t80) cc_final: 0.7303 (t80) REVERT: C 574 MET cc_start: 0.9171 (mtp) cc_final: 0.8904 (mtm) REVERT: C 698 ARG cc_start: 0.7967 (mtp85) cc_final: 0.6928 (mtt90) REVERT: C 714 ARG cc_start: 0.8195 (ttm-80) cc_final: 0.7527 (ttt-90) REVERT: D 479 MET cc_start: 0.2675 (OUTLIER) cc_final: 0.0060 (tpt) REVERT: D 574 MET cc_start: 0.9153 (mtp) cc_final: 0.8880 (mtm) REVERT: D 584 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7670 (mp) REVERT: D 683 ASN cc_start: 0.7383 (OUTLIER) cc_final: 0.7156 (m-40) REVERT: D 698 ARG cc_start: 0.7979 (mtp85) cc_final: 0.6953 (mtt90) REVERT: D 714 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7559 (ttt-90) REVERT: D 738 LYS cc_start: 0.8874 (tptt) cc_final: 0.8608 (ptmt) outliers start: 45 outliers final: 17 residues processed: 321 average time/residue: 0.6095 time to fit residues: 223.8783 Evaluate side-chains 329 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 301 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 683 ASN Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 683 ASN Chi-restraints excluded: chain D residue 687 GLU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 97 optimal weight: 20.0000 chunk 152 optimal weight: 0.9980 chunk 124 optimal weight: 20.0000 chunk 229 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN B 279 GLN B 585 HIS C 279 GLN D 279 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.172868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.137238 restraints weight = 22892.280| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.52 r_work: 0.3136 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22700 Z= 0.119 Angle : 0.509 7.001 30352 Z= 0.261 Chirality : 0.037 0.128 3244 Planarity : 0.003 0.038 3632 Dihedral : 19.280 170.903 4272 Min Nonbonded Distance : 1.561 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.84 % Allowed : 14.34 % Favored : 83.81 % 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: -0.19 (0.17), residues: 2492 helix: 0.74 (0.13), residues: 1592 sheet: 0.48 (0.51), residues: 112 loop : -1.99 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 122 TYR 0.015 0.001 TYR B 540 PHE 0.023 0.001 PHE D 193 TRP 0.008 0.001 TRP A 742 HIS 0.006 0.001 HIS B 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (22696) covalent geometry : angle 0.50946 / 0.26 (30344) SS BOND : bond 0.00005 / 0.00 ( 4) SS BOND : angle 0.13703 / 0.09 ( 8) hydrogen bonds : bond 0.03154 / 2.07 ( 896) hydrogen bonds : angle 3.46813 / 2.41 ( 2640) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 301 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7346 (ttp-110) cc_final: 0.7076 (mtp180) REVERT: A 185 GLU cc_start: 0.7528 (mp0) cc_final: 0.7211 (mp0) REVERT: A 251 ASN cc_start: 0.8231 (m110) cc_final: 0.7764 (m-40) REVERT: A 351 MET cc_start: 0.9005 (mtp) cc_final: 0.8791 (mtp) REVERT: A 401 ASN cc_start: 0.7762 (p0) cc_final: 0.7464 (p0) REVERT: A 431 MET cc_start: 0.8452 (mtp) cc_final: 0.8164 (mtm) REVERT: A 479 MET cc_start: 0.2375 (OUTLIER) cc_final: -0.0121 (tpt) REVERT: A 538 PHE cc_start: 0.7560 (t80) cc_final: 0.7246 (t80) REVERT: A 687 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7403 (tp30) REVERT: A 698 ARG cc_start: 0.7969 (mtp85) cc_final: 0.6906 (mtt90) REVERT: A 714 ARG cc_start: 0.8201 (ttm-80) cc_final: 0.7549 (ttt-90) REVERT: A 716 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7053 (tpm170) REVERT: B 188 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7579 (mtt-85) REVERT: B 251 ASN cc_start: 0.8278 (m110) cc_final: 0.7813 (m-40) REVERT: B 351 MET cc_start: 0.8994 (mtp) cc_final: 0.8771 (mtp) REVERT: B 431 MET cc_start: 0.8474 (mtp) cc_final: 0.8187 (mtm) REVERT: B 479 MET cc_start: 0.2642 (OUTLIER) cc_final: 0.0043 (tpt) REVERT: B 538 PHE cc_start: 0.7480 (t80) cc_final: 0.6206 (m-80) REVERT: B 574 MET cc_start: 0.9150 (mtp) cc_final: 0.8875 (mtm) REVERT: B 581 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7453 (mppt) REVERT: B 585 HIS cc_start: 0.7526 (t-90) cc_final: 0.7128 (m-70) REVERT: B 683 ASN cc_start: 0.7398 (OUTLIER) cc_final: 0.7166 (m-40) REVERT: B 698 ARG cc_start: 0.8014 (mtp85) cc_final: 0.6950 (mtt90) REVERT: B 714 ARG cc_start: 0.8195 (ttm-80) cc_final: 0.7541 (ttt-90) REVERT: B 738 LYS cc_start: 0.8855 (tptt) cc_final: 0.8590 (ptmt) REVERT: C 122 ARG cc_start: 0.7382 (ttp-110) cc_final: 0.7068 (mtp-110) REVERT: C 185 GLU cc_start: 0.7487 (mp0) cc_final: 0.7159 (mp0) REVERT: C 251 ASN cc_start: 0.8200 (m110) cc_final: 0.7742 (m-40) REVERT: C 351 MET cc_start: 0.9039 (mtp) cc_final: 0.8831 (mtp) REVERT: C 431 MET cc_start: 0.8416 (mtp) cc_final: 0.8132 (mtm) REVERT: C 479 MET cc_start: 0.2322 (OUTLIER) cc_final: -0.0151 (tpt) REVERT: C 538 PHE cc_start: 0.7571 (t80) cc_final: 0.7264 (t80) REVERT: C 574 MET cc_start: 0.9174 (mtp) cc_final: 0.8909 (mtm) REVERT: C 698 ARG cc_start: 0.7966 (mtp85) cc_final: 0.6906 (mtt90) REVERT: C 714 ARG cc_start: 0.8204 (ttm-80) cc_final: 0.7543 (ttt-90) REVERT: C 716 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7262 (tpm170) REVERT: D 122 ARG cc_start: 0.7372 (ttp-110) cc_final: 0.7091 (mtp85) REVERT: D 351 MET cc_start: 0.8980 (mtp) cc_final: 0.8771 (mtp) REVERT: D 479 MET cc_start: 0.2648 (OUTLIER) cc_final: 0.0038 (tpt) REVERT: D 574 MET cc_start: 0.9143 (mtp) cc_final: 0.8866 (mtm) REVERT: D 683 ASN cc_start: 0.7376 (OUTLIER) cc_final: 0.7151 (m-40) REVERT: D 698 ARG cc_start: 0.8015 (mtp85) cc_final: 0.6949 (mtt90) REVERT: D 714 ARG cc_start: 0.8227 (ttm-80) cc_final: 0.7577 (ttt-90) REVERT: D 738 LYS cc_start: 0.8875 (tptt) cc_final: 0.8595 (ptmt) outliers start: 41 outliers final: 22 residues processed: 321 average time/residue: 0.6207 time to fit residues: 227.9963 Evaluate side-chains 330 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 298 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 683 ASN Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 683 ASN Chi-restraints excluded: chain D residue 687 GLU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 146 optimal weight: 1.9990 chunk 245 optimal weight: 0.1980 chunk 101 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 180 optimal weight: 0.7980 chunk 217 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 237 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN B 279 GLN C 279 GLN C 514 GLN D 279 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.173922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.138194 restraints weight = 22848.755| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.53 r_work: 0.3142 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22700 Z= 0.099 Angle : 0.493 7.995 30352 Z= 0.254 Chirality : 0.036 0.132 3244 Planarity : 0.003 0.038 3632 Dihedral : 19.095 171.396 4272 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.48 % Allowed : 14.93 % Favored : 83.59 % 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: -0.10 (0.17), residues: 2492 helix: 0.83 (0.13), residues: 1592 sheet: 0.57 (0.51), residues: 112 loop : -2.01 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 122 TYR 0.015 0.001 TYR B 540 PHE 0.022 0.001 PHE C 193 TRP 0.008 0.001 TRP A 742 HIS 0.006 0.001 HIS B 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (22696) covalent geometry : angle 0.49343 / 0.25 (30344) SS BOND : bond 0.00024 / 0.01 ( 4) SS BOND : angle 0.15552 / 0.11 ( 8) hydrogen bonds : bond 0.02920 / 1.92 ( 896) hydrogen bonds : angle 3.42869 / 2.39 ( 2640) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 307 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7358 (ttp-110) cc_final: 0.7085 (mtp180) REVERT: A 185 GLU cc_start: 0.7498 (mp0) cc_final: 0.7204 (mp0) REVERT: A 251 ASN cc_start: 0.8193 (m110) cc_final: 0.7736 (m-40) REVERT: A 315 ASP cc_start: 0.7420 (p0) cc_final: 0.6961 (t0) REVERT: A 351 MET cc_start: 0.8992 (mtp) cc_final: 0.8774 (mtp) REVERT: A 401 ASN cc_start: 0.7752 (p0) cc_final: 0.7408 (p0) REVERT: A 431 MET cc_start: 0.8443 (mtp) cc_final: 0.8163 (mtm) REVERT: A 479 MET cc_start: 0.2369 (OUTLIER) cc_final: -0.0096 (tpt) REVERT: A 538 PHE cc_start: 0.7560 (t80) cc_final: 0.7263 (t80) REVERT: A 687 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7346 (mm-30) REVERT: A 698 ARG cc_start: 0.7940 (mtp85) cc_final: 0.6905 (mtt90) REVERT: A 714 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7559 (ttt-90) REVERT: A 716 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.6990 (tpm170) REVERT: B 188 ARG cc_start: 0.8053 (mtm-85) cc_final: 0.7583 (mtt-85) REVERT: B 251 ASN cc_start: 0.8203 (m110) cc_final: 0.7759 (m-40) REVERT: B 351 MET cc_start: 0.8964 (mtp) cc_final: 0.8758 (mtp) REVERT: B 431 MET cc_start: 0.8451 (mtp) cc_final: 0.8172 (mtm) REVERT: B 479 MET cc_start: 0.2610 (OUTLIER) cc_final: 0.0026 (tpt) REVERT: B 538 PHE cc_start: 0.7518 (t80) cc_final: 0.6220 (m-80) REVERT: B 574 MET cc_start: 0.9151 (mtp) cc_final: 0.8877 (mtm) REVERT: B 581 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7409 (mppt) REVERT: B 585 HIS cc_start: 0.7597 (t-90) cc_final: 0.7154 (m-70) REVERT: B 683 ASN cc_start: 0.7375 (OUTLIER) cc_final: 0.7153 (m-40) REVERT: B 698 ARG cc_start: 0.7994 (mtp85) cc_final: 0.6951 (mtt90) REVERT: B 714 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7550 (ttt-90) REVERT: C 122 ARG cc_start: 0.7362 (ttp-110) cc_final: 0.7044 (mtp-110) REVERT: C 185 GLU cc_start: 0.7476 (mp0) cc_final: 0.7160 (mp0) REVERT: C 251 ASN cc_start: 0.8157 (m110) cc_final: 0.7708 (m-40) REVERT: C 315 ASP cc_start: 0.7426 (p0) cc_final: 0.6998 (OUTLIER) REVERT: C 351 MET cc_start: 0.9027 (mtp) cc_final: 0.8819 (mtp) REVERT: C 367 GLU cc_start: 0.6484 (mp0) cc_final: 0.6269 (tm-30) REVERT: C 431 MET cc_start: 0.8430 (mtp) cc_final: 0.8148 (mtm) REVERT: C 479 MET cc_start: 0.2334 (OUTLIER) cc_final: -0.0148 (tpt) REVERT: C 538 PHE cc_start: 0.7559 (t80) cc_final: 0.7272 (t80) REVERT: C 574 MET cc_start: 0.9177 (mtp) cc_final: 0.8909 (mtm) REVERT: C 698 ARG cc_start: 0.7945 (mtp85) cc_final: 0.6926 (mtt90) REVERT: C 714 ARG cc_start: 0.8216 (ttm-80) cc_final: 0.7558 (ttt-90) REVERT: C 716 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7278 (tpm170) REVERT: D 122 ARG cc_start: 0.7390 (ttp-110) cc_final: 0.7097 (mtp85) REVERT: D 251 ASN cc_start: 0.8200 (m110) cc_final: 0.7764 (m-40) REVERT: D 351 MET cc_start: 0.8956 (mtp) cc_final: 0.8754 (mtp) REVERT: D 367 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6743 (pm20) REVERT: D 479 MET cc_start: 0.2619 (OUTLIER) cc_final: 0.0026 (tpt) REVERT: D 574 MET cc_start: 0.9148 (mtp) cc_final: 0.8877 (mtm) REVERT: D 683 ASN cc_start: 0.7392 (OUTLIER) cc_final: 0.7173 (m-40) REVERT: D 698 ARG cc_start: 0.7985 (mtp85) cc_final: 0.6945 (mtt90) REVERT: D 714 ARG cc_start: 0.8213 (ttm-80) cc_final: 0.7574 (ttt-90) REVERT: D 738 LYS cc_start: 0.8877 (tptt) cc_final: 0.8614 (ptmt) outliers start: 33 outliers final: 18 residues processed: 323 average time/residue: 0.6225 time to fit residues: 229.5310 Evaluate side-chains 332 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 305 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 683 ASN Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 683 ASN Chi-restraints excluded: chain D residue 687 GLU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 82 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 238 optimal weight: 0.8980 chunk 230 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 83 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN B 279 GLN C 279 GLN D 279 GLN D 514 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.171842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.136274 restraints weight = 22924.960| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.51 r_work: 0.3117 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22700 Z= 0.134 Angle : 0.532 7.320 30352 Z= 0.271 Chirality : 0.038 0.140 3244 Planarity : 0.004 0.039 3632 Dihedral : 19.055 169.811 4272 Min Nonbonded Distance : 1.545 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.80 % Allowed : 14.84 % Favored : 83.36 % 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: -0.21 (0.17), residues: 2492 helix: 0.71 (0.13), residues: 1588 sheet: 0.52 (0.51), residues: 112 loop : -1.95 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 122 TYR 0.016 0.002 TYR B 540 PHE 0.022 0.001 PHE C 193 TRP 0.010 0.001 TRP B 742 HIS 0.006 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.13 (22696) covalent geometry : angle 0.53175 / 0.27 (30344) SS BOND : bond 0.00004 / 0.00 ( 4) SS BOND : angle 0.12400 / 0.08 ( 8) hydrogen bonds : bond 0.03394 / 2.23 ( 896) hydrogen bonds : angle 3.57309 / 2.49 ( 2640) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8254.37 seconds wall clock time: 141 minutes 13.88 seconds (8473.88 seconds total)