Starting phenix.real_space_refine on Fri Aug 7 15:44:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13ln_77138/08_2026/13ln_77138.cif Found real_map, /net/cci-nas-00/data/ceres_data/13ln_77138/08_2026/13ln_77138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/13ln_77138/08_2026/13ln_77138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13ln_77138/08_2026/13ln_77138.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/13ln_77138/08_2026/13ln_77138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13ln_77138/08_2026/13ln_77138.map" } resolution = 3.02 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= 0.025 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 32 5.49 5 S 128 5.16 5 Na 3 4.78 5 C 14600 2.51 5 N 3396 2.21 5 O 3988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 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: 22147 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5094 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 16, 'TRANS': 609} Chain breaks: 1 Chain: "B" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5094 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 16, 'TRANS': 609} Chain breaks: 1 Chain: "C" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5094 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 16, 'TRANS': 609} Chain breaks: 1 Chain: "D" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5094 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 16, 'TRANS': 609} Chain breaks: 1 Chain: "A" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 471 Unusual residues: {' NA': 3, 'POV': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 364 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "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: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 364 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Time building chain proxies: 5.08, per 1000 atoms: 0.23 Number of scatterers: 22147 At special positions: 0 Unit cell: (159.428, 159.428, 128.544, 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 32 15.00 Na 3 11.00 O 3988 8.00 N 3396 7.00 C 14600 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=2.05 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.05 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.05 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.05 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: 1.83 Conformation dependent library (CDL) restraints added in 1.0 seconds 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4784 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 4 sheets defined 62.3% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 118 through 129 removed outlier: 3.604A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 145 removed outlier: 3.941A pdb=" N VAL A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.574A pdb=" N THR A 163 " --> pdb=" O MET A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.629A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.778A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.535A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 225 removed outlier: 3.623A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 238 removed outlier: 3.522A pdb=" N LEU A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.670A pdb=" N LEU A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.559A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.501A pdb=" N ASP A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 removed outlier: 3.628A pdb=" N THR A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.775A 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 Processing helix chain 'A' and resid 422 through 434 removed outlier: 4.067A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 458 removed outlier: 3.873A pdb=" N TYR A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR A 454 " --> pdb=" O PHE A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 488 removed outlier: 4.190A pdb=" N LEU A 484 " --> pdb=" O GLY A 480 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 485 " --> pdb=" O TRP A 481 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 507 removed outlier: 3.642A pdb=" N ALA A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 removed outlier: 3.518A pdb=" N SER A 518 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP A 519 " --> pdb=" O ILE A 516 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ALA A 520 " --> pdb=" O LEU A 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 515 through 520' Processing helix chain 'A' and resid 521 through 542 removed outlier: 3.524A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 559 removed outlier: 4.023A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 567 removed outlier: 3.547A pdb=" N LEU A 563 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 576 removed outlier: 3.617A pdb=" N TYR A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 584 Processing helix chain 'A' and resid 586 through 599 removed outlier: 3.782A pdb=" N PHE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 608 removed outlier: 3.895A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 removed outlier: 3.583A pdb=" N THR A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 681 removed outlier: 3.681A pdb=" N VAL A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 669 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL A 681 " --> pdb=" O MET A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.647A pdb=" N ILE A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 removed outlier: 4.121A pdb=" N SER A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 removed outlier: 3.605A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 145 removed outlier: 3.940A pdb=" N VAL B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.573A pdb=" N THR B 163 " --> pdb=" O MET B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.629A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.778A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.534A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 225 removed outlier: 3.624A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 238 removed outlier: 3.522A pdb=" N LEU B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.670A pdb=" N LEU B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.560A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.501A pdb=" N ASP B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 336 removed outlier: 3.627A pdb=" N THR B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 351 removed outlier: 3.583A pdb=" N MET B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.775A 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 Processing helix chain 'B' and resid 422 through 434 removed outlier: 4.068A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 458 removed outlier: 3.874A pdb=" N TYR B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR B 454 " --> pdb=" O PHE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 488 removed outlier: 4.190A pdb=" N LEU B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 485 " --> pdb=" O TRP B 481 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 507 removed outlier: 3.642A pdb=" N ALA B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS B 500 " --> pdb=" O CYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 520 removed outlier: 3.518A pdb=" N SER B 518 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP B 519 " --> pdb=" O ILE B 516 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ALA B 520 " --> pdb=" O LEU B 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 515 through 520' Processing helix chain 'B' and resid 521 through 542 removed outlier: 3.524A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN B 529 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 559 removed outlier: 4.023A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 567 removed outlier: 3.547A pdb=" N LEU B 563 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B 566 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 576 removed outlier: 3.617A pdb=" N TYR B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 584 Processing helix chain 'B' and resid 586 through 599 removed outlier: 3.782A pdb=" N PHE B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 595 " --> pdb=" O LEU B 591 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 608 removed outlier: 3.895A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 637 removed outlier: 3.584A pdb=" N THR B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 681 removed outlier: 3.681A pdb=" N VAL B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU B 669 " --> pdb=" O THR B 665 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL B 681 " --> pdb=" O MET B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.647A pdb=" N ILE B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 removed outlier: 4.121A pdb=" N SER B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 129 removed outlier: 3.604A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 145 removed outlier: 3.940A pdb=" N VAL C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 163 removed outlier: 3.574A pdb=" N THR C 163 " --> pdb=" O MET C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.628A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.778A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.535A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 225 removed outlier: 3.622A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 238 removed outlier: 3.522A pdb=" N LEU C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.670A pdb=" N LEU C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.560A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.501A pdb=" N ASP C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 324 " --> pdb=" O MET C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 336 removed outlier: 3.627A pdb=" N THR C 336 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.776A 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 Processing helix chain 'C' and resid 422 through 434 removed outlier: 4.067A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 458 removed outlier: 3.874A pdb=" N TYR C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR C 454 " --> pdb=" O PHE C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 488 removed outlier: 4.190A pdb=" N LEU C 484 " --> pdb=" O GLY C 480 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU C 485 " --> pdb=" O TRP C 481 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 507 removed outlier: 3.642A pdb=" N ALA C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 520 removed outlier: 3.519A pdb=" N SER C 518 " --> pdb=" O SER C 515 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP C 519 " --> pdb=" O ILE C 516 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ALA C 520 " --> pdb=" O LEU C 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 515 through 520' Processing helix chain 'C' and resid 521 through 542 removed outlier: 3.524A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 559 removed outlier: 4.023A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 567 removed outlier: 3.547A pdb=" N LEU C 563 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR C 566 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 576 removed outlier: 3.617A pdb=" N TYR C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 584 Processing helix chain 'C' and resid 586 through 599 removed outlier: 3.781A pdb=" N PHE C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE C 595 " --> pdb=" O LEU C 591 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 608 removed outlier: 3.895A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 removed outlier: 3.583A pdb=" N THR C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 681 removed outlier: 3.680A pdb=" N VAL C 662 " --> pdb=" O LEU C 658 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU C 669 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL C 681 " --> pdb=" O MET C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 707 removed outlier: 3.646A pdb=" N ILE C 691 " --> pdb=" O GLU C 687 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS C 705 " --> pdb=" O LEU C 701 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 removed outlier: 4.120A pdb=" N SER C 713 " --> pdb=" O GLU C 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 129 removed outlier: 3.604A pdb=" N PHE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 145 removed outlier: 3.940A pdb=" N VAL D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 163 removed outlier: 3.574A pdb=" N THR D 163 " --> pdb=" O MET D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.628A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.778A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 removed outlier: 3.535A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 225 removed outlier: 3.623A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 238 removed outlier: 3.522A pdb=" N LEU D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.670A pdb=" N LEU D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.560A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.501A pdb=" N ASP D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 324 " --> pdb=" O MET D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 336 removed outlier: 3.627A pdb=" N THR D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 removed outlier: 3.649A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.775A 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 Processing helix chain 'D' and resid 422 through 434 removed outlier: 4.067A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 458 removed outlier: 3.874A pdb=" N TYR D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR D 454 " --> pdb=" O PHE D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 488 removed outlier: 4.191A pdb=" N LEU D 484 " --> pdb=" O GLY D 480 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU D 485 " --> pdb=" O TRP D 481 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 507 removed outlier: 3.643A pdb=" N ALA D 494 " --> pdb=" O VAL D 490 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS D 500 " --> pdb=" O CYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 520 removed outlier: 3.519A pdb=" N SER D 518 " --> pdb=" O SER D 515 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP D 519 " --> pdb=" O ILE D 516 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ALA D 520 " --> pdb=" O LEU D 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 515 through 520' Processing helix chain 'D' and resid 521 through 542 removed outlier: 3.524A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 559 removed outlier: 4.023A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 567 removed outlier: 3.547A pdb=" N LEU D 563 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR D 566 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 576 removed outlier: 3.617A pdb=" N TYR D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 584 Processing helix chain 'D' and resid 586 through 599 removed outlier: 3.781A pdb=" N PHE D 590 " --> pdb=" O ASP D 586 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 595 " --> pdb=" O LEU D 591 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 608 removed outlier: 3.895A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 637 removed outlier: 3.584A pdb=" N THR D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 681 removed outlier: 3.680A pdb=" N VAL D 662 " --> pdb=" O LEU D 658 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU D 669 " --> pdb=" O THR D 665 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL D 681 " --> pdb=" O MET D 677 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 707 removed outlier: 3.647A pdb=" N ILE D 691 " --> pdb=" O GLU D 687 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 removed outlier: 4.120A 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 381 removed outlier: 6.767A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 734 " --> pdb=" O SER A 388 " (cutoff:3.500A) removed outlier: 7.096A 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 381 removed outlier: 6.768A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 734 " --> pdb=" O SER B 388 " (cutoff:3.500A) removed outlier: 7.096A 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 381 removed outlier: 6.768A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 734 " --> pdb=" O SER C 388 " (cutoff:3.500A) removed outlier: 7.097A 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 381 removed outlier: 6.768A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE D 734 " --> pdb=" O SER D 388 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 837 hydrogen bonds defined for protein. 2475 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: 3.69 Time building geometry restraints manager: 2.42 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: 3446 1.32 - 1.44: 5665 1.44 - 1.57: 13069 1.57 - 1.69: 64 1.69 - 1.81: 212 Bond restraints: 22456 Sorted by residual: bond pdb=" O12 POV C1105 " pdb=" P POV C1105 " ideal model delta sigma weight residual 1.657 1.590 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" O12 POV A1104 " pdb=" P POV A1104 " 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 D1105 " pdb=" P POV D1105 " 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 B1104 " pdb=" P POV B1104 " ideal model delta sigma weight residual 1.657 1.591 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" N LEU B 347 " pdb=" CA LEU B 347 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.33e-02 5.65e+03 1.07e+01 ... (remaining 22451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 28553 2.21 - 4.42: 1324 4.42 - 6.63: 119 6.63 - 8.83: 52 8.83 - 11.04: 12 Bond angle restraints: 30060 Sorted by residual: angle pdb=" N ILE D 505 " pdb=" CA ILE D 505 " pdb=" C ILE D 505 " ideal model delta sigma weight residual 112.96 106.88 6.08 1.00e+00 1.00e+00 3.69e+01 angle pdb=" N ILE B 505 " pdb=" CA ILE B 505 " pdb=" C ILE B 505 " ideal model delta sigma weight residual 112.96 106.89 6.07 1.00e+00 1.00e+00 3.68e+01 angle pdb=" N ILE C 505 " pdb=" CA ILE C 505 " pdb=" C ILE C 505 " ideal model delta sigma weight residual 112.96 106.90 6.06 1.00e+00 1.00e+00 3.67e+01 angle pdb=" N ILE A 505 " pdb=" CA ILE A 505 " pdb=" C ILE A 505 " ideal model delta sigma weight residual 112.96 106.91 6.05 1.00e+00 1.00e+00 3.66e+01 angle pdb=" C LYS B 368 " pdb=" N ARG B 369 " pdb=" CA ARG B 369 " ideal model delta sigma weight residual 121.54 132.58 -11.04 1.91e+00 2.74e-01 3.34e+01 ... (remaining 30055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.56: 13282 35.56 - 71.12: 396 71.12 - 106.68: 71 106.68 - 142.24: 32 142.24 - 177.80: 27 Dihedral angle restraints: 13808 sinusoidal: 6436 harmonic: 7372 Sorted by residual: dihedral pdb=" CB CYS C 612 " pdb=" SG CYS C 612 " pdb=" SG CYS C 619 " pdb=" CB CYS C 619 " ideal model delta sinusoidal sigma weight residual -86.00 -167.59 81.59 1 1.00e+01 1.00e-02 8.20e+01 dihedral pdb=" CB CYS D 612 " pdb=" SG CYS D 612 " pdb=" SG CYS D 619 " pdb=" CB CYS D 619 " ideal model delta sinusoidal sigma weight residual -86.00 -167.57 81.57 1 1.00e+01 1.00e-02 8.19e+01 dihedral pdb=" CB CYS A 612 " pdb=" SG CYS A 612 " pdb=" SG CYS A 619 " pdb=" CB CYS A 619 " ideal model delta sinusoidal sigma weight residual -86.00 -167.56 81.56 1 1.00e+01 1.00e-02 8.19e+01 ... (remaining 13805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2761 0.066 - 0.131: 397 0.131 - 0.197: 57 0.197 - 0.263: 17 0.263 - 0.329: 4 Chirality restraints: 3236 Sorted by residual: 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 -2.26 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CG LEU C 429 " pdb=" CB LEU C 429 " pdb=" CD1 LEU C 429 " pdb=" CD2 LEU C 429 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.67e+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 -2.27 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 3233 not shown) Planarity restraints: 3612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 682 " 0.015 2.00e-02 2.50e+03 3.10e-02 9.60e+00 pdb=" C GLU B 682 " -0.054 2.00e-02 2.50e+03 pdb=" O GLU B 682 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN B 683 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 682 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.61e+00 pdb=" C GLU A 682 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU A 682 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN A 683 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 682 " -0.013 2.00e-02 2.50e+03 2.73e-02 7.43e+00 pdb=" C GLU D 682 " 0.047 2.00e-02 2.50e+03 pdb=" O GLU D 682 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN D 683 " -0.016 2.00e-02 2.50e+03 ... (remaining 3609 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 242 2.65 - 3.21: 17727 3.21 - 3.77: 32463 3.77 - 4.34: 48543 4.34 - 4.90: 78528 Nonbonded interactions: 177503 Sorted by model distance: nonbonded pdb="NA NA A1110 " pdb="NA NA A1111 " model vdw 2.083 1.900 nonbonded pdb=" O PRO A 753 " pdb=" OH TYR B 213 " model vdw 2.176 3.040 nonbonded pdb=" O PRO B 753 " pdb=" OH TYR C 213 " model vdw 2.223 3.040 nonbonded pdb=" O PRO C 753 " pdb=" OH TYR D 213 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR A 213 " pdb=" O PRO D 753 " model vdw 2.249 3.040 ... (remaining 177498 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 1107) selection = chain 'B' selection = (chain 'C' and resid 118 through 1107) 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 20.320 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5055 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 : 0.007 0.082 22460 Z= 0.328 Angle : 1.032 11.044 30068 Z= 0.514 Chirality : 0.052 0.329 3236 Planarity : 0.006 0.060 3612 Dihedral : 19.568 177.801 9012 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.59 % Favored : 93.25 % Rotamer: Outliers : 0.36 % Allowed : 3.78 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.04 (0.11), residues: 2488 helix: -4.54 (0.06), residues: 1544 sheet: -2.31 (0.49), residues: 84 loop : -2.61 (0.18), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 226 TYR 0.013 0.003 TYR A 564 PHE 0.034 0.003 PHE D 526 TRP 0.014 0.002 TRP D 692 HIS 0.012 0.003 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00713 / 0.33 (22456) covalent geometry : angle 1.03249 / 0.51 (30060) SS BOND : bond 0.01589 / 0.80 ( 4) SS BOND : angle 0.79011 / 0.50 ( 8) hydrogen bonds : bond 0.33081 / 21.59 ( 837) hydrogen bonds : angle 10.01546 / 6.92 ( 2475) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 348 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 MET cc_start: 0.2421 (mpp) cc_final: 0.2190 (pmm) REVERT: B 583 ILE cc_start: 0.6597 (mt) cc_final: 0.6359 (mt) REVERT: C 159 MET cc_start: 0.4717 (tpt) cc_final: 0.4362 (mtt) outliers start: 8 outliers final: 2 residues processed: 354 average time/residue: 0.1691 time to fit residues: 92.2171 Evaluate side-chains 219 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 217 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain C residue 684 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 247 optimal weight: 0.0370 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 HIS A 160 HIS ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 417 HIS A 426 HIS A 452 ASN A 483 GLN A 616 ASN B 150 HIS B 160 HIS B 178 ASN B 298 ASN B 412 ASN B 483 GLN B 616 ASN C 150 HIS C 160 HIS C 178 ASN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN C 452 ASN C 483 GLN C 616 ASN D 150 HIS D 160 HIS D 298 ASN D 452 ASN D 483 GLN D 616 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.222706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.173808 restraints weight = 23281.105| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.13 r_work: 0.3761 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3777 r_free = 0.3777 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 22460 Z= 0.207 Angle : 0.749 12.632 30068 Z= 0.376 Chirality : 0.044 0.271 3236 Planarity : 0.006 0.056 3612 Dihedral : 21.196 173.107 4099 Min Nonbonded Distance : 1.543 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.75 % Favored : 94.09 % Rotamer: Outliers : 1.80 % Allowed : 7.75 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.22 (0.14), residues: 2488 helix: -2.83 (0.10), residues: 1556 sheet: -1.89 (0.51), residues: 84 loop : -2.44 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 363 TYR 0.031 0.003 TYR D 208 PHE 0.025 0.002 PHE C 489 TRP 0.024 0.003 TRP A 692 HIS 0.008 0.002 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.21 (22456) covalent geometry : angle 0.74927 / 0.38 (30060) SS BOND : bond 0.00532 / 0.27 ( 4) SS BOND : angle 0.65274 / 0.40 ( 8) hydrogen bonds : bond 0.03953 / 2.56 ( 837) hydrogen bonds : angle 4.46740 / 3.10 ( 2475) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 338 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 ASP cc_start: 0.7419 (m-30) cc_final: 0.6865 (t0) REVERT: A 440 MET cc_start: 0.7148 (mtt) cc_final: 0.6842 (mtt) REVERT: A 479 MET cc_start: 0.2507 (mpp) cc_final: 0.2240 (pmm) REVERT: A 546 GLU cc_start: 0.6627 (pm20) cc_final: 0.5723 (tt0) REVERT: A 578 MET cc_start: 0.6969 (mmm) cc_final: 0.6665 (mmp) REVERT: A 716 ARG cc_start: 0.5146 (ttp-170) cc_final: 0.4063 (mmt-90) REVERT: B 578 MET cc_start: 0.6152 (mmt) cc_final: 0.5885 (ptt) REVERT: B 706 MET cc_start: 0.6677 (mmt) cc_final: 0.6389 (mtt) REVERT: C 293 ASP cc_start: 0.6811 (p0) cc_final: 0.5722 (m-30) REVERT: C 320 MET cc_start: 0.6947 (mmt) cc_final: 0.6585 (mmt) REVERT: C 355 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: C 369 ARG cc_start: 0.7373 (ptm-80) cc_final: 0.7098 (ptt-90) REVERT: C 563 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7829 (mp) REVERT: C 687 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6912 (mm-30) REVERT: C 736 GLU cc_start: 0.7424 (tt0) cc_final: 0.7024 (pt0) REVERT: D 159 MET cc_start: 0.6308 (mmm) cc_final: 0.5990 (mmt) REVERT: D 279 GLN cc_start: 0.7367 (tt0) cc_final: 0.7100 (mt0) REVERT: D 323 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6931 (ttm) REVERT: D 586 ASP cc_start: 0.7047 (t70) cc_final: 0.6669 (t0) REVERT: D 702 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6813 (mt-10) REVERT: D 716 ARG cc_start: 0.5562 (ttp-170) cc_final: 0.4723 (tpm170) outliers start: 40 outliers final: 16 residues processed: 366 average time/residue: 0.1528 time to fit residues: 88.0142 Evaluate side-chains 265 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 246 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 684 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 114 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 0.0770 chunk 47 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 24 optimal weight: 0.0870 chunk 120 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN A 216 GLN ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN B 178 ASN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN C 452 ASN D 452 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.224165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.173589 restraints weight = 22814.422| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.60 r_work: 0.3748 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22460 Z= 0.104 Angle : 0.523 7.912 30068 Z= 0.267 Chirality : 0.037 0.142 3236 Planarity : 0.004 0.051 3612 Dihedral : 19.233 155.491 4097 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.94 % Favored : 94.90 % Rotamer: Outliers : 2.39 % Allowed : 9.73 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.15), residues: 2488 helix: -1.45 (0.12), residues: 1604 sheet: -1.56 (0.55), residues: 84 loop : -2.49 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 698 TYR 0.013 0.001 TYR B 208 PHE 0.026 0.001 PHE B 489 TRP 0.012 0.001 TRP A 692 HIS 0.008 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (22456) covalent geometry : angle 0.52294 / 0.27 (30060) SS BOND : bond 0.00252 / 0.13 ( 4) SS BOND : angle 0.26891 / 0.18 ( 8) hydrogen bonds : bond 0.03570 / 2.32 ( 837) hydrogen bonds : angle 3.55173 / 2.51 ( 2475) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 297 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 216 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: A 293 ASP cc_start: 0.7444 (p0) cc_final: 0.6815 (p0) REVERT: A 340 ASP cc_start: 0.7634 (m-30) cc_final: 0.6983 (t0) REVERT: A 546 GLU cc_start: 0.6720 (pm20) cc_final: 0.6503 (pm20) REVERT: A 578 MET cc_start: 0.7081 (mmm) cc_final: 0.6829 (mmp) REVERT: A 716 ARG cc_start: 0.5315 (ttp-170) cc_final: 0.4089 (mmt-90) REVERT: B 279 GLN cc_start: 0.6897 (mt0) cc_final: 0.6689 (mt0) REVERT: B 319 ARG cc_start: 0.7312 (ttp80) cc_final: 0.6961 (mtm110) REVERT: B 488 MET cc_start: 0.7236 (mmp) cc_final: 0.7013 (mmp) REVERT: B 741 GLU cc_start: 0.7097 (tp30) cc_final: 0.6880 (tp30) REVERT: C 293 ASP cc_start: 0.6808 (p0) cc_final: 0.5744 (m-30) REVERT: C 369 ARG cc_start: 0.7545 (ptm-80) cc_final: 0.7117 (ptt-90) REVERT: C 569 PHE cc_start: 0.8201 (m-80) cc_final: 0.7962 (m-80) REVERT: C 687 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6879 (mm-30) REVERT: C 736 GLU cc_start: 0.7556 (tt0) cc_final: 0.7049 (pt0) REVERT: D 159 MET cc_start: 0.6083 (mmm) cc_final: 0.5861 (mmm) REVERT: D 293 ASP cc_start: 0.6945 (p0) cc_final: 0.6650 (p0) REVERT: D 338 ASN cc_start: 0.7920 (m-40) cc_final: 0.7314 (m-40) REVERT: D 450 PHE cc_start: 0.7359 (m-10) cc_final: 0.7131 (m-10) REVERT: D 495 MET cc_start: 0.6784 (mtp) cc_final: 0.6360 (mtt) REVERT: D 535 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6480 (tt) REVERT: D 586 ASP cc_start: 0.7267 (t70) cc_final: 0.6973 (t0) REVERT: D 677 MET cc_start: 0.5968 (tpt) cc_final: 0.5602 (mmt) REVERT: D 716 ARG cc_start: 0.5420 (ttp-170) cc_final: 0.4521 (mmt-90) REVERT: D 734 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7779 (mt) outliers start: 53 outliers final: 21 residues processed: 333 average time/residue: 0.1534 time to fit residues: 81.3553 Evaluate side-chains 275 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 251 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 1 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 136 optimal weight: 20.0000 chunk 109 optimal weight: 0.6980 chunk 239 optimal weight: 3.9990 chunk 243 optimal weight: 0.1980 chunk 245 optimal weight: 4.9990 chunk 246 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 ASN ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN C 178 ASN D 646 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.221297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.168336 restraints weight = 22784.384| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.46 r_work: 0.3667 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.7004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.142 22460 Z= 0.109 Angle : 0.521 7.926 30068 Z= 0.266 Chirality : 0.037 0.150 3236 Planarity : 0.004 0.060 3612 Dihedral : 18.008 152.256 4097 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.14 % Favored : 94.69 % Rotamer: Outliers : 2.39 % Allowed : 10.50 % Favored : 87.12 % 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: -1.79 (0.16), residues: 2488 helix: -0.56 (0.13), residues: 1580 sheet: -1.33 (0.56), residues: 84 loop : -2.27 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 690 TYR 0.015 0.001 TYR B 208 PHE 0.016 0.001 PHE B 316 TRP 0.012 0.001 TRP A 710 HIS 0.008 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (22456) covalent geometry : angle 0.51959 / 0.27 (30060) SS BOND : bond 0.00896 / 0.47 ( 4) SS BOND : angle 2.14819 / 1.24 ( 8) hydrogen bonds : bond 0.03056 / 1.94 ( 837) hydrogen bonds : angle 3.36677 / 2.40 ( 2475) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 278 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7748 (tm-30) REVERT: A 282 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7281 (mtm) REVERT: A 369 ARG cc_start: 0.6132 (ttp-110) cc_final: 0.5913 (ttp-110) REVERT: A 546 GLU cc_start: 0.6962 (pm20) cc_final: 0.6730 (mp0) REVERT: A 578 MET cc_start: 0.7478 (mmt) cc_final: 0.7162 (mmp) REVERT: A 716 ARG cc_start: 0.6049 (ttp-170) cc_final: 0.4871 (mmt-90) REVERT: B 279 GLN cc_start: 0.7222 (mt0) cc_final: 0.7016 (mt0) REVERT: B 319 ARG cc_start: 0.7711 (ttp80) cc_final: 0.7472 (mtm110) REVERT: B 343 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8131 (p) REVERT: B 536 SER cc_start: 0.7605 (t) cc_final: 0.7144 (m) REVERT: B 546 GLU cc_start: 0.6513 (tt0) cc_final: 0.6254 (mp0) REVERT: B 690 ARG cc_start: 0.7469 (ttt90) cc_final: 0.7017 (ttm-80) REVERT: C 293 ASP cc_start: 0.7308 (p0) cc_final: 0.5801 (m-30) REVERT: C 386 SER cc_start: 0.8598 (m) cc_final: 0.8372 (p) REVERT: C 535 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7094 (tt) REVERT: C 668 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7821 (mp) REVERT: C 736 GLU cc_start: 0.7815 (tt0) cc_final: 0.7234 (pt0) REVERT: D 159 MET cc_start: 0.6043 (mmm) cc_final: 0.5489 (mmt) REVERT: D 323 MET cc_start: 0.8137 (ttm) cc_final: 0.7912 (ttm) REVERT: D 338 ASN cc_start: 0.8091 (m-40) cc_final: 0.7449 (m-40) REVERT: D 450 PHE cc_start: 0.7539 (m-10) cc_final: 0.7300 (m-10) REVERT: D 495 MET cc_start: 0.6940 (mtp) cc_final: 0.6576 (mtt) REVERT: D 562 MET cc_start: 0.8993 (tpp) cc_final: 0.8781 (tpp) REVERT: D 716 ARG cc_start: 0.5967 (ttp-170) cc_final: 0.5147 (mmt-90) REVERT: D 734 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.7982 (mt) outliers start: 53 outliers final: 26 residues processed: 321 average time/residue: 0.1424 time to fit residues: 73.0272 Evaluate side-chains 275 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 247 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 94 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 167 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 ASN A 216 GLN A 274 GLN ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN C 178 ASN C 227 GLN D 452 ASN D 735 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.208624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.153936 restraints weight = 22548.943| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.70 r_work: 0.3508 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.9539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 22460 Z= 0.218 Angle : 0.742 10.500 30068 Z= 0.370 Chirality : 0.044 0.273 3236 Planarity : 0.005 0.079 3612 Dihedral : 18.447 146.433 4097 Min Nonbonded Distance : 1.441 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.63 % Favored : 94.17 % Rotamer: Outliers : 3.42 % Allowed : 10.05 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.60 (0.17), residues: 2488 helix: -0.39 (0.13), residues: 1588 sheet: -1.40 (0.54), residues: 92 loop : -2.21 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 462 TYR 0.023 0.002 TYR D 451 PHE 0.030 0.002 PHE B 666 TRP 0.016 0.002 TRP A 521 HIS 0.010 0.002 HIS D 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.22 (22456) covalent geometry : angle 0.73694 / 0.37 (30060) SS BOND : bond 0.01343 / 0.65 ( 4) SS BOND : angle 5.48088 / 3.24 ( 8) hydrogen bonds : bond 0.04944 / 3.22 ( 837) hydrogen bonds : angle 3.89582 / 2.75 ( 2475) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 302 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.7812 (tt0) cc_final: 0.7548 (tp30) REVERT: A 285 GLU cc_start: 0.7676 (pp20) cc_final: 0.7326 (pm20) REVERT: A 368 LYS cc_start: 0.8022 (tppt) cc_final: 0.7767 (mmtp) REVERT: A 369 ARG cc_start: 0.6939 (ttp-110) cc_final: 0.6638 (ttp-110) REVERT: A 385 VAL cc_start: 0.8185 (OUTLIER) cc_final: 0.7960 (m) REVERT: A 574 MET cc_start: 0.8662 (mtt) cc_final: 0.8153 (mtp) REVERT: A 578 MET cc_start: 0.7621 (mmm) cc_final: 0.7257 (mmp) REVERT: A 610 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6877 (mt-10) REVERT: A 716 ARG cc_start: 0.7264 (ttp-170) cc_final: 0.6242 (tpm170) REVERT: B 214 GLU cc_start: 0.7727 (tt0) cc_final: 0.7289 (tp30) REVERT: B 223 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8248 (mt) REVERT: B 279 GLN cc_start: 0.7768 (mt0) cc_final: 0.7556 (mt0) REVERT: B 280 LEU cc_start: 0.8265 (tt) cc_final: 0.8044 (tp) REVERT: B 320 MET cc_start: 0.8503 (mmt) cc_final: 0.8086 (mmt) REVERT: B 546 GLU cc_start: 0.7074 (tt0) cc_final: 0.6574 (mp0) REVERT: B 669 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8291 (mm) REVERT: B 690 ARG cc_start: 0.7799 (ttt90) cc_final: 0.7292 (ttm-80) REVERT: B 716 ARG cc_start: 0.7166 (ttp-170) cc_final: 0.6469 (tpm170) REVERT: B 741 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: C 289 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7686 (mt) REVERT: C 430 HIS cc_start: 0.7721 (t70) cc_final: 0.6928 (m90) REVERT: C 690 ARG cc_start: 0.6896 (ttp80) cc_final: 0.6612 (ttm-80) REVERT: C 736 GLU cc_start: 0.8175 (tt0) cc_final: 0.7346 (pt0) REVERT: D 159 MET cc_start: 0.5913 (mmm) cc_final: 0.5570 (mmt) REVERT: D 327 ARG cc_start: 0.7752 (tpt170) cc_final: 0.7479 (mmm-85) REVERT: D 430 HIS cc_start: 0.7764 (t70) cc_final: 0.6994 (m170) REVERT: D 495 MET cc_start: 0.7257 (mtp) cc_final: 0.6873 (mmt) REVERT: D 677 MET cc_start: 0.6832 (tpt) cc_final: 0.6548 (mmp) REVERT: D 716 ARG cc_start: 0.7399 (ttp-170) cc_final: 0.6496 (mmt-90) REVERT: D 734 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8106 (mt) REVERT: D 736 GLU cc_start: 0.8219 (tt0) cc_final: 0.7194 (pt0) outliers start: 76 outliers final: 26 residues processed: 361 average time/residue: 0.1604 time to fit residues: 90.3327 Evaluate side-chains 286 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 254 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 621 SER Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 734 ILE Chi-restraints excluded: chain D residue 756 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 130 optimal weight: 5.9990 chunk 55 optimal weight: 0.0060 chunk 124 optimal weight: 30.0000 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 163 optimal weight: 0.0980 chunk 112 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 GLN C 274 GLN C 646 GLN D 452 ASN D 570 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.212697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.159392 restraints weight = 22711.295| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.71 r_work: 0.3559 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.9681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 22460 Z= 0.100 Angle : 0.520 6.857 30068 Z= 0.268 Chirality : 0.037 0.158 3236 Planarity : 0.004 0.058 3612 Dihedral : 17.370 144.721 4097 Min Nonbonded Distance : 1.584 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.39 % Favored : 94.45 % Rotamer: Outliers : 1.62 % Allowed : 12.21 % Favored : 86.17 % 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: -1.03 (0.17), residues: 2488 helix: 0.16 (0.13), residues: 1588 sheet: -1.15 (0.56), residues: 84 loop : -2.25 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 369 TYR 0.015 0.001 TYR B 208 PHE 0.014 0.001 PHE B 316 TRP 0.013 0.001 TRP B 710 HIS 0.007 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (22456) covalent geometry : angle 0.51712 / 0.27 (30060) SS BOND : bond 0.01499 / 0.74 ( 4) SS BOND : angle 3.22592 / 1.77 ( 8) hydrogen bonds : bond 0.03060 / 1.98 ( 837) hydrogen bonds : angle 3.37721 / 2.40 ( 2475) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 273 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 214 GLU cc_start: 0.7797 (tt0) cc_final: 0.7452 (tp30) REVERT: A 285 GLU cc_start: 0.7737 (pp20) cc_final: 0.7211 (pm20) REVERT: A 369 ARG cc_start: 0.6848 (ttp-110) cc_final: 0.6494 (ttp80) REVERT: A 488 MET cc_start: 0.6800 (tpp) cc_final: 0.6560 (mmt) REVERT: A 574 MET cc_start: 0.8391 (mtt) cc_final: 0.8155 (mtt) REVERT: A 578 MET cc_start: 0.7564 (mmm) cc_final: 0.7205 (mmp) REVERT: A 716 ARG cc_start: 0.7227 (ttp-170) cc_final: 0.6145 (tpm170) REVERT: B 214 GLU cc_start: 0.7558 (tt0) cc_final: 0.7124 (tp30) REVERT: B 251 ASN cc_start: 0.7523 (OUTLIER) cc_final: 0.6481 (t0) REVERT: B 280 LEU cc_start: 0.8144 (tt) cc_final: 0.7923 (tp) REVERT: B 323 MET cc_start: 0.8826 (ttt) cc_final: 0.8618 (ttm) REVERT: B 430 HIS cc_start: 0.7700 (t70) cc_final: 0.6677 (m-70) REVERT: B 519 ASP cc_start: 0.6443 (OUTLIER) cc_final: 0.6199 (m-30) REVERT: B 546 GLU cc_start: 0.6913 (tt0) cc_final: 0.6410 (mp0) REVERT: B 669 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8094 (mm) REVERT: B 690 ARG cc_start: 0.7408 (ttt90) cc_final: 0.6931 (ttm-80) REVERT: B 716 ARG cc_start: 0.7091 (ttp-170) cc_final: 0.6453 (tpm170) REVERT: B 734 ILE cc_start: 0.8249 (pt) cc_final: 0.8032 (mt) REVERT: B 741 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: C 289 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7728 (mt) REVERT: C 338 ASN cc_start: 0.7418 (m-40) cc_final: 0.7081 (m-40) REVERT: C 369 ARG cc_start: 0.7622 (ttp-110) cc_final: 0.7349 (ttp80) REVERT: C 430 HIS cc_start: 0.7674 (t70) cc_final: 0.6892 (m90) REVERT: C 479 MET cc_start: 0.3874 (mmm) cc_final: 0.1660 (ptm) REVERT: C 734 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7882 (mt) REVERT: C 736 GLU cc_start: 0.8121 (tt0) cc_final: 0.7293 (pt0) REVERT: D 159 MET cc_start: 0.5632 (mmm) cc_final: 0.5276 (mmt) REVERT: D 327 ARG cc_start: 0.7611 (tpt170) cc_final: 0.7370 (mmm-85) REVERT: D 430 HIS cc_start: 0.7661 (t70) cc_final: 0.6935 (m170) REVERT: D 435 LYS cc_start: 0.8128 (mttp) cc_final: 0.7801 (tttt) REVERT: D 495 MET cc_start: 0.7089 (mtp) cc_final: 0.6757 (mmt) REVERT: D 586 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7278 (m-30) REVERT: D 677 MET cc_start: 0.6534 (tpt) cc_final: 0.6153 (mmp) REVERT: D 716 ARG cc_start: 0.7256 (ttp-170) cc_final: 0.6189 (mmt-90) REVERT: D 734 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.7975 (mt) REVERT: D 736 GLU cc_start: 0.8268 (tt0) cc_final: 0.7272 (pt0) outliers start: 36 outliers final: 18 residues processed: 297 average time/residue: 0.1581 time to fit residues: 74.1154 Evaluate side-chains 275 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 249 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 734 ILE Chi-restraints excluded: chain D residue 756 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 64 optimal weight: 4.9990 chunk 197 optimal weight: 0.8980 chunk 105 optimal weight: 0.2980 chunk 175 optimal weight: 5.9990 chunk 44 optimal weight: 0.0070 chunk 149 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 53 optimal weight: 0.0170 chunk 111 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.213183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.158709 restraints weight = 22612.902| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.59 r_work: 0.3536 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.9869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22460 Z= 0.087 Angle : 0.477 6.216 30068 Z= 0.246 Chirality : 0.036 0.143 3236 Planarity : 0.004 0.054 3612 Dihedral : 16.389 139.676 4097 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.10 % Favored : 94.73 % Rotamer: Outliers : 1.17 % Allowed : 13.24 % Favored : 85.59 % 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: -0.46 (0.17), residues: 2488 helix: 0.64 (0.14), residues: 1596 sheet: -0.75 (0.58), residues: 84 loop : -2.17 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 369 TYR 0.018 0.001 TYR D 208 PHE 0.014 0.001 PHE B 316 TRP 0.017 0.001 TRP B 710 HIS 0.008 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00184 / 0.09 (22456) covalent geometry : angle 0.47596 / 0.25 (30060) SS BOND : bond 0.00261 / 0.13 ( 4) SS BOND : angle 2.15840 / 1.22 ( 8) hydrogen bonds : bond 0.02608 / 1.67 ( 837) hydrogen bonds : angle 3.08478 / 2.18 ( 2475) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 268 time to evaluate : 0.791 Fit side-chains REVERT: A 214 GLU cc_start: 0.7797 (tt0) cc_final: 0.7490 (tp30) REVERT: A 257 GLU cc_start: 0.5689 (pm20) cc_final: 0.5353 (pt0) REVERT: A 285 GLU cc_start: 0.7748 (pp20) cc_final: 0.7311 (pm20) REVERT: A 488 MET cc_start: 0.6827 (tpp) cc_final: 0.6607 (mmt) REVERT: A 574 MET cc_start: 0.8127 (mtt) cc_final: 0.7894 (mtt) REVERT: A 578 MET cc_start: 0.7564 (mmm) cc_final: 0.7252 (mmp) REVERT: A 716 ARG cc_start: 0.7315 (ttp-170) cc_final: 0.6234 (tpm170) REVERT: A 732 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8279 (tp) REVERT: B 214 GLU cc_start: 0.7569 (tt0) cc_final: 0.7187 (tp30) REVERT: B 251 ASN cc_start: 0.7243 (OUTLIER) cc_final: 0.6672 (t0) REVERT: B 546 GLU cc_start: 0.7002 (tt0) cc_final: 0.6506 (mp0) REVERT: B 586 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7672 (m-30) REVERT: B 690 ARG cc_start: 0.7223 (ttt90) cc_final: 0.6785 (ttm-80) REVERT: B 716 ARG cc_start: 0.7012 (ttp-170) cc_final: 0.6561 (tpm170) REVERT: C 159 MET cc_start: 0.3833 (mtt) cc_final: 0.2067 (mmm) REVERT: C 289 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7612 (mt) REVERT: C 479 MET cc_start: 0.3786 (mmm) cc_final: 0.1672 (ptm) REVERT: C 734 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7724 (mt) REVERT: C 736 GLU cc_start: 0.8035 (tt0) cc_final: 0.7325 (pt0) REVERT: D 320 MET cc_start: 0.8126 (mmt) cc_final: 0.7806 (mmt) REVERT: D 430 HIS cc_start: 0.7723 (t70) cc_final: 0.7115 (m170) REVERT: D 435 LYS cc_start: 0.8118 (mttp) cc_final: 0.7830 (ttmt) REVERT: D 495 MET cc_start: 0.7230 (mtp) cc_final: 0.6915 (mmt) REVERT: D 546 GLU cc_start: 0.7574 (mm-30) cc_final: 0.6706 (mp0) REVERT: D 578 MET cc_start: 0.7545 (mmm) cc_final: 0.7224 (mmt) REVERT: D 677 MET cc_start: 0.6675 (tpt) cc_final: 0.6251 (mmp) REVERT: D 716 ARG cc_start: 0.7147 (ttp-170) cc_final: 0.6132 (mmt-90) REVERT: D 734 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.7903 (mt) REVERT: D 736 GLU cc_start: 0.8251 (tt0) cc_final: 0.7384 (pt0) outliers start: 26 outliers final: 16 residues processed: 288 average time/residue: 0.1626 time to fit residues: 73.5343 Evaluate side-chains 266 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 244 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 734 ILE Chi-restraints excluded: chain D residue 756 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 131 optimal weight: 8.9990 chunk 152 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 99 optimal weight: 0.0170 chunk 227 optimal weight: 6.9990 chunk 201 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 193 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 GLN B 646 GLN C 646 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.207026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.153575 restraints weight = 22471.542| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.50 r_work: 0.3491 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 1.0098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22460 Z= 0.105 Angle : 0.508 6.093 30068 Z= 0.260 Chirality : 0.037 0.145 3236 Planarity : 0.004 0.053 3612 Dihedral : 16.112 130.672 4097 Min Nonbonded Distance : 1.603 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.55 % Favored : 94.29 % Rotamer: Outliers : 1.62 % Allowed : 12.75 % Favored : 85.63 % 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: -0.29 (0.17), residues: 2488 helix: 0.82 (0.14), residues: 1588 sheet: -0.72 (0.56), residues: 84 loop : -2.16 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 416 TYR 0.014 0.001 TYR B 208 PHE 0.027 0.001 PHE B 489 TRP 0.016 0.001 TRP B 710 HIS 0.007 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (22456) covalent geometry : angle 0.50691 / 0.26 (30060) SS BOND : bond 0.00249 / 0.12 ( 4) SS BOND : angle 2.29715 / 1.30 ( 8) hydrogen bonds : bond 0.03028 / 1.96 ( 837) hydrogen bonds : angle 3.15693 / 2.23 ( 2475) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 257 time to evaluate : 0.817 Fit side-chains REVERT: A 188 ARG cc_start: 0.7802 (tpp80) cc_final: 0.7582 (ttp80) REVERT: A 214 GLU cc_start: 0.7889 (tt0) cc_final: 0.7479 (tp30) REVERT: A 279 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7380 (mt0) REVERT: A 285 GLU cc_start: 0.7792 (pp20) cc_final: 0.7333 (pm20) REVERT: A 338 ASN cc_start: 0.7960 (m-40) cc_final: 0.7599 (m-40) REVERT: A 488 MET cc_start: 0.6855 (tpp) cc_final: 0.6627 (mmt) REVERT: A 578 MET cc_start: 0.7603 (mmm) cc_final: 0.7283 (mmp) REVERT: A 716 ARG cc_start: 0.7339 (ttp-170) cc_final: 0.6268 (tpm170) REVERT: A 732 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8277 (tp) REVERT: A 734 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7907 (mt) REVERT: A 736 GLU cc_start: 0.8434 (tt0) cc_final: 0.7581 (pt0) REVERT: B 214 GLU cc_start: 0.7608 (tt0) cc_final: 0.7143 (tp30) REVERT: B 251 ASN cc_start: 0.7433 (OUTLIER) cc_final: 0.6624 (t0) REVERT: B 430 HIS cc_start: 0.7816 (t70) cc_final: 0.6893 (m90) REVERT: B 546 GLU cc_start: 0.7034 (tt0) cc_final: 0.6536 (mp0) REVERT: B 669 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8098 (mm) REVERT: B 690 ARG cc_start: 0.7263 (ttt90) cc_final: 0.6853 (ttm-80) REVERT: B 716 ARG cc_start: 0.7254 (ttp-170) cc_final: 0.6642 (tpm170) REVERT: B 741 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: C 159 MET cc_start: 0.3810 (mtt) cc_final: 0.2043 (mmp) REVERT: C 289 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7774 (mt) REVERT: C 479 MET cc_start: 0.3951 (mmm) cc_final: 0.1617 (ptm) REVERT: C 610 GLU cc_start: 0.7653 (mm-30) cc_final: 0.6378 (mt-10) REVERT: C 612 CYS cc_start: 0.5566 (OUTLIER) cc_final: 0.4767 (m) REVERT: C 690 ARG cc_start: 0.6753 (ttp80) cc_final: 0.6406 (ttm-80) REVERT: C 734 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7946 (mt) REVERT: C 736 GLU cc_start: 0.8101 (tt0) cc_final: 0.7321 (pt0) REVERT: D 369 ARG cc_start: 0.7104 (ttp-110) cc_final: 0.6852 (ttp-110) REVERT: D 430 HIS cc_start: 0.7752 (t70) cc_final: 0.7051 (m170) REVERT: D 435 LYS cc_start: 0.8139 (mttp) cc_final: 0.7803 (tttt) REVERT: D 546 GLU cc_start: 0.7562 (mm-30) cc_final: 0.6677 (mp0) REVERT: D 578 MET cc_start: 0.7535 (mmm) cc_final: 0.7204 (mmt) REVERT: D 677 MET cc_start: 0.6785 (tpt) cc_final: 0.6425 (mmp) REVERT: D 716 ARG cc_start: 0.7462 (ttp-170) cc_final: 0.6341 (tpm170) REVERT: D 732 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8265 (tp) REVERT: D 734 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.7986 (mt) REVERT: D 736 GLU cc_start: 0.8315 (tt0) cc_final: 0.7357 (pt0) outliers start: 36 outliers final: 18 residues processed: 283 average time/residue: 0.1618 time to fit residues: 71.1448 Evaluate side-chains 276 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 248 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 612 CYS Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 734 ILE Chi-restraints excluded: chain D residue 756 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 200 optimal weight: 4.9990 chunk 242 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 223 optimal weight: 0.0570 chunk 167 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 187 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.205949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.151871 restraints weight = 22370.681| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.23 r_work: 0.3482 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 1.0280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22460 Z= 0.089 Angle : 0.477 8.369 30068 Z= 0.245 Chirality : 0.036 0.169 3236 Planarity : 0.004 0.053 3612 Dihedral : 15.512 118.143 4097 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.31 % Favored : 94.53 % Rotamer: Outliers : 1.53 % Allowed : 13.02 % Favored : 85.45 % 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: -0.00 (0.18), residues: 2488 helix: 1.04 (0.14), residues: 1592 sheet: -0.54 (0.57), residues: 84 loop : -2.08 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 416 TYR 0.013 0.001 TYR B 208 PHE 0.023 0.001 PHE B 489 TRP 0.015 0.001 TRP B 710 HIS 0.010 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (22456) covalent geometry : angle 0.47645 / 0.24 (30060) SS BOND : bond 0.00126 / 0.06 ( 4) SS BOND : angle 1.93804 / 1.09 ( 8) hydrogen bonds : bond 0.02627 / 1.70 ( 837) hydrogen bonds : angle 3.01082 / 2.12 ( 2475) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 255 time to evaluate : 0.728 Fit side-chains REVERT: A 214 GLU cc_start: 0.7909 (tt0) cc_final: 0.7491 (tp30) REVERT: A 257 GLU cc_start: 0.5885 (pm20) cc_final: 0.5561 (pt0) REVERT: A 279 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7499 (mt0) REVERT: A 488 MET cc_start: 0.6839 (tpp) cc_final: 0.6639 (mmt) REVERT: A 578 MET cc_start: 0.7615 (mmm) cc_final: 0.7297 (mmp) REVERT: A 716 ARG cc_start: 0.7330 (ttp-170) cc_final: 0.6379 (mmt-90) REVERT: A 726 ASP cc_start: 0.7190 (m-30) cc_final: 0.6865 (t0) REVERT: A 732 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8300 (tp) REVERT: A 736 GLU cc_start: 0.8341 (tt0) cc_final: 0.7663 (pt0) REVERT: B 214 GLU cc_start: 0.7651 (tt0) cc_final: 0.7228 (tp30) REVERT: B 229 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.7103 (p0) REVERT: B 251 ASN cc_start: 0.7318 (OUTLIER) cc_final: 0.6687 (t0) REVERT: B 546 GLU cc_start: 0.6878 (tt0) cc_final: 0.6494 (mp0) REVERT: B 669 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8099 (mm) REVERT: B 690 ARG cc_start: 0.7125 (ttt90) cc_final: 0.6767 (ttm-80) REVERT: B 716 ARG cc_start: 0.7258 (ttp-170) cc_final: 0.6761 (tpm170) REVERT: C 159 MET cc_start: 0.4123 (mtt) cc_final: 0.2299 (mmp) REVERT: C 286 GLN cc_start: 0.8176 (mt0) cc_final: 0.7565 (mm-40) REVERT: C 289 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7783 (mt) REVERT: C 479 MET cc_start: 0.3942 (mmm) cc_final: 0.1675 (ptm) REVERT: C 610 GLU cc_start: 0.7690 (mm-30) cc_final: 0.6508 (mt-10) REVERT: C 612 CYS cc_start: 0.5653 (OUTLIER) cc_final: 0.4675 (m) REVERT: C 690 ARG cc_start: 0.6714 (ttp80) cc_final: 0.6417 (ttm-80) REVERT: C 716 ARG cc_start: 0.7186 (ttp-170) cc_final: 0.6122 (tpp-160) REVERT: C 734 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7767 (mt) REVERT: C 736 GLU cc_start: 0.7920 (tt0) cc_final: 0.7264 (pt0) REVERT: D 173 MET cc_start: 0.7071 (mtp) cc_final: 0.6787 (mtp) REVERT: D 369 ARG cc_start: 0.7101 (ttp-110) cc_final: 0.6804 (ttp80) REVERT: D 435 LYS cc_start: 0.8077 (mttp) cc_final: 0.7761 (tttt) REVERT: D 479 MET cc_start: 0.4895 (mmp) cc_final: 0.4535 (mtm) REVERT: D 495 MET cc_start: 0.7119 (mtp) cc_final: 0.6905 (mtt) REVERT: D 546 GLU cc_start: 0.7531 (mm-30) cc_final: 0.6740 (mp0) REVERT: D 578 MET cc_start: 0.7591 (mmm) cc_final: 0.7279 (mmt) REVERT: D 586 ASP cc_start: 0.7631 (t0) cc_final: 0.7429 (m-30) REVERT: D 716 ARG cc_start: 0.7459 (ttp-170) cc_final: 0.6476 (mmt-90) REVERT: D 734 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7876 (mt) REVERT: D 736 GLU cc_start: 0.8177 (tt0) cc_final: 0.7347 (pt0) outliers start: 34 outliers final: 20 residues processed: 280 average time/residue: 0.1549 time to fit residues: 67.9521 Evaluate side-chains 270 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 242 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 612 CYS Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 734 ILE Chi-restraints excluded: chain D residue 756 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 36 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 223 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 646 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.204055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.148095 restraints weight = 22609.588| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.81 r_work: 0.3374 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3396 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3396 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 1.0526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22460 Z= 0.116 Angle : 0.530 8.429 30068 Z= 0.268 Chirality : 0.038 0.158 3236 Planarity : 0.004 0.053 3612 Dihedral : 15.309 112.663 4097 Min Nonbonded Distance : 1.572 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.55 % Favored : 94.29 % Rotamer: Outliers : 1.26 % Allowed : 13.06 % Favored : 85.68 % 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: -0.02 (0.17), residues: 2488 helix: 1.03 (0.14), residues: 1588 sheet: -0.49 (0.57), residues: 84 loop : -2.08 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 416 TYR 0.015 0.001 TYR C 451 PHE 0.021 0.001 PHE B 489 TRP 0.018 0.001 TRP B 710 HIS 0.007 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (22456) covalent geometry : angle 0.52863 / 0.27 (30060) SS BOND : bond 0.00223 / 0.11 ( 4) SS BOND : angle 2.11760 / 1.19 ( 8) hydrogen bonds : bond 0.03184 / 2.07 ( 837) hydrogen bonds : angle 3.14877 / 2.21 ( 2475) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 260 time to evaluate : 0.832 Fit side-chains REVERT: A 188 ARG cc_start: 0.7595 (ttp80) cc_final: 0.7297 (mtt180) REVERT: A 257 GLU cc_start: 0.5997 (pm20) cc_final: 0.5568 (pt0) REVERT: A 279 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7558 (mt0) REVERT: A 338 ASN cc_start: 0.7988 (m-40) cc_final: 0.7343 (m-40) REVERT: A 488 MET cc_start: 0.6984 (tpp) cc_final: 0.6777 (mmt) REVERT: A 578 MET cc_start: 0.7597 (mmm) cc_final: 0.7274 (mmp) REVERT: A 716 ARG cc_start: 0.7350 (ttp-170) cc_final: 0.6289 (mmt-90) REVERT: A 726 ASP cc_start: 0.7255 (m-30) cc_final: 0.6907 (t0) REVERT: B 159 MET cc_start: 0.4872 (mmp) cc_final: 0.4305 (mmp) REVERT: B 229 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7157 (p0) REVERT: B 251 ASN cc_start: 0.7611 (OUTLIER) cc_final: 0.6675 (t0) REVERT: B 289 ILE cc_start: 0.8209 (mp) cc_final: 0.7800 (mt) REVERT: B 430 HIS cc_start: 0.7792 (t70) cc_final: 0.6840 (m90) REVERT: B 546 GLU cc_start: 0.6953 (tt0) cc_final: 0.6525 (mp0) REVERT: B 669 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8142 (mm) REVERT: B 690 ARG cc_start: 0.7292 (ttt90) cc_final: 0.6846 (ttm-80) REVERT: B 716 ARG cc_start: 0.7301 (ttp-170) cc_final: 0.6560 (tpm170) REVERT: C 159 MET cc_start: 0.4247 (mtt) cc_final: 0.2628 (mmp) REVERT: C 214 GLU cc_start: 0.7443 (tt0) cc_final: 0.7059 (tp30) REVERT: C 286 GLN cc_start: 0.8362 (mt0) cc_final: 0.7773 (mm-40) REVERT: C 289 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7954 (mt) REVERT: C 430 HIS cc_start: 0.7869 (t70) cc_final: 0.7061 (m90) REVERT: C 479 MET cc_start: 0.3953 (mmm) cc_final: 0.1619 (ptm) REVERT: C 610 GLU cc_start: 0.7713 (mm-30) cc_final: 0.6508 (mt-10) REVERT: C 612 CYS cc_start: 0.5624 (OUTLIER) cc_final: 0.4556 (m) REVERT: C 690 ARG cc_start: 0.6899 (ttp80) cc_final: 0.6692 (ttp80) REVERT: C 716 ARG cc_start: 0.7363 (ttp-170) cc_final: 0.6065 (mmt180) REVERT: C 734 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8002 (mt) REVERT: C 736 GLU cc_start: 0.8144 (tt0) cc_final: 0.7360 (pt0) REVERT: D 214 GLU cc_start: 0.7413 (tt0) cc_final: 0.7004 (tp30) REVERT: D 338 ASN cc_start: 0.8007 (m-40) cc_final: 0.7217 (m-40) REVERT: D 369 ARG cc_start: 0.7213 (ttp-110) cc_final: 0.6846 (ttp80) REVERT: D 435 LYS cc_start: 0.8163 (mttp) cc_final: 0.7773 (tttt) REVERT: D 546 GLU cc_start: 0.7570 (mm-30) cc_final: 0.6738 (mp0) REVERT: D 578 MET cc_start: 0.7584 (mmm) cc_final: 0.7288 (mmt) REVERT: D 586 ASP cc_start: 0.7835 (t0) cc_final: 0.7452 (m-30) REVERT: D 716 ARG cc_start: 0.7459 (ttp-170) cc_final: 0.6401 (tpm170) REVERT: D 732 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8311 (tp) REVERT: D 734 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7982 (mt) REVERT: D 736 GLU cc_start: 0.8316 (tt0) cc_final: 0.7373 (pt0) outliers start: 28 outliers final: 17 residues processed: 281 average time/residue: 0.1592 time to fit residues: 69.1724 Evaluate side-chains 273 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 248 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 612 CYS Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 734 ILE Chi-restraints excluded: chain D residue 756 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 20 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 122 optimal weight: 0.2980 chunk 169 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 180 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 570 GLN C 683 ASN D 178 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.214194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.159882 restraints weight = 22473.333| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.81 r_work: 0.3547 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 1.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22460 Z= 0.126 Angle : 0.543 8.519 30068 Z= 0.273 Chirality : 0.039 0.159 3236 Planarity : 0.004 0.053 3612 Dihedral : 15.240 111.444 4097 Min Nonbonded Distance : 1.569 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.31 % Favored : 94.53 % Rotamer: Outliers : 1.31 % Allowed : 13.29 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.17), residues: 2488 helix: 0.98 (0.14), residues: 1588 sheet: -0.55 (0.56), residues: 84 loop : -2.07 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 416 TYR 0.014 0.001 TYR C 451 PHE 0.021 0.001 PHE B 489 TRP 0.012 0.001 TRP B 710 HIS 0.007 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (22456) covalent geometry : angle 0.54175 / 0.27 (30060) SS BOND : bond 0.00205 / 0.10 ( 4) SS BOND : angle 2.07938 / 1.18 ( 8) hydrogen bonds : bond 0.03331 / 2.16 ( 837) hydrogen bonds : angle 3.24050 / 2.27 ( 2475) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6020.81 seconds wall clock time: 103 minutes 39.63 seconds (6219.63 seconds total)