Starting phenix.real_space_refine on Fri Aug 7 01:22:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30jw_57834/08_2026/30jw_57834.cif Found real_map, /net/cci-nas-00/data/ceres_data/30jw_57834/08_2026/30jw_57834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/30jw_57834/08_2026/30jw_57834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30jw_57834/08_2026/30jw_57834.map" model { file = "/net/cci-nas-00/data/ceres_data/30jw_57834/08_2026/30jw_57834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30jw_57834/08_2026/30jw_57834.cif" } resolution = 2.51 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= -0.000 sd= 0.008 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 120 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 11136 2.51 5 N 3068 2.21 5 O 3558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 17940 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4943 Classifications: {'peptide': 608} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 574} Chain breaks: 3 Chain: "B" Number of atoms: 4943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4943 Classifications: {'peptide': 608} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 574} Chain breaks: 3 Chain: "C" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2775 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 19, 'TRANS': 316} Chain breaks: 2 Chain: "D" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2775 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 19, 'TRANS': 316} Chain breaks: 2 Chain: "E" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 591 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "F" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 660 Classifications: {'DNA': 33} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 32} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan': 1, ' DA%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 591 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "H" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 660 Classifications: {'DNA': 33} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 32} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan': 1, ' DA%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.92, per 1000 atoms: 0.22 Number of scatterers: 17940 At special positions: 0 Unit cell: (152.75, 103.35, 118.3, 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 56 16.00 P 120 15.00 Mg 2 11.99 O 3558 8.00 N 3068 7.00 C 11136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.74 Conformation dependent library (CDL) restraints added in 766.4 milliseconds 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3620 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 18 sheets defined 47.2% alpha, 14.2% beta 56 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 31 through 43 removed outlier: 3.658A pdb=" N PHE A 39 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 94 through 110 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.689A pdb=" N TYR A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 159 Processing helix chain 'A' and resid 163 through 170 Processing helix chain 'A' and resid 173 through 188 Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.787A pdb=" N VAL A 262 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 278 through 299 Processing helix chain 'A' and resid 304 through 316 Proline residue: A 310 - end of helix Processing helix chain 'A' and resid 325 through 339 Processing helix chain 'A' and resid 342 through 347 Processing helix chain 'A' and resid 363 through 375 Processing helix chain 'A' and resid 381 through 399 removed outlier: 4.338A pdb=" N SER A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 419 Processing helix chain 'A' and resid 421 through 439 removed outlier: 3.505A pdb=" N VAL A 425 " --> pdb=" O PRO A 421 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LYS A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 9.483A pdb=" N PHE A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS A 434 " --> pdb=" O HIS A 430 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TRP A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 515 Processing helix chain 'A' and resid 518 through 522 removed outlier: 4.154A pdb=" N ALA A 521 " --> pdb=" O SER A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 559 Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.645A pdb=" N ARG A 579 " --> pdb=" O PRO A 575 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 630 Processing helix chain 'A' and resid 642 through 654 removed outlier: 3.514A pdb=" N ALA A 653 " --> pdb=" O GLN A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'B' and resid 31 through 43 removed outlier: 3.658A pdb=" N PHE B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 43 " --> pdb=" O PHE B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 94 through 110 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 127 through 138 removed outlier: 3.688A pdb=" N TYR B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 159 Processing helix chain 'B' and resid 163 through 170 Processing helix chain 'B' and resid 173 through 188 Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.787A pdb=" N VAL B 262 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 277 Processing helix chain 'B' and resid 278 through 299 Processing helix chain 'B' and resid 304 through 316 Proline residue: B 310 - end of helix Processing helix chain 'B' and resid 325 through 339 Processing helix chain 'B' and resid 342 through 347 Processing helix chain 'B' and resid 363 through 375 Processing helix chain 'B' and resid 381 through 399 removed outlier: 4.338A pdb=" N SER B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 419 Processing helix chain 'B' and resid 421 through 439 removed outlier: 3.504A pdb=" N VAL B 425 " --> pdb=" O PRO B 421 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LYS B 432 " --> pdb=" O ALA B 428 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N PHE B 433 " --> pdb=" O ARG B 429 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS B 434 " --> pdb=" O HIS B 430 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TRP B 438 " --> pdb=" O LYS B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 515 Processing helix chain 'B' and resid 518 through 522 removed outlier: 4.155A pdb=" N ALA B 521 " --> pdb=" O SER B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 559 Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.645A pdb=" N ARG B 579 " --> pdb=" O PRO B 575 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE B 580 " --> pdb=" O PHE B 576 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 630 Processing helix chain 'B' and resid 642 through 654 removed outlier: 3.514A pdb=" N ALA B 653 " --> pdb=" O GLN B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'C' and resid 501 through 515 removed outlier: 3.859A pdb=" N SER C 505 " --> pdb=" O PRO C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 522 Processing helix chain 'C' and resid 549 through 559 removed outlier: 3.598A pdb=" N ALA C 559 " --> pdb=" O ALA C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 584 removed outlier: 4.138A pdb=" N ARG C 579 " --> pdb=" O PRO C 575 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE C 580 " --> pdb=" O PHE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 630 Processing helix chain 'C' and resid 642 through 654 Processing helix chain 'C' and resid 660 through 669 removed outlier: 3.706A pdb=" N ARG C 666 " --> pdb=" O GLU C 662 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE C 667 " --> pdb=" O GLU C 663 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 668 " --> pdb=" O GLU C 664 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N MET C 669 " --> pdb=" O THR C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 672 No H-bonds generated for 'chain 'C' and resid 670 through 672' Processing helix chain 'C' and resid 693 through 703 Processing helix chain 'C' and resid 750 through 769 Processing helix chain 'C' and resid 770 through 795 Processing helix chain 'D' and resid 501 through 515 removed outlier: 3.859A pdb=" N SER D 505 " --> pdb=" O PRO D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 522 Processing helix chain 'D' and resid 549 through 559 removed outlier: 3.582A pdb=" N ALA D 559 " --> pdb=" O ALA D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 584 removed outlier: 4.165A pdb=" N ARG D 579 " --> pdb=" O PRO D 575 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE D 580 " --> pdb=" O PHE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 630 Processing helix chain 'D' and resid 642 through 654 Processing helix chain 'D' and resid 660 through 669 removed outlier: 3.722A pdb=" N ARG D 666 " --> pdb=" O GLU D 662 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE D 667 " --> pdb=" O GLU D 663 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER D 668 " --> pdb=" O GLU D 664 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N MET D 669 " --> pdb=" O THR D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 672 No H-bonds generated for 'chain 'D' and resid 670 through 672' Processing helix chain 'D' and resid 693 through 703 Processing helix chain 'D' and resid 750 through 769 Processing helix chain 'D' and resid 770 through 795 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 29 removed outlier: 3.916A pdb=" N VAL A 15 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL A 455 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ASP A 542 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N ILE A 457 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY A 493 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASP A 485 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL A 491 " --> pdb=" O ASP A 485 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.396A pdb=" N TYR A 83 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 118 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLU A 85 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 57 through 60 removed outlier: 3.574A pdb=" N PHE A 57 " --> pdb=" O TYR A 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 271 removed outlier: 7.102A pdb=" N LYS C 723 " --> pdb=" O ASP C 717 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP C 717 " --> pdb=" O LYS C 723 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU C 713 " --> pdb=" O TYR C 727 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 474 through 476 removed outlier: 6.961A pdb=" N LEU A 466 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 26 through 29 removed outlier: 3.916A pdb=" N VAL B 15 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL B 455 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ASP B 542 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N ILE B 457 " --> pdb=" O ASP B 542 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 493 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASP B 485 " --> pdb=" O VAL B 491 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL B 491 " --> pdb=" O ASP B 485 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.396A pdb=" N TYR B 83 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL B 118 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLU B 85 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 60 removed outlier: 3.573A pdb=" N PHE B 57 " --> pdb=" O TYR B 68 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AB2, first strand: chain 'B' and resid 270 through 271 removed outlier: 7.101A pdb=" N LYS D 723 " --> pdb=" O ASP D 717 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASP D 717 " --> pdb=" O LYS D 723 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU D 713 " --> pdb=" O TYR D 727 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 474 through 476 removed outlier: 6.961A pdb=" N LEU B 466 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 491 through 497 removed outlier: 6.604A pdb=" N VAL C 491 " --> pdb=" O ASP C 485 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ASP C 485 " --> pdb=" O VAL C 491 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY C 493 " --> pdb=" O LEU C 483 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL C 455 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N ASP C 542 " --> pdb=" O VAL C 455 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N ILE C 457 " --> pdb=" O ASP C 542 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU C 539 " --> pdb=" O GLN C 564 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ASN C 566 " --> pdb=" O LEU C 539 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL C 541 " --> pdb=" O ASN C 566 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 474 through 476 removed outlier: 7.011A pdb=" N LEU C 466 " --> pdb=" O ILE C 475 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET C 614 " --> pdb=" O ILE C 465 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 684 through 686 Processing sheet with id=AB7, first strand: chain 'D' and resid 491 through 497 removed outlier: 6.618A pdb=" N VAL D 491 " --> pdb=" O ASP D 485 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASP D 485 " --> pdb=" O VAL D 491 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY D 493 " --> pdb=" O LEU D 483 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL D 455 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N ASP D 542 " --> pdb=" O VAL D 455 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N ILE D 457 " --> pdb=" O ASP D 542 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU D 539 " --> pdb=" O GLN D 564 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ASN D 566 " --> pdb=" O LEU D 539 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL D 541 " --> pdb=" O ASN D 566 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 474 through 476 removed outlier: 7.009A pdb=" N LEU D 466 " --> pdb=" O ILE D 475 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET D 614 " --> pdb=" O ILE D 465 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 684 through 686 712 hydrogen bonds defined for protein. 2022 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 142 hydrogen bonds 284 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 4.05 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4487 1.33 - 1.45: 4134 1.45 - 1.57: 9679 1.57 - 1.69: 240 1.69 - 1.81: 90 Bond restraints: 18630 Sorted by residual: bond pdb=" C3' DG E -6 " pdb=" C2' DG E -6 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" C3' DG G -6 " pdb=" C2' DG G -6 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 bond pdb=" C3' DA G -1 " pdb=" C2' DA G -1 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DA E -1 " pdb=" C2' DA E -1 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C1' DT F 1 " pdb=" N1 DT F 1 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.30e+00 ... (remaining 18625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 25105 1.95 - 3.90: 574 3.90 - 5.85: 31 5.85 - 7.80: 22 7.80 - 9.76: 6 Bond angle restraints: 25738 Sorted by residual: angle pdb=" N3 DT E -16 " pdb=" C4 DT E -16 " pdb=" O4 DT E -16 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.07e+01 angle pdb=" N3 DT G -16 " pdb=" C4 DT G -16 " pdb=" O4 DT G -16 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT E -26 " pdb=" C4 DT E -26 " pdb=" O4 DT E -26 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT E -22 " pdb=" C4 DT E -22 " pdb=" O4 DT E -22 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT G -22 " pdb=" C4 DT G -22 " pdb=" O4 DT G -22 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 ... (remaining 25733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 10135 35.76 - 71.52: 731 71.52 - 107.28: 22 107.28 - 143.04: 8 143.04 - 178.79: 2 Dihedral angle restraints: 10898 sinusoidal: 5322 harmonic: 5576 Sorted by residual: dihedral pdb=" C4' DT E -26 " pdb=" C3' DT E -26 " pdb=" O3' DT E -26 " pdb=" P DA E -25 " ideal model delta sinusoidal sigma weight residual -140.00 38.79 -178.79 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT G -26 " pdb=" C3' DT G -26 " pdb=" O3' DT G -26 " pdb=" P DA G -25 " ideal model delta sinusoidal sigma weight residual -140.00 38.29 -178.29 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC G -17 " pdb=" C3' DC G -17 " pdb=" O3' DC G -17 " pdb=" P DT G -16 " ideal model delta sinusoidal sigma weight residual 220.00 79.27 140.73 1 3.50e+01 8.16e-04 1.39e+01 ... (remaining 10895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1848 0.034 - 0.068: 620 0.068 - 0.102: 236 0.102 - 0.137: 84 0.137 - 0.171: 16 Chirality restraints: 2804 Sorted by residual: chirality pdb=" CG LEU A 312 " pdb=" CB LEU A 312 " pdb=" CD1 LEU A 312 " pdb=" CD2 LEU A 312 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CG LEU B 312 " pdb=" CB LEU B 312 " pdb=" CD1 LEU B 312 " pdb=" CD2 LEU B 312 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.10e-01 chirality pdb=" CA GLU A 60 " pdb=" N GLU A 60 " pdb=" C GLU A 60 " pdb=" CB GLU A 60 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 2801 not shown) Planarity restraints: 2862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 661 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.86e+00 pdb=" CD GLU D 661 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU D 661 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU D 661 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 83 " 0.016 2.00e-02 2.50e+03 1.29e-02 3.33e+00 pdb=" CG TYR B 83 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 83 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 83 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 83 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B 83 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 83 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 83 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 83 " -0.016 2.00e-02 2.50e+03 1.28e-02 3.29e+00 pdb=" CG TYR A 83 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 83 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 83 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 83 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 83 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 83 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 83 " 0.000 2.00e-02 2.50e+03 ... (remaining 2859 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 37 2.60 - 3.17: 14797 3.17 - 3.75: 30459 3.75 - 4.32: 41742 4.32 - 4.90: 65800 Nonbonded interactions: 152835 Sorted by model distance: nonbonded pdb=" O TYR B 86 " pdb="MG MG B1000 " model vdw 2.024 2.170 nonbonded pdb=" O TYR A 86 " pdb="MG MG A1000 " model vdw 2.025 2.170 nonbonded pdb=" OP2 DA H -2 " pdb="MG MG B1000 " model vdw 2.078 2.170 nonbonded pdb=" OP2 DA F -2 " pdb="MG MG A1000 " model vdw 2.078 2.170 nonbonded pdb=" OD2 ASP B 71 " pdb="MG MG B1000 " model vdw 2.110 2.170 ... (remaining 152830 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } 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=1.00 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: 10.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.190 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 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 : 0.004 0.043 18630 Z= 0.307 Angle : 0.655 9.756 25738 Z= 0.447 Chirality : 0.044 0.171 2804 Planarity : 0.004 0.044 2862 Dihedral : 20.694 178.795 7278 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.47 % Allowed : 22.61 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.27 (0.19), residues: 1860 helix: 1.81 (0.18), residues: 804 sheet: 0.21 (0.32), residues: 264 loop : 0.16 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 379 TYR 0.031 0.001 TYR B 83 PHE 0.022 0.001 PHE A 667 TRP 0.006 0.001 TRP C 647 HIS 0.010 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.31 (18630) covalent geometry : angle 0.65456 / 0.45 (25738) hydrogen bonds : bond 0.13955 / 8.96 ( 854) hydrogen bonds : angle 5.71950 / 4.12 ( 2306) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.8367 (tmm) cc_final: 0.8060 (tmm) REVERT: A 30 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8026 (tt0) REVERT: A 48 GLU cc_start: 0.8522 (pt0) cc_final: 0.8032 (pp20) REVERT: A 65 SER cc_start: 0.8817 (OUTLIER) cc_final: 0.8615 (t) REVERT: A 193 ASP cc_start: 0.8215 (t0) cc_final: 0.7916 (t70) REVERT: B 28 MET cc_start: 0.8362 (tmm) cc_final: 0.8050 (tmm) REVERT: B 30 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8028 (tt0) REVERT: B 48 GLU cc_start: 0.8518 (pt0) cc_final: 0.8037 (pp20) REVERT: B 65 SER cc_start: 0.8819 (OUTLIER) cc_final: 0.8612 (t) REVERT: B 193 ASP cc_start: 0.8214 (t0) cc_final: 0.7917 (t70) REVERT: C 569 ARG cc_start: 0.8832 (mmm160) cc_final: 0.8593 (mmm160) REVERT: C 614 MET cc_start: 0.8875 (ptp) cc_final: 0.8657 (ptm) REVERT: C 661 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8067 (tm-30) REVERT: D 614 MET cc_start: 0.8931 (ptp) cc_final: 0.8690 (ptm) REVERT: D 649 GLN cc_start: 0.8993 (pp30) cc_final: 0.8743 (pp30) outliers start: 25 outliers final: 13 residues processed: 122 average time/residue: 0.6594 time to fit residues: 89.8492 Evaluate side-chains 120 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain C residue 490 CYS Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain D residue 490 CYS Chi-restraints excluded: chain D residue 551 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.112466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.076479 restraints weight = 33382.174| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.51 r_work: 0.2987 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.0496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18630 Z= 0.153 Angle : 0.581 10.198 25738 Z= 0.312 Chirality : 0.042 0.234 2804 Planarity : 0.004 0.037 2862 Dihedral : 22.336 176.129 3413 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.18 % Allowed : 19.79 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.40 (0.19), residues: 1860 helix: 1.97 (0.18), residues: 810 sheet: 0.16 (0.29), residues: 296 loop : 0.20 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 379 TYR 0.019 0.001 TYR A 389 PHE 0.012 0.001 PHE A 50 TRP 0.009 0.001 TRP B 548 HIS 0.005 0.001 HIS A 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (18630) covalent geometry : angle 0.58056 / 0.31 (25738) hydrogen bonds : bond 0.04470 / 2.88 ( 854) hydrogen bonds : angle 4.61723 / 3.33 ( 2306) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 105 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.8468 (tmm) cc_final: 0.8232 (tmm) REVERT: A 30 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8143 (mm-30) REVERT: A 48 GLU cc_start: 0.8633 (pt0) cc_final: 0.8190 (pp20) REVERT: A 83 TYR cc_start: 0.7363 (OUTLIER) cc_final: 0.7046 (t80) REVERT: A 193 ASP cc_start: 0.8305 (t0) cc_final: 0.8065 (t70) REVERT: B 28 MET cc_start: 0.8471 (tmm) cc_final: 0.8234 (tmm) REVERT: B 30 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8149 (mm-30) REVERT: B 48 GLU cc_start: 0.8622 (pt0) cc_final: 0.8185 (pp20) REVERT: B 83 TYR cc_start: 0.7362 (OUTLIER) cc_final: 0.7090 (t80) REVERT: B 193 ASP cc_start: 0.8319 (t0) cc_final: 0.8078 (t70) REVERT: C 661 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8151 (tm-30) outliers start: 54 outliers final: 18 residues processed: 154 average time/residue: 0.6035 time to fit residues: 104.6512 Evaluate side-chains 122 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain C residue 490 CYS Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 669 MET Chi-restraints excluded: chain D residue 490 CYS Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 668 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 125 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 140 optimal weight: 0.0670 chunk 152 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 40 optimal weight: 0.0070 chunk 137 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 83 optimal weight: 0.2980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 702 HIS D 702 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.113445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.077614 restraints weight = 33786.735| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.55 r_work: 0.3010 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18630 Z= 0.117 Angle : 0.552 8.719 25738 Z= 0.297 Chirality : 0.041 0.243 2804 Planarity : 0.004 0.040 2862 Dihedral : 22.386 175.296 3402 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.71 % Allowed : 20.67 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.48 (0.19), residues: 1860 helix: 2.05 (0.18), residues: 810 sheet: 0.19 (0.29), residues: 296 loop : 0.24 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 379 TYR 0.017 0.001 TYR A 389 PHE 0.010 0.001 PHE B 50 TRP 0.006 0.001 TRP B 548 HIS 0.009 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.12 (18630) covalent geometry : angle 0.55168 / 0.30 (25738) hydrogen bonds : bond 0.03901 / 2.50 ( 854) hydrogen bonds : angle 4.37313 / 3.16 ( 2306) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 112 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.8457 (tmm) cc_final: 0.8192 (tmm) REVERT: A 30 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8314 (mt-10) REVERT: A 48 GLU cc_start: 0.8629 (pt0) cc_final: 0.8196 (pp20) REVERT: A 83 TYR cc_start: 0.7342 (OUTLIER) cc_final: 0.7103 (t80) REVERT: A 193 ASP cc_start: 0.8314 (t0) cc_final: 0.8003 (t70) REVERT: B 28 MET cc_start: 0.8454 (tmm) cc_final: 0.8186 (tmm) REVERT: B 30 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8325 (mt-10) REVERT: B 48 GLU cc_start: 0.8622 (pt0) cc_final: 0.8182 (pp20) REVERT: B 83 TYR cc_start: 0.7324 (OUTLIER) cc_final: 0.7085 (t80) REVERT: B 193 ASP cc_start: 0.8330 (t0) cc_final: 0.8018 (t70) REVERT: C 661 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8140 (tm-30) REVERT: C 709 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8904 (p) REVERT: D 709 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8908 (p) outliers start: 46 outliers final: 17 residues processed: 155 average time/residue: 0.6427 time to fit residues: 111.0373 Evaluate side-chains 123 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain C residue 490 CYS Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 669 MET Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain D residue 490 CYS Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 793 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 60 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 191 optimal weight: 20.0000 chunk 33 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 119 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 HIS ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS C 632 HIS C 649 GLN C 789 GLN D 632 HIS D 649 GLN D 789 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.108995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.072522 restraints weight = 33642.191| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.51 r_work: 0.2908 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 18630 Z= 0.274 Angle : 0.645 8.418 25738 Z= 0.340 Chirality : 0.046 0.249 2804 Planarity : 0.004 0.049 2862 Dihedral : 22.822 177.296 3398 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.77 % Allowed : 19.26 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.32 (0.20), residues: 1860 helix: 1.94 (0.18), residues: 812 sheet: -0.04 (0.29), residues: 306 loop : 0.21 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 379 TYR 0.024 0.002 TYR A 389 PHE 0.016 0.002 PHE B 439 TRP 0.010 0.002 TRP B 548 HIS 0.011 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.27 (18630) covalent geometry : angle 0.64526 / 0.34 (25738) hydrogen bonds : bond 0.04705 / 3.00 ( 854) hydrogen bonds : angle 4.45294 / 3.22 ( 2306) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 101 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.8380 (tmm) cc_final: 0.8141 (tmm) REVERT: A 30 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8320 (mt-10) REVERT: A 48 GLU cc_start: 0.8679 (pt0) cc_final: 0.8243 (pp20) REVERT: A 83 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.7161 (t80) REVERT: A 193 ASP cc_start: 0.8375 (t0) cc_final: 0.8136 (t70) REVERT: B 28 MET cc_start: 0.8376 (tmm) cc_final: 0.8133 (tmm) REVERT: B 30 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8324 (mt-10) REVERT: B 48 GLU cc_start: 0.8679 (pt0) cc_final: 0.8242 (pp20) REVERT: B 83 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.7160 (t80) REVERT: B 193 ASP cc_start: 0.8379 (t0) cc_final: 0.8148 (t70) REVERT: C 456 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7655 (tp30) REVERT: C 552 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9010 (tt) REVERT: C 649 GLN cc_start: 0.9222 (OUTLIER) cc_final: 0.8974 (pp30) REVERT: C 661 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8155 (tm-30) REVERT: D 456 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7654 (tp30) REVERT: D 552 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9010 (tt) outliers start: 64 outliers final: 27 residues processed: 158 average time/residue: 0.6165 time to fit residues: 108.6422 Evaluate side-chains 131 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 645 LYS Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 490 CYS Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 649 GLN Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain D residue 490 CYS Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 668 SER Chi-restraints excluded: chain D residue 674 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 50 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 18 optimal weight: 0.0870 chunk 194 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 649 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.111471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.075404 restraints weight = 33486.430| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.53 r_work: 0.2967 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18630 Z= 0.125 Angle : 0.568 10.361 25738 Z= 0.301 Chirality : 0.042 0.242 2804 Planarity : 0.004 0.046 2862 Dihedral : 22.696 174.509 3398 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.77 % Allowed : 21.55 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.40 (0.19), residues: 1860 helix: 2.02 (0.18), residues: 810 sheet: 0.04 (0.30), residues: 286 loop : 0.19 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 379 TYR 0.017 0.001 TYR B 389 PHE 0.011 0.001 PHE B 439 TRP 0.012 0.001 TRP C 647 HIS 0.006 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 (18630) covalent geometry : angle 0.56817 / 0.30 (25738) hydrogen bonds : bond 0.03747 / 2.40 ( 854) hydrogen bonds : angle 4.20790 / 3.05 ( 2306) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 103 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.8378 (tmm) cc_final: 0.8155 (tmm) REVERT: A 30 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8181 (mm-30) REVERT: A 48 GLU cc_start: 0.8667 (pt0) cc_final: 0.8222 (pp20) REVERT: A 83 TYR cc_start: 0.7349 (OUTLIER) cc_final: 0.7125 (t80) REVERT: A 121 ARG cc_start: 0.9410 (mmt90) cc_final: 0.9163 (mmt90) REVERT: A 193 ASP cc_start: 0.8395 (t0) cc_final: 0.8112 (t70) REVERT: A 669 MET cc_start: 0.8885 (tmm) cc_final: 0.8656 (pp-130) REVERT: B 28 MET cc_start: 0.8363 (tmm) cc_final: 0.8144 (tmm) REVERT: B 30 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8206 (mm-30) REVERT: B 48 GLU cc_start: 0.8661 (pt0) cc_final: 0.8220 (pp20) REVERT: B 193 ASP cc_start: 0.8367 (t0) cc_final: 0.8067 (t70) REVERT: B 669 MET cc_start: 0.8879 (tmm) cc_final: 0.8648 (pp-130) REVERT: C 456 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7776 (tp30) REVERT: C 552 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9006 (tt) REVERT: C 614 MET cc_start: 0.8791 (ptp) cc_final: 0.8562 (ptm) REVERT: C 661 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8102 (tm-30) REVERT: D 552 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9008 (tt) REVERT: D 649 GLN cc_start: 0.8988 (pp30) cc_final: 0.8705 (pp30) outliers start: 47 outliers final: 17 residues processed: 142 average time/residue: 0.6433 time to fit residues: 101.1064 Evaluate side-chains 117 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 490 CYS Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain D residue 490 CYS Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 669 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 27 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 85 optimal weight: 0.0030 chunk 28 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 145 optimal weight: 0.5980 chunk 188 optimal weight: 10.0000 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 789 GLN D 789 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.111534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.075435 restraints weight = 33238.199| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.52 r_work: 0.2965 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18630 Z= 0.136 Angle : 0.561 11.681 25738 Z= 0.297 Chirality : 0.041 0.240 2804 Planarity : 0.004 0.045 2862 Dihedral : 22.586 174.511 3398 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.12 % Allowed : 22.14 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.51 (0.20), residues: 1860 helix: 2.08 (0.18), residues: 814 sheet: 0.17 (0.29), residues: 296 loop : 0.25 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 379 TYR 0.017 0.001 TYR B 389 PHE 0.010 0.001 PHE B 367 TRP 0.008 0.001 TRP C 647 HIS 0.012 0.001 HIS A 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (18630) covalent geometry : angle 0.56110 / 0.30 (25738) hydrogen bonds : bond 0.03655 / 2.34 ( 854) hydrogen bonds : angle 4.15465 / 3.01 ( 2306) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.8412 (tmm) cc_final: 0.8182 (tmm) REVERT: A 30 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8222 (mm-30) REVERT: A 48 GLU cc_start: 0.8665 (pt0) cc_final: 0.8237 (pp20) REVERT: A 83 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.7162 (t80) REVERT: A 193 ASP cc_start: 0.8396 (t0) cc_final: 0.8118 (t70) REVERT: A 669 MET cc_start: 0.8881 (tmm) cc_final: 0.8664 (pp-130) REVERT: B 28 MET cc_start: 0.8431 (tmm) cc_final: 0.8061 (tmm) REVERT: B 48 GLU cc_start: 0.8676 (pt0) cc_final: 0.8244 (pp20) REVERT: B 83 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.7016 (t80) REVERT: B 121 ARG cc_start: 0.9401 (mmt90) cc_final: 0.9155 (mmt90) REVERT: B 193 ASP cc_start: 0.8395 (t0) cc_final: 0.8114 (t70) REVERT: B 669 MET cc_start: 0.8856 (tmm) cc_final: 0.8628 (pp-130) REVERT: C 456 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7839 (tp30) REVERT: C 552 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9084 (tt) REVERT: C 661 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8110 (tm-30) REVERT: D 552 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9086 (tt) REVERT: D 649 GLN cc_start: 0.9012 (pp30) cc_final: 0.8708 (pp30) outliers start: 36 outliers final: 21 residues processed: 133 average time/residue: 0.6660 time to fit residues: 97.6705 Evaluate side-chains 124 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 490 CYS Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 669 MET Chi-restraints excluded: chain D residue 490 CYS Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 668 SER Chi-restraints excluded: chain D residue 669 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 142 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 108 optimal weight: 0.0980 chunk 5 optimal weight: 0.2980 chunk 181 optimal weight: 0.9980 chunk 189 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 147 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.112129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.076177 restraints weight = 33543.844| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.53 r_work: 0.2980 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18630 Z= 0.121 Angle : 0.563 13.298 25738 Z= 0.298 Chirality : 0.041 0.239 2804 Planarity : 0.003 0.045 2862 Dihedral : 22.556 174.063 3398 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.00 % Allowed : 21.85 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.53 (0.20), residues: 1860 helix: 2.09 (0.18), residues: 814 sheet: 0.26 (0.29), residues: 292 loop : 0.24 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 379 TYR 0.016 0.001 TYR A 389 PHE 0.010 0.001 PHE B 439 TRP 0.012 0.001 TRP C 647 HIS 0.010 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (18630) covalent geometry : angle 0.56316 / 0.30 (25738) hydrogen bonds : bond 0.03504 / 2.24 ( 854) hydrogen bonds : angle 4.08748 / 2.97 ( 2306) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.8418 (tmm) cc_final: 0.8118 (tmm) REVERT: A 48 GLU cc_start: 0.8668 (pt0) cc_final: 0.8226 (pp20) REVERT: A 83 TYR cc_start: 0.7363 (OUTLIER) cc_final: 0.7082 (t80) REVERT: A 121 ARG cc_start: 0.9397 (mmt90) cc_final: 0.8908 (mtt-85) REVERT: A 193 ASP cc_start: 0.8387 (t0) cc_final: 0.8112 (t70) REVERT: A 669 MET cc_start: 0.8916 (tmm) cc_final: 0.8704 (pp-130) REVERT: B 28 MET cc_start: 0.8409 (tmm) cc_final: 0.8112 (tmm) REVERT: B 48 GLU cc_start: 0.8671 (pt0) cc_final: 0.8238 (pp20) REVERT: B 121 ARG cc_start: 0.9397 (mmt90) cc_final: 0.9154 (mmt90) REVERT: B 193 ASP cc_start: 0.8385 (t0) cc_final: 0.8113 (t70) REVERT: B 669 MET cc_start: 0.8920 (tmm) cc_final: 0.8701 (pp-130) REVERT: C 552 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9126 (tt) REVERT: C 569 ARG cc_start: 0.8844 (mmm160) cc_final: 0.8606 (mmm160) REVERT: C 661 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8087 (tm-30) REVERT: D 552 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9131 (tt) REVERT: D 569 ARG cc_start: 0.8851 (mmm160) cc_final: 0.8623 (mmm160) REVERT: D 649 GLN cc_start: 0.9017 (pp30) cc_final: 0.8742 (pp30) outliers start: 34 outliers final: 14 residues processed: 127 average time/residue: 0.6936 time to fit residues: 97.1709 Evaluate side-chains 114 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain C residue 490 CYS Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 669 MET Chi-restraints excluded: chain D residue 490 CYS Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 563 ILE Chi-restraints excluded: chain D residue 669 MET Chi-restraints excluded: chain D residue 674 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 68 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 789 GLN D 789 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.108702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.072303 restraints weight = 33724.381| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.49 r_work: 0.2902 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 18630 Z= 0.296 Angle : 0.653 15.735 25738 Z= 0.339 Chirality : 0.046 0.245 2804 Planarity : 0.004 0.043 2862 Dihedral : 22.813 176.043 3396 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.24 % Allowed : 21.79 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.41 (0.20), residues: 1860 helix: 2.03 (0.18), residues: 814 sheet: -0.00 (0.29), residues: 302 loop : 0.22 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 379 TYR 0.022 0.002 TYR A 389 PHE 0.015 0.002 PHE B 439 TRP 0.010 0.002 TRP B 548 HIS 0.011 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.30 (18630) covalent geometry : angle 0.65284 / 0.34 (25738) hydrogen bonds : bond 0.04424 / 2.83 ( 854) hydrogen bonds : angle 4.28313 / 3.10 ( 2306) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.8353 (tmm) cc_final: 0.7729 (tmm) REVERT: A 48 GLU cc_start: 0.8702 (pt0) cc_final: 0.8277 (pp20) REVERT: A 83 TYR cc_start: 0.7392 (OUTLIER) cc_final: 0.7075 (t80) REVERT: A 121 ARG cc_start: 0.9401 (mmt90) cc_final: 0.9162 (mmt90) REVERT: A 193 ASP cc_start: 0.8418 (t0) cc_final: 0.8196 (t70) REVERT: A 669 MET cc_start: 0.8972 (tmm) cc_final: 0.8740 (pp-130) REVERT: B 28 MET cc_start: 0.8326 (tmm) cc_final: 0.7710 (tmm) REVERT: B 48 GLU cc_start: 0.8722 (pt0) cc_final: 0.8292 (pp20) REVERT: B 193 ASP cc_start: 0.8403 (t0) cc_final: 0.8183 (t70) REVERT: B 520 ASP cc_start: 0.9302 (m-30) cc_final: 0.9100 (p0) REVERT: B 669 MET cc_start: 0.8961 (tmm) cc_final: 0.8724 (pp-130) REVERT: C 552 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9014 (tt) REVERT: C 661 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8159 (tm-30) REVERT: D 552 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9014 (tt) REVERT: D 589 LEU cc_start: 0.8006 (tt) cc_final: 0.7790 (tt) REVERT: D 649 GLN cc_start: 0.9048 (pp30) cc_final: 0.8726 (pp30) outliers start: 38 outliers final: 22 residues processed: 139 average time/residue: 0.6163 time to fit residues: 95.8379 Evaluate side-chains 122 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain C residue 490 CYS Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain D residue 490 CYS Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 563 ILE Chi-restraints excluded: chain D residue 668 SER Chi-restraints excluded: chain D residue 674 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 120 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 81 optimal weight: 0.0060 chunk 15 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 106 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 632 HIS D 632 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.111503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.075687 restraints weight = 33069.030| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.50 r_work: 0.2975 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18630 Z= 0.121 Angle : 0.599 16.005 25738 Z= 0.314 Chirality : 0.041 0.237 2804 Planarity : 0.004 0.040 2862 Dihedral : 22.648 173.716 3396 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.41 % Allowed : 22.91 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.46 (0.20), residues: 1860 helix: 2.09 (0.18), residues: 812 sheet: 0.01 (0.30), residues: 286 loop : 0.23 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 379 TYR 0.016 0.001 TYR A 389 PHE 0.009 0.001 PHE B 439 TRP 0.010 0.001 TRP C 647 HIS 0.006 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (18630) covalent geometry : angle 0.59851 / 0.31 (25738) hydrogen bonds : bond 0.03617 / 2.31 ( 854) hydrogen bonds : angle 4.08894 / 2.97 ( 2306) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.8350 (tmm) cc_final: 0.8059 (tmm) REVERT: A 48 GLU cc_start: 0.8665 (pt0) cc_final: 0.8241 (pp20) REVERT: A 83 TYR cc_start: 0.7337 (OUTLIER) cc_final: 0.7071 (t80) REVERT: A 193 ASP cc_start: 0.8382 (t0) cc_final: 0.8113 (t70) REVERT: A 669 MET cc_start: 0.8933 (tmm) cc_final: 0.8728 (pp-130) REVERT: B 28 MET cc_start: 0.8343 (tmm) cc_final: 0.8050 (tmm) REVERT: B 48 GLU cc_start: 0.8678 (pt0) cc_final: 0.8261 (pp20) REVERT: B 121 ARG cc_start: 0.9393 (mmt90) cc_final: 0.9138 (mmt90) REVERT: B 193 ASP cc_start: 0.8374 (t0) cc_final: 0.8092 (t70) REVERT: C 552 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9025 (tt) REVERT: C 661 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8075 (tm-30) REVERT: D 552 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9023 (tt) REVERT: D 589 LEU cc_start: 0.7944 (tt) cc_final: 0.7738 (tt) REVERT: D 649 GLN cc_start: 0.9021 (pp30) cc_final: 0.8711 (pp30) outliers start: 24 outliers final: 11 residues processed: 125 average time/residue: 0.6781 time to fit residues: 93.8630 Evaluate side-chains 109 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain C residue 490 CYS Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain D residue 490 CYS Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 552 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 24 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 96 optimal weight: 0.0970 chunk 38 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 789 GLN D 789 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.111085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.074940 restraints weight = 33183.997| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.51 r_work: 0.2957 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18630 Z= 0.152 Angle : 0.609 16.270 25738 Z= 0.317 Chirality : 0.042 0.237 2804 Planarity : 0.004 0.054 2862 Dihedral : 22.559 174.238 3396 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.35 % Allowed : 23.09 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.51 (0.20), residues: 1860 helix: 2.11 (0.18), residues: 814 sheet: 0.21 (0.29), residues: 292 loop : 0.20 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 121 TYR 0.017 0.001 TYR A 389 PHE 0.011 0.001 PHE A 367 TRP 0.007 0.001 TRP D 647 HIS 0.012 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (18630) covalent geometry : angle 0.60902 / 0.32 (25738) hydrogen bonds : bond 0.03691 / 2.34 ( 854) hydrogen bonds : angle 4.07643 / 2.96 ( 2306) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.8401 (tmm) cc_final: 0.8107 (tmm) REVERT: A 48 GLU cc_start: 0.8687 (pt0) cc_final: 0.8265 (pp20) REVERT: A 83 TYR cc_start: 0.7388 (OUTLIER) cc_final: 0.7100 (t80) REVERT: A 193 ASP cc_start: 0.8415 (t0) cc_final: 0.8153 (t70) REVERT: A 669 MET cc_start: 0.8947 (tmm) cc_final: 0.8737 (pp-130) REVERT: B 28 MET cc_start: 0.8388 (tmm) cc_final: 0.8095 (tmm) REVERT: B 48 GLU cc_start: 0.8708 (pt0) cc_final: 0.8294 (pp20) REVERT: B 121 ARG cc_start: 0.9401 (mmt90) cc_final: 0.9157 (mmt90) REVERT: B 193 ASP cc_start: 0.8404 (t0) cc_final: 0.8143 (t70) REVERT: C 552 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9089 (tt) REVERT: C 589 LEU cc_start: 0.7996 (tt) cc_final: 0.7783 (tt) REVERT: C 661 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8115 (tm-30) REVERT: D 552 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9075 (tt) REVERT: D 589 LEU cc_start: 0.7989 (tt) cc_final: 0.7781 (tt) REVERT: D 649 GLN cc_start: 0.9020 (pp30) cc_final: 0.8688 (pp30) outliers start: 23 outliers final: 17 residues processed: 120 average time/residue: 0.6294 time to fit residues: 83.5707 Evaluate side-chains 119 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 459 HIS Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain C residue 490 CYS Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain D residue 490 CYS Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 552 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 121 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 8 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 191 optimal weight: 20.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.110273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.074188 restraints weight = 33326.975| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.50 r_work: 0.2937 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18630 Z= 0.184 Angle : 0.620 16.185 25738 Z= 0.322 Chirality : 0.042 0.239 2804 Planarity : 0.004 0.064 2862 Dihedral : 22.567 174.577 3396 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.35 % Allowed : 23.38 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.47 (0.20), residues: 1860 helix: 2.04 (0.18), residues: 816 sheet: 0.16 (0.29), residues: 294 loop : 0.23 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 121 TYR 0.019 0.001 TYR A 389 PHE 0.022 0.001 PHE C 619 TRP 0.006 0.001 TRP B 548 HIS 0.014 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (18630) covalent geometry : angle 0.61990 / 0.32 (25738) hydrogen bonds : bond 0.03811 / 2.42 ( 854) hydrogen bonds : angle 4.08917 / 2.97 ( 2306) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7009.37 seconds wall clock time: 119 minutes 57.47 seconds (7197.47 seconds total)