Starting phenix.real_space_refine on Fri Jul 3 00:35:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8iab_35299/07_2026/8iab_35299.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iab_35299/07_2026/8iab_35299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iab_35299/07_2026/8iab_35299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iab_35299/07_2026/8iab_35299.map" model { file = "/net/cci-nas-00/data/ceres_data/8iab_35299/07_2026/8iab_35299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iab_35299/07_2026/8iab_35299.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8iab_35299/07_2026/8iab_35299.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8iab_35299/07_2026/8iab_35299.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 12 5.49 5 Mg 2 5.21 5 S 58 5.16 5 Cl 6 4.86 5 C 7192 2.51 5 N 1836 2.21 5 O 1988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11094 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5465 Classifications: {'peptide': 704} Link IDs: {'PTRANS': 28, 'TRANS': 675} Chain breaks: 2 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 82 Unusual residues: {' CL': 3, ' MG': 1, 'ATP': 1, 'PIO': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Restraints were copied for chains: B Time building chain proxies: 4.34, per 1000 atoms: 0.39 Number of scatterers: 11094 At special positions: 0 Unit cell: (110.39, 87.15, 107.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 6 17.00 S 58 16.00 P 12 15.00 Mg 2 11.99 O 1988 8.00 N 1836 7.00 C 7192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 419 " distance=2.04 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 419 " distance=2.04 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: 0.85 Conformation dependent library (CDL) restraints added in 403.2 milliseconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 66.8% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 75 through 124 removed outlier: 3.564A pdb=" N PHE A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 109 " --> pdb=" O ASN A 105 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 154 removed outlier: 3.533A pdb=" N VAL A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 removed outlier: 3.857A pdb=" N ALA A 158 " --> pdb=" O PRO A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 158' Processing helix chain 'A' and resid 161 through 169 Processing helix chain 'A' and resid 179 through 195 removed outlier: 3.542A pdb=" N ALA A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 220 removed outlier: 3.813A pdb=" N VAL A 207 " --> pdb=" O GLU A 203 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.877A pdb=" N TYR A 234 " --> pdb=" O TRP A 231 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN A 236 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 258 removed outlier: 3.595A pdb=" N ASP A 243 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 276 through 301 removed outlier: 3.512A pdb=" N VAL A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 330 through 364 removed outlier: 3.533A pdb=" N LYS A 354 " --> pdb=" O HIS A 350 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 357 " --> pdb=" O HIS A 353 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 361 " --> pdb=" O ARG A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 388 removed outlier: 3.681A pdb=" N LYS A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 388 " --> pdb=" O CYS A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.569A pdb=" N LEU A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 443 removed outlier: 3.739A pdb=" N ARG A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 471 removed outlier: 3.524A pdb=" N ILE A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 468 " --> pdb=" O CYS A 464 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 499 removed outlier: 3.618A pdb=" N ILE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR A 490 " --> pdb=" O MET A 486 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 499 " --> pdb=" O GLY A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 523 Processing helix chain 'A' and resid 525 through 537 removed outlier: 3.600A pdb=" N VAL A 530 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 536 " --> pdb=" O PHE A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 540 No H-bonds generated for 'chain 'A' and resid 538 through 540' Processing helix chain 'A' and resid 541 through 558 removed outlier: 3.648A pdb=" N VAL A 548 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 558 " --> pdb=" O THR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 571 Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.656A pdb=" N ARG A 585 " --> pdb=" O PRO A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 593 Processing helix chain 'A' and resid 594 through 596 No H-bonds generated for 'chain 'A' and resid 594 through 596' Processing helix chain 'A' and resid 608 through 618 removed outlier: 3.671A pdb=" N THR A 618 " --> pdb=" O VAL A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 653 removed outlier: 3.734A pdb=" N LYS A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 671 removed outlier: 4.280A pdb=" N VAL A 667 " --> pdb=" O GLU A 663 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG A 668 " --> pdb=" O GLU A 664 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU A 669 " --> pdb=" O TRP A 665 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 removed outlier: 3.598A pdb=" N ALA A 677 " --> pdb=" O PRO A 673 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 678 " --> pdb=" O VAL A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 686 removed outlier: 3.668A pdb=" N ASP A 685 " --> pdb=" O ASN A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 703 removed outlier: 3.525A pdb=" N THR A 703 " --> pdb=" O HIS A 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 700 through 703' Processing helix chain 'A' and resid 715 through 727 Processing helix chain 'A' and resid 755 through 763 removed outlier: 4.090A pdb=" N GLN A 761 " --> pdb=" O TYR A 757 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 762 " --> pdb=" O ASN A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 767 removed outlier: 4.197A pdb=" N ASP A 767 " --> pdb=" O PRO A 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 764 through 767' Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 75 through 124 removed outlier: 3.564A pdb=" N PHE B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 124 " --> pdb=" O GLY B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 154 removed outlier: 3.533A pdb=" N VAL B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 158 removed outlier: 3.857A pdb=" N ALA B 158 " --> pdb=" O PRO B 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 158' Processing helix chain 'B' and resid 161 through 169 Processing helix chain 'B' and resid 179 through 195 removed outlier: 3.542A pdb=" N ALA B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 220 removed outlier: 3.813A pdb=" N VAL B 207 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 236 removed outlier: 3.877A pdb=" N TYR B 234 " --> pdb=" O TRP B 231 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN B 236 " --> pdb=" O ARG B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 258 removed outlier: 3.595A pdb=" N ASP B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 276 through 301 removed outlier: 3.512A pdb=" N VAL B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 329 No H-bonds generated for 'chain 'B' and resid 327 through 329' Processing helix chain 'B' and resid 330 through 364 removed outlier: 3.533A pdb=" N LYS B 354 " --> pdb=" O HIS B 350 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 357 " --> pdb=" O HIS B 353 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 388 removed outlier: 3.681A pdb=" N LYS B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 388 " --> pdb=" O CYS B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 391 No H-bonds generated for 'chain 'B' and resid 389 through 391' Processing helix chain 'B' and resid 427 through 432 removed outlier: 3.569A pdb=" N LEU B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 443 removed outlier: 3.739A pdb=" N ARG B 440 " --> pdb=" O ASP B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 471 removed outlier: 3.524A pdb=" N ILE B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 468 " --> pdb=" O CYS B 464 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE B 471 " --> pdb=" O GLY B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 499 removed outlier: 3.618A pdb=" N ILE B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR B 490 " --> pdb=" O MET B 486 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 499 " --> pdb=" O GLY B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 523 Processing helix chain 'B' and resid 525 through 537 removed outlier: 3.600A pdb=" N VAL B 530 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 536 " --> pdb=" O PHE B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 540 No H-bonds generated for 'chain 'B' and resid 538 through 540' Processing helix chain 'B' and resid 541 through 558 removed outlier: 3.648A pdb=" N VAL B 548 " --> pdb=" O ILE B 544 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 558 " --> pdb=" O THR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 571 Processing helix chain 'B' and resid 581 through 586 removed outlier: 3.656A pdb=" N ARG B 585 " --> pdb=" O PRO B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 593 Processing helix chain 'B' and resid 594 through 596 No H-bonds generated for 'chain 'B' and resid 594 through 596' Processing helix chain 'B' and resid 608 through 618 removed outlier: 3.671A pdb=" N THR B 618 " --> pdb=" O VAL B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 653 removed outlier: 3.734A pdb=" N LYS B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 671 removed outlier: 4.280A pdb=" N VAL B 667 " --> pdb=" O GLU B 663 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG B 668 " --> pdb=" O GLU B 664 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU B 669 " --> pdb=" O TRP B 665 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.598A pdb=" N ALA B 677 " --> pdb=" O PRO B 673 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 678 " --> pdb=" O VAL B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 686 removed outlier: 3.668A pdb=" N ASP B 685 " --> pdb=" O ASN B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 703 removed outlier: 3.525A pdb=" N THR B 703 " --> pdb=" O HIS B 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 700 through 703' Processing helix chain 'B' and resid 715 through 727 Processing helix chain 'B' and resid 755 through 763 removed outlier: 4.090A pdb=" N GLN B 761 " --> pdb=" O TYR B 757 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 762 " --> pdb=" O ASN B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 767 removed outlier: 4.197A pdb=" N ASP B 767 " --> pdb=" O PRO B 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 764 through 767' Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 47 Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 56 removed outlier: 4.221A pdb=" N GLU A 55 " --> pdb=" O ASP A 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 394 through 396 Processing sheet with id=AA4, first strand: chain 'A' and resid 602 through 603 removed outlier: 6.494A pdb=" N LEU A 602 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY A 639 " --> pdb=" O VAL A 625 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 605 through 607 Processing sheet with id=AA6, first strand: chain 'A' and resid 709 through 711 removed outlier: 6.321A pdb=" N VAL A 710 " --> pdb=" O VAL A 734 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A 747 " --> pdb=" O VAL A 733 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 47 Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 56 removed outlier: 4.221A pdb=" N GLU B 55 " --> pdb=" O ASP B 173 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 394 through 396 Processing sheet with id=AB1, first strand: chain 'B' and resid 602 through 603 removed outlier: 6.494A pdb=" N LEU B 602 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 639 " --> pdb=" O VAL B 625 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 605 through 607 Processing sheet with id=AB3, first strand: chain 'B' and resid 709 through 711 removed outlier: 6.321A pdb=" N VAL B 710 " --> pdb=" O VAL B 734 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY B 747 " --> pdb=" O VAL B 733 " (cutoff:3.500A) 606 hydrogen bonds defined for protein. 1758 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1724 1.30 - 1.43: 2944 1.43 - 1.56: 6560 1.56 - 1.68: 18 1.68 - 1.81: 92 Bond restraints: 11338 Sorted by residual: bond pdb=" C4 ATP B 800 " pdb=" C5 ATP B 800 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.25e+01 bond pdb=" C4 ATP A 800 " pdb=" C5 ATP A 800 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.25e+01 bond pdb=" C5 ATP A 800 " pdb=" C6 ATP A 800 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.90e+01 bond pdb=" C5 ATP B 800 " pdb=" C6 ATP B 800 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.90e+01 bond pdb=" C4 ATP B 800 " pdb=" N9 ATP B 800 " ideal model delta sigma weight residual 1.374 1.328 0.046 1.00e-02 1.00e+04 2.08e+01 ... (remaining 11333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 15224 3.28 - 6.57: 172 6.57 - 9.85: 32 9.85 - 13.13: 6 13.13 - 16.41: 4 Bond angle restraints: 15438 Sorted by residual: angle pdb=" PB ATP B 800 " pdb=" O3B ATP B 800 " pdb=" PG ATP B 800 " ideal model delta sigma weight residual 139.87 123.46 16.41 1.00e+00 1.00e+00 2.69e+02 angle pdb=" PB ATP A 800 " pdb=" O3B ATP A 800 " pdb=" PG ATP A 800 " ideal model delta sigma weight residual 139.87 123.46 16.41 1.00e+00 1.00e+00 2.69e+02 angle pdb=" PA ATP B 800 " pdb=" O3A ATP B 800 " pdb=" PB ATP B 800 " ideal model delta sigma weight residual 136.83 123.66 13.17 1.00e+00 1.00e+00 1.73e+02 angle pdb=" PA ATP A 800 " pdb=" O3A ATP A 800 " pdb=" PB ATP A 800 " ideal model delta sigma weight residual 136.83 123.66 13.17 1.00e+00 1.00e+00 1.73e+02 angle pdb=" C5 ATP B 800 " pdb=" C4 ATP B 800 " pdb=" N3 ATP B 800 " ideal model delta sigma weight residual 126.80 119.15 7.65 1.00e+00 1.00e+00 5.86e+01 ... (remaining 15433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 6034 17.68 - 35.37: 452 35.37 - 53.05: 88 53.05 - 70.73: 10 70.73 - 88.42: 8 Dihedral angle restraints: 6592 sinusoidal: 2572 harmonic: 4020 Sorted by residual: dihedral pdb=" CB CYS A 394 " pdb=" SG CYS A 394 " pdb=" SG CYS A 419 " pdb=" CB CYS A 419 " ideal model delta sinusoidal sigma weight residual -86.00 -121.10 35.10 1 1.00e+01 1.00e-02 1.75e+01 dihedral pdb=" CB CYS B 394 " pdb=" SG CYS B 394 " pdb=" SG CYS B 419 " pdb=" CB CYS B 419 " ideal model delta sinusoidal sigma weight residual -86.00 -121.10 35.10 1 1.00e+01 1.00e-02 1.75e+01 dihedral pdb=" CA TYR B 463 " pdb=" C TYR B 463 " pdb=" N CYS B 464 " pdb=" CA CYS B 464 " ideal model delta harmonic sigma weight residual 180.00 162.27 17.73 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 6589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1134 0.040 - 0.079: 538 0.079 - 0.119: 112 0.119 - 0.159: 26 0.159 - 0.198: 4 Chirality restraints: 1814 Sorted by residual: chirality pdb=" C1 PIO B 802 " pdb=" C2 PIO B 802 " pdb=" C6 PIO B 802 " pdb=" O1 PIO B 802 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.20 2.00e-01 2.50e+01 9.85e-01 chirality pdb=" C1 PIO A 802 " pdb=" C2 PIO A 802 " pdb=" C6 PIO A 802 " pdb=" O1 PIO A 802 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.48e-01 chirality pdb=" CA GLU A 323 " pdb=" N GLU A 323 " pdb=" C GLU A 323 " pdb=" CB GLU A 323 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.33e-01 ... (remaining 1811 not shown) Planarity restraints: 1902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 388 " 0.044 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO B 389 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 389 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 389 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 388 " -0.044 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO A 389 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 389 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 389 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 481 " 0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO A 482 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 482 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 482 " 0.032 5.00e-02 4.00e+02 ... (remaining 1899 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 23 2.41 - 3.03: 5301 3.03 - 3.65: 16401 3.65 - 4.28: 26424 4.28 - 4.90: 43577 Nonbonded interactions: 91726 Sorted by model distance: nonbonded pdb=" OE2 GLU A 55 " pdb="MG MG A 801 " model vdw 1.783 2.170 nonbonded pdb=" O1B ATP A 800 " pdb="MG MG A 801 " model vdw 2.023 2.170 nonbonded pdb=" OH TYR A 564 " pdb="CL CL A 804 " model vdw 2.023 3.190 nonbonded pdb=" OH TYR B 564 " pdb="CL CL B 804 " model vdw 2.024 3.190 nonbonded pdb=" OE2 GLU B 55 " pdb="MG MG B 801 " model vdw 2.102 2.170 ... (remaining 91721 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.010 Normalize map: mean=0, sd=1: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.960 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:8.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 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 : 0.005 0.079 11342 Z= 0.299 Angle : 0.929 16.413 15446 Z= 0.536 Chirality : 0.046 0.198 1814 Planarity : 0.006 0.065 1902 Dihedral : 13.234 88.417 4004 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.05 (0.15), residues: 1396 helix: -4.13 (0.07), residues: 814 sheet: -1.86 (1.22), residues: 20 loop : -1.82 (0.23), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 523 TYR 0.013 0.001 TYR B 490 PHE 0.010 0.001 PHE A 683 TRP 0.012 0.002 TRP A 274 HIS 0.002 0.001 HIS A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.30 (11338) covalent geometry : angle 0.92888 / 0.54 (15438) SS BOND : bond 0.00483 / 0.24 ( 4) SS BOND : angle 1.48799 / 0.96 ( 8) hydrogen bonds : bond 0.30034 / 19.83 ( 606) hydrogen bonds : angle 9.87313 / 6.81 ( 1758) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TYR cc_start: 0.7485 (t80) cc_final: 0.7169 (t80) REVERT: A 123 ILE cc_start: 0.8444 (pt) cc_final: 0.8162 (mt) REVERT: A 367 LYS cc_start: 0.8563 (mttt) cc_final: 0.8283 (mtmt) REVERT: A 577 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7233 (mm-30) REVERT: A 678 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7712 (mt-10) REVERT: A 757 TYR cc_start: 0.7339 (t80) cc_final: 0.7012 (t80) REVERT: B 121 TYR cc_start: 0.7483 (t80) cc_final: 0.7165 (t80) REVERT: B 123 ILE cc_start: 0.8437 (pt) cc_final: 0.8157 (mt) REVERT: B 367 LYS cc_start: 0.8561 (mttt) cc_final: 0.8282 (mtmt) REVERT: B 577 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7232 (mm-30) REVERT: B 678 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7715 (mt-10) REVERT: B 757 TYR cc_start: 0.7342 (t80) cc_final: 0.7016 (t80) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.6515 time to fit residues: 123.4465 Evaluate side-chains 124 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 ASN A 657 ASN A 758 ASN B 237 ASN B 657 ASN B 758 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.116876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.083857 restraints weight = 12837.802| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 1.73 r_work: 0.2589 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2447 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11342 Z= 0.169 Angle : 0.604 9.121 15446 Z= 0.312 Chirality : 0.043 0.308 1814 Planarity : 0.006 0.048 1902 Dihedral : 6.565 73.382 1544 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.60 % Allowed : 9.36 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.38 (0.20), residues: 1396 helix: -0.57 (0.16), residues: 784 sheet: -0.97 (0.98), residues: 30 loop : -1.26 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 258 TYR 0.015 0.001 TYR B 463 PHE 0.013 0.002 PHE B 284 TRP 0.014 0.002 TRP A 87 HIS 0.003 0.001 HIS B 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (11338) covalent geometry : angle 0.59406 / 0.31 (15438) SS BOND : bond 0.01140 / 0.52 ( 4) SS BOND : angle 4.84771 / 2.55 ( 8) hydrogen bonds : bond 0.05776 / 3.77 ( 606) hydrogen bonds : angle 4.58867 / 3.13 ( 1758) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.300 Fit side-chains REVERT: A 367 LYS cc_start: 0.8464 (mttt) cc_final: 0.8164 (mtmt) REVERT: A 577 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7742 (mm-30) REVERT: A 678 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7991 (mt-10) REVERT: A 742 MET cc_start: 0.6845 (mmt) cc_final: 0.6567 (mmt) REVERT: A 757 TYR cc_start: 0.7852 (t80) cc_final: 0.7599 (t80) REVERT: B 367 LYS cc_start: 0.8461 (mttt) cc_final: 0.8160 (mtmt) REVERT: B 577 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7737 (mm-30) REVERT: B 678 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7984 (mt-10) REVERT: B 742 MET cc_start: 0.6845 (mmt) cc_final: 0.6564 (mmt) REVERT: B 757 TYR cc_start: 0.7854 (t80) cc_final: 0.7603 (t80) outliers start: 19 outliers final: 6 residues processed: 136 average time/residue: 0.5704 time to fit residues: 82.8693 Evaluate side-chains 123 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 546 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 58 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 54 optimal weight: 0.2980 chunk 98 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 657 ASN B 657 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.117064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.083862 restraints weight = 12876.722| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 1.75 r_work: 0.2592 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2448 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11342 Z= 0.138 Angle : 0.535 7.154 15446 Z= 0.273 Chirality : 0.042 0.209 1814 Planarity : 0.004 0.044 1902 Dihedral : 6.380 77.011 1544 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.36 % Allowed : 10.96 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.22), residues: 1396 helix: 0.85 (0.18), residues: 782 sheet: -0.56 (0.98), residues: 30 loop : -0.96 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 258 TYR 0.015 0.001 TYR A 463 PHE 0.012 0.001 PHE B 723 TRP 0.015 0.001 TRP B 87 HIS 0.002 0.000 HIS B 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (11338) covalent geometry : angle 0.53237 / 0.27 (15438) SS BOND : bond 0.00264 / 0.12 ( 4) SS BOND : angle 2.55175 / 1.36 ( 8) hydrogen bonds : bond 0.04939 / 3.22 ( 606) hydrogen bonds : angle 4.18860 / 2.85 ( 1758) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.367 Fit side-chains REVERT: A 76 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8434 (tptt) REVERT: A 316 MET cc_start: 0.7623 (mmm) cc_final: 0.7208 (tpp) REVERT: A 367 LYS cc_start: 0.8402 (mttt) cc_final: 0.8148 (mtmt) REVERT: A 577 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7793 (mm-30) REVERT: A 659 LYS cc_start: 0.8746 (mtpt) cc_final: 0.8457 (mttp) REVERT: A 678 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7909 (mt-10) REVERT: A 742 MET cc_start: 0.7068 (mmt) cc_final: 0.6763 (mmt) REVERT: A 757 TYR cc_start: 0.7907 (t80) cc_final: 0.7659 (t80) REVERT: B 76 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8430 (tptt) REVERT: B 316 MET cc_start: 0.7632 (mmm) cc_final: 0.7221 (tpp) REVERT: B 367 LYS cc_start: 0.8395 (mttt) cc_final: 0.8140 (mtmt) REVERT: B 577 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7797 (mm-30) REVERT: B 659 LYS cc_start: 0.8742 (mtpt) cc_final: 0.8458 (mttp) REVERT: B 678 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7919 (mt-10) REVERT: B 742 MET cc_start: 0.7053 (mmt) cc_final: 0.6748 (mmt) REVERT: B 757 TYR cc_start: 0.7896 (t80) cc_final: 0.7652 (t80) outliers start: 28 outliers final: 14 residues processed: 136 average time/residue: 0.5648 time to fit residues: 82.4449 Evaluate side-chains 128 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 365 LYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 635 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 82 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 HIS B 321 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.116533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.082985 restraints weight = 12937.452| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 1.80 r_work: 0.2564 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2418 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11342 Z= 0.164 Angle : 0.550 6.746 15446 Z= 0.278 Chirality : 0.042 0.193 1814 Planarity : 0.004 0.045 1902 Dihedral : 6.539 80.531 1544 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.53 % Allowed : 11.97 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.22), residues: 1396 helix: 1.31 (0.18), residues: 786 sheet: -0.43 (1.00), residues: 30 loop : -0.80 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 258 TYR 0.018 0.001 TYR B 463 PHE 0.012 0.001 PHE A 723 TRP 0.016 0.001 TRP B 87 HIS 0.002 0.000 HIS A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.16 (11338) covalent geometry : angle 0.54749 / 0.28 (15438) SS BOND : bond 0.00180 / 0.08 ( 4) SS BOND : angle 2.20787 / 1.17 ( 8) hydrogen bonds : bond 0.05021 / 3.26 ( 606) hydrogen bonds : angle 4.18037 / 2.84 ( 1758) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.268 Fit side-chains REVERT: A 76 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8378 (tptt) REVERT: A 316 MET cc_start: 0.7596 (mmm) cc_final: 0.7130 (tpp) REVERT: A 367 LYS cc_start: 0.8399 (mttt) cc_final: 0.8161 (mtmt) REVERT: A 577 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7755 (mm-30) REVERT: A 659 LYS cc_start: 0.8728 (mtpt) cc_final: 0.8420 (mttp) REVERT: A 678 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7905 (mt-10) REVERT: A 742 MET cc_start: 0.6855 (mmt) cc_final: 0.6581 (mmt) REVERT: A 757 TYR cc_start: 0.7876 (t80) cc_final: 0.7623 (t80) REVERT: B 76 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8373 (tptt) REVERT: B 316 MET cc_start: 0.7603 (mmm) cc_final: 0.7139 (tpp) REVERT: B 367 LYS cc_start: 0.8396 (mttt) cc_final: 0.8159 (mtmt) REVERT: B 577 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7754 (mm-30) REVERT: B 659 LYS cc_start: 0.8714 (mtpt) cc_final: 0.8402 (mttp) REVERT: B 678 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7905 (mt-10) REVERT: B 742 MET cc_start: 0.6839 (mmt) cc_final: 0.6561 (mmt) REVERT: B 757 TYR cc_start: 0.7870 (t80) cc_final: 0.7619 (t80) outliers start: 30 outliers final: 16 residues processed: 138 average time/residue: 0.5576 time to fit residues: 82.2635 Evaluate side-chains 136 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 635 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 69 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3185 r_free = 0.3185 target = 0.115805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.082082 restraints weight = 12801.342| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 1.80 r_work: 0.2637 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11342 Z= 0.169 Angle : 0.548 6.578 15446 Z= 0.278 Chirality : 0.043 0.181 1814 Planarity : 0.004 0.045 1902 Dihedral : 6.702 82.669 1544 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.45 % Allowed : 12.90 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.23), residues: 1396 helix: 1.55 (0.18), residues: 788 sheet: -0.34 (1.00), residues: 30 loop : -0.73 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 258 TYR 0.018 0.001 TYR B 463 PHE 0.011 0.001 PHE A 723 TRP 0.016 0.001 TRP B 87 HIS 0.002 0.000 HIS B 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 (11338) covalent geometry : angle 0.54592 / 0.28 (15438) SS BOND : bond 0.00133 / 0.06 ( 4) SS BOND : angle 2.06168 / 1.10 ( 8) hydrogen bonds : bond 0.04986 / 3.24 ( 606) hydrogen bonds : angle 4.17452 / 2.84 ( 1758) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8384 (tptt) REVERT: A 305 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.6635 (mtpt) REVERT: A 316 MET cc_start: 0.7599 (mmm) cc_final: 0.7139 (tpp) REVERT: A 367 LYS cc_start: 0.8449 (mttt) cc_final: 0.8210 (mtmt) REVERT: A 577 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7741 (mm-30) REVERT: A 659 LYS cc_start: 0.8736 (mtpt) cc_final: 0.8434 (mttp) REVERT: A 678 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7950 (mt-10) REVERT: A 742 MET cc_start: 0.6883 (mmt) cc_final: 0.6604 (mmt) REVERT: A 757 TYR cc_start: 0.7906 (t80) cc_final: 0.7653 (t80) REVERT: B 76 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8379 (tptt) REVERT: B 305 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.6635 (mtpt) REVERT: B 316 MET cc_start: 0.7609 (mmm) cc_final: 0.7148 (tpp) REVERT: B 367 LYS cc_start: 0.8444 (mttt) cc_final: 0.8205 (mtmt) REVERT: B 577 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7749 (mm-30) REVERT: B 659 LYS cc_start: 0.8729 (mtpt) cc_final: 0.8428 (mttp) REVERT: B 678 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7939 (mt-10) REVERT: B 742 MET cc_start: 0.6873 (mmt) cc_final: 0.6593 (mmt) REVERT: B 757 TYR cc_start: 0.7897 (t80) cc_final: 0.7641 (t80) outliers start: 29 outliers final: 20 residues processed: 137 average time/residue: 0.5158 time to fit residues: 75.9770 Evaluate side-chains 146 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 691 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 68 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 35 optimal weight: 0.2980 chunk 8 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.3184 r_free = 0.3184 target = 0.115770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.082782 restraints weight = 12932.645| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 1.72 r_work: 0.2657 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11342 Z= 0.170 Angle : 0.550 6.554 15446 Z= 0.278 Chirality : 0.043 0.176 1814 Planarity : 0.004 0.046 1902 Dihedral : 6.567 83.394 1544 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.95 % Allowed : 13.07 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 1.01 (0.23), residues: 1396 helix: 1.72 (0.18), residues: 786 sheet: -0.26 (1.00), residues: 30 loop : -0.74 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 258 TYR 0.018 0.001 TYR A 463 PHE 0.011 0.001 PHE B 723 TRP 0.016 0.002 TRP A 87 HIS 0.002 0.000 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (11338) covalent geometry : angle 0.54782 / 0.28 (15438) SS BOND : bond 0.00091 / 0.04 ( 4) SS BOND : angle 1.98092 / 1.05 ( 8) hydrogen bonds : bond 0.04955 / 3.22 ( 606) hydrogen bonds : angle 4.16474 / 2.83 ( 1758) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8375 (tptt) REVERT: A 305 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.6764 (mtpt) REVERT: A 367 LYS cc_start: 0.8465 (mttt) cc_final: 0.8229 (mtmt) REVERT: A 577 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7762 (mm-30) REVERT: A 659 LYS cc_start: 0.8725 (mtpt) cc_final: 0.8437 (mttp) REVERT: A 678 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7941 (mt-10) REVERT: A 691 SER cc_start: 0.8546 (OUTLIER) cc_final: 0.8321 (p) REVERT: A 712 GLN cc_start: 0.8546 (mt0) cc_final: 0.8012 (mt0) REVERT: A 742 MET cc_start: 0.6832 (mmt) cc_final: 0.6554 (mmt) REVERT: A 757 TYR cc_start: 0.7915 (t80) cc_final: 0.7650 (t80) REVERT: B 76 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8354 (tptt) REVERT: B 305 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.6762 (mtpt) REVERT: B 367 LYS cc_start: 0.8459 (mttt) cc_final: 0.8220 (mtmt) REVERT: B 577 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7761 (mm-30) REVERT: B 659 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8431 (mttp) REVERT: B 678 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7924 (mt-10) REVERT: B 691 SER cc_start: 0.8546 (OUTLIER) cc_final: 0.8319 (p) REVERT: B 712 GLN cc_start: 0.8542 (mt0) cc_final: 0.8013 (mt0) REVERT: B 742 MET cc_start: 0.6820 (mmt) cc_final: 0.6541 (mmt) REVERT: B 757 TYR cc_start: 0.7905 (t80) cc_final: 0.7638 (t80) outliers start: 35 outliers final: 18 residues processed: 137 average time/residue: 0.5093 time to fit residues: 75.2976 Evaluate side-chains 146 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 691 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 96 optimal weight: 6.9990 chunk 137 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 72 optimal weight: 0.0070 chunk 118 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 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 = 0.3189 r_free = 0.3189 target = 0.116129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.082586 restraints weight = 12871.536| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 1.78 r_work: 0.2570 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2424 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11342 Z= 0.153 Angle : 0.532 6.301 15446 Z= 0.270 Chirality : 0.042 0.171 1814 Planarity : 0.004 0.046 1902 Dihedral : 6.467 84.427 1544 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.53 % Allowed : 13.49 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 1.16 (0.23), residues: 1396 helix: 1.87 (0.18), residues: 784 sheet: -0.22 (0.99), residues: 30 loop : -0.72 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 258 TYR 0.017 0.001 TYR B 463 PHE 0.011 0.001 PHE A 723 TRP 0.016 0.001 TRP A 87 HIS 0.002 0.000 HIS B 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 (11338) covalent geometry : angle 0.53048 / 0.27 (15438) SS BOND : bond 0.00057 / 0.03 ( 4) SS BOND : angle 1.86690 / 0.99 ( 8) hydrogen bonds : bond 0.04727 / 3.08 ( 606) hydrogen bonds : angle 4.13039 / 2.81 ( 1758) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8351 (tptt) REVERT: A 228 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7984 (tppt) REVERT: A 305 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6680 (mtpt) REVERT: A 367 LYS cc_start: 0.8407 (mttt) cc_final: 0.8145 (mtmt) REVERT: A 577 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7792 (mm-30) REVERT: A 678 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7892 (mt-10) REVERT: A 691 SER cc_start: 0.8523 (OUTLIER) cc_final: 0.8298 (p) REVERT: A 712 GLN cc_start: 0.8544 (mt0) cc_final: 0.7965 (mt0) REVERT: A 742 MET cc_start: 0.6806 (mmt) cc_final: 0.6511 (mmt) REVERT: A 757 TYR cc_start: 0.7899 (t80) cc_final: 0.7643 (t80) REVERT: B 76 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8333 (tptt) REVERT: B 228 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7974 (tppt) REVERT: B 305 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.6679 (mtpt) REVERT: B 367 LYS cc_start: 0.8403 (mttt) cc_final: 0.8134 (mtmt) REVERT: B 577 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7800 (mm-30) REVERT: B 678 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7896 (mt-10) REVERT: B 691 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8297 (p) REVERT: B 712 GLN cc_start: 0.8541 (mt0) cc_final: 0.7965 (mt0) REVERT: B 742 MET cc_start: 0.6784 (mmt) cc_final: 0.6492 (mmt) REVERT: B 757 TYR cc_start: 0.7891 (t80) cc_final: 0.7635 (t80) outliers start: 30 outliers final: 14 residues processed: 136 average time/residue: 0.5247 time to fit residues: 76.8852 Evaluate side-chains 146 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 691 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 111 optimal weight: 0.0170 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 122 optimal weight: 0.0770 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 ASN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.117750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.084351 restraints weight = 12867.618| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 1.78 r_work: 0.2603 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11342 Z= 0.115 Angle : 0.494 5.598 15446 Z= 0.251 Chirality : 0.041 0.159 1814 Planarity : 0.004 0.045 1902 Dihedral : 6.282 86.861 1544 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.11 % Allowed : 13.83 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.23), residues: 1396 helix: 2.12 (0.18), residues: 782 sheet: -0.19 (0.96), residues: 30 loop : -0.69 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 258 TYR 0.013 0.001 TYR B 463 PHE 0.011 0.001 PHE B 723 TRP 0.016 0.001 TRP A 87 HIS 0.001 0.000 HIS B 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (11338) covalent geometry : angle 0.49258 / 0.25 (15438) SS BOND : bond 0.00053 / 0.03 ( 4) SS BOND : angle 1.64479 / 0.87 ( 8) hydrogen bonds : bond 0.04130 / 2.69 ( 606) hydrogen bonds : angle 4.02924 / 2.73 ( 1758) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8325 (tptt) REVERT: A 223 ASP cc_start: 0.8124 (t70) cc_final: 0.7860 (m-30) REVERT: A 305 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6495 (mtpt) REVERT: A 316 MET cc_start: 0.7587 (mmm) cc_final: 0.7185 (tpp) REVERT: A 367 LYS cc_start: 0.8351 (mttt) cc_final: 0.8111 (mtmt) REVERT: A 486 MET cc_start: 0.8887 (ttm) cc_final: 0.8620 (mtp) REVERT: A 577 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7789 (mm-30) REVERT: A 659 LYS cc_start: 0.8696 (mtpt) cc_final: 0.8394 (mttp) REVERT: A 678 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7844 (mt-10) REVERT: A 691 SER cc_start: 0.8539 (OUTLIER) cc_final: 0.8319 (p) REVERT: A 742 MET cc_start: 0.6820 (mmt) cc_final: 0.6597 (mpp) REVERT: A 757 TYR cc_start: 0.7901 (t80) cc_final: 0.7659 (t80) REVERT: B 76 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8313 (tptt) REVERT: B 223 ASP cc_start: 0.8110 (t70) cc_final: 0.7845 (m-30) REVERT: B 305 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6496 (mtpt) REVERT: B 316 MET cc_start: 0.7590 (mmm) cc_final: 0.7191 (tpp) REVERT: B 367 LYS cc_start: 0.8307 (mttt) cc_final: 0.8068 (mtmt) REVERT: B 486 MET cc_start: 0.8889 (ttm) cc_final: 0.8621 (mtp) REVERT: B 577 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7788 (mm-30) REVERT: B 659 LYS cc_start: 0.8688 (mtpt) cc_final: 0.8391 (mttp) REVERT: B 678 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7840 (mt-10) REVERT: B 691 SER cc_start: 0.8541 (OUTLIER) cc_final: 0.8322 (p) REVERT: B 742 MET cc_start: 0.6802 (mmt) cc_final: 0.6579 (mpp) REVERT: B 757 TYR cc_start: 0.7890 (t80) cc_final: 0.7648 (t80) outliers start: 25 outliers final: 8 residues processed: 137 average time/residue: 0.5691 time to fit residues: 83.5592 Evaluate side-chains 136 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 691 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 68 optimal weight: 0.0470 chunk 63 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- 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 = 0.3205 r_free = 0.3205 target = 0.117421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.083929 restraints weight = 12800.124| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 1.77 r_work: 0.2603 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11342 Z= 0.123 Angle : 0.508 6.011 15446 Z= 0.257 Chirality : 0.041 0.160 1814 Planarity : 0.004 0.045 1902 Dihedral : 6.257 86.160 1544 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.69 % Allowed : 14.25 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.23), residues: 1396 helix: 2.13 (0.18), residues: 784 sheet: -0.70 (0.85), residues: 40 loop : -0.59 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 258 TYR 0.014 0.001 TYR A 463 PHE 0.011 0.001 PHE B 723 TRP 0.015 0.001 TRP A 87 HIS 0.002 0.000 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (11338) covalent geometry : angle 0.50668 / 0.26 (15438) SS BOND : bond 0.00032 / 0.02 ( 4) SS BOND : angle 1.67450 / 0.89 ( 8) hydrogen bonds : bond 0.04280 / 2.79 ( 606) hydrogen bonds : angle 4.03662 / 2.74 ( 1758) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8329 (tptt) REVERT: A 316 MET cc_start: 0.7564 (mmm) cc_final: 0.7178 (tpp) REVERT: A 367 LYS cc_start: 0.8373 (mttt) cc_final: 0.8123 (mtmt) REVERT: A 486 MET cc_start: 0.8915 (ttm) cc_final: 0.8640 (mtp) REVERT: A 659 LYS cc_start: 0.8698 (mtpt) cc_final: 0.8402 (mttp) REVERT: A 678 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7853 (mt-10) REVERT: A 691 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.8326 (p) REVERT: A 712 GLN cc_start: 0.8402 (mt0) cc_final: 0.7827 (mt0) REVERT: A 742 MET cc_start: 0.6838 (mmt) cc_final: 0.6553 (mmt) REVERT: A 757 TYR cc_start: 0.7898 (t80) cc_final: 0.7651 (t80) REVERT: B 76 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8318 (tptt) REVERT: B 316 MET cc_start: 0.7570 (mmm) cc_final: 0.7186 (tpp) REVERT: B 367 LYS cc_start: 0.8369 (mttt) cc_final: 0.8120 (mtmt) REVERT: B 486 MET cc_start: 0.8918 (ttm) cc_final: 0.8642 (mtp) REVERT: B 659 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8397 (mttp) REVERT: B 678 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7845 (mt-10) REVERT: B 691 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.8326 (p) REVERT: B 712 GLN cc_start: 0.8408 (mt0) cc_final: 0.7832 (mt0) REVERT: B 742 MET cc_start: 0.6820 (mmt) cc_final: 0.6535 (mmt) REVERT: B 757 TYR cc_start: 0.7886 (t80) cc_final: 0.7637 (t80) outliers start: 20 outliers final: 10 residues processed: 132 average time/residue: 0.5515 time to fit residues: 78.4312 Evaluate side-chains 140 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 691 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 87 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3171 r_free = 0.3171 target = 0.114794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.080773 restraints weight = 12969.454| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 1.83 r_work: 0.2540 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2393 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11342 Z= 0.199 Angle : 0.577 7.411 15446 Z= 0.291 Chirality : 0.044 0.173 1814 Planarity : 0.004 0.046 1902 Dihedral : 6.510 84.273 1544 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.85 % Allowed : 14.33 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.23), residues: 1396 helix: 1.93 (0.18), residues: 786 sheet: -0.71 (0.86), residues: 40 loop : -0.60 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 258 TYR 0.021 0.002 TYR A 463 PHE 0.010 0.001 PHE B 723 TRP 0.013 0.002 TRP B 87 HIS 0.005 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.20 (11338) covalent geometry : angle 0.57553 / 0.29 (15438) SS BOND : bond 0.00165 / 0.08 ( 4) SS BOND : angle 2.07155 / 1.10 ( 8) hydrogen bonds : bond 0.05184 / 3.37 ( 606) hydrogen bonds : angle 4.19104 / 2.85 ( 1758) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8407 (tptt) REVERT: A 305 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.6738 (mtpt) REVERT: A 367 LYS cc_start: 0.8441 (mttt) cc_final: 0.8183 (mtmt) REVERT: A 449 ASN cc_start: 0.8257 (m-40) cc_final: 0.8057 (m-40) REVERT: A 678 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7933 (mt-10) REVERT: A 691 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.8301 (p) REVERT: A 712 GLN cc_start: 0.8472 (mt0) cc_final: 0.7838 (mt0) REVERT: A 742 MET cc_start: 0.6836 (mmt) cc_final: 0.6586 (mpp) REVERT: A 757 TYR cc_start: 0.7932 (t80) cc_final: 0.7710 (t80) REVERT: B 76 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8382 (tptt) REVERT: B 305 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.6742 (mtpt) REVERT: B 367 LYS cc_start: 0.8428 (mttt) cc_final: 0.8165 (mtmt) REVERT: B 449 ASN cc_start: 0.8259 (m-40) cc_final: 0.8059 (m-40) REVERT: B 678 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7919 (mt-10) REVERT: B 691 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.8299 (p) REVERT: B 712 GLN cc_start: 0.8473 (mt0) cc_final: 0.7836 (mt0) REVERT: B 742 MET cc_start: 0.6832 (mmt) cc_final: 0.6581 (mpp) REVERT: B 757 TYR cc_start: 0.7920 (t80) cc_final: 0.7695 (t80) outliers start: 22 outliers final: 12 residues processed: 134 average time/residue: 0.5305 time to fit residues: 76.4845 Evaluate side-chains 142 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 691 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 42 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3200 r_free = 0.3200 target = 0.116988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.083511 restraints weight = 12932.831| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 1.79 r_work: 0.2602 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2457 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11342 Z= 0.124 Angle : 0.513 6.147 15446 Z= 0.260 Chirality : 0.041 0.164 1814 Planarity : 0.004 0.045 1902 Dihedral : 6.337 87.813 1544 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.85 % Allowed : 14.50 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.23), residues: 1396 helix: 2.12 (0.18), residues: 786 sheet: -0.68 (0.86), residues: 40 loop : -0.56 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 258 TYR 0.014 0.001 TYR A 463 PHE 0.011 0.001 PHE B 723 TRP 0.015 0.001 TRP A 87 HIS 0.002 0.000 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (11338) covalent geometry : angle 0.51152 / 0.26 (15438) SS BOND : bond 0.00032 / 0.02 ( 4) SS BOND : angle 1.74714 / 0.93 ( 8) hydrogen bonds : bond 0.04309 / 2.81 ( 606) hydrogen bonds : angle 4.06478 / 2.76 ( 1758) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3105.92 seconds wall clock time: 53 minutes 32.98 seconds (3212.98 seconds total)