Starting phenix.real_space_refine on Thu Mar 5 22:02:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sto_25435/03_2026/7sto_25435_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sto_25435/03_2026/7sto_25435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sto_25435/03_2026/7sto_25435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sto_25435/03_2026/7sto_25435.map" model { file = "/net/cci-nas-00/data/ceres_data/7sto_25435/03_2026/7sto_25435_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sto_25435/03_2026/7sto_25435_trim.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 56 5.16 5 C 8478 2.51 5 N 2064 2.21 5 O 2336 1.98 5 H 12268 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25210 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 12410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 12410 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 24, 'TRANS': 765} Chain breaks: 3 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 56 Chain: "A" Number of atoms: 12410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 12410 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 24, 'TRANS': 765} Chain breaks: 3 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 158 Unusual residues: {'3PE': 3, 'BJ9': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "A" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 232 Unusual residues: {'3PE': 5, 'BJ9': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 59 Time building chain proxies: 4.25, per 1000 atoms: 0.17 Number of scatterers: 25210 At special positions: 0 Unit cell: (93.96, 126.36, 119.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 8 15.00 O 2336 8.00 N 2064 7.00 C 8478 6.00 H 12268 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 641.1 milliseconds 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 6 sheets defined 60.9% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'B' and resid 147 through 155 removed outlier: 3.571A pdb=" N ARG B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 254 through 261 removed outlier: 3.750A pdb=" N PHE B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.611A pdb=" N TYR B 304 " --> pdb=" O ARG B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 343 Processing helix chain 'B' and resid 352 through 355 removed outlier: 3.656A pdb=" N LYS B 355 " --> pdb=" O ASP B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 355' Processing helix chain 'B' and resid 370 through 381 Processing helix chain 'B' and resid 439 through 451 removed outlier: 3.835A pdb=" N ASN B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 444 " --> pdb=" O LYS B 440 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 451 " --> pdb=" O TRP B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 457 removed outlier: 3.563A pdb=" N VAL B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 485 removed outlier: 3.871A pdb=" N ASP B 485 " --> pdb=" O GLU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 532 removed outlier: 4.791A pdb=" N LYS B 525 " --> pdb=" O ASN B 521 " (cutoff:3.500A) Proline residue: B 526 - end of helix Processing helix chain 'B' and resid 545 through 550 removed outlier: 3.572A pdb=" N LEU B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN B 550 " --> pdb=" O PHE B 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 545 through 550' Processing helix chain 'B' and resid 557 through 569 removed outlier: 4.044A pdb=" N GLY B 565 " --> pdb=" O LYS B 561 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLU B 566 " --> pdb=" O TYR B 562 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE B 567 " --> pdb=" O PHE B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 590 Processing helix chain 'B' and resid 593 through 598 Processing helix chain 'B' and resid 599 through 602 Processing helix chain 'B' and resid 603 through 613 removed outlier: 4.386A pdb=" N LEU B 607 " --> pdb=" O GLU B 603 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N CYS B 608 " --> pdb=" O ASP B 604 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE B 609 " --> pdb=" O ARG B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 661 removed outlier: 4.071A pdb=" N ARG B 646 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP B 647 " --> pdb=" O GLN B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 667 removed outlier: 3.519A pdb=" N VAL B 665 " --> pdb=" O PHE B 662 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR B 667 " --> pdb=" O LYS B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 694 Processing helix chain 'B' and resid 694 through 710 removed outlier: 3.581A pdb=" N LEU B 710 " --> pdb=" O LEU B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 745 Processing helix chain 'B' and resid 750 through 787 removed outlier: 3.943A pdb=" N TYR B 754 " --> pdb=" O THR B 750 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER B 786 " --> pdb=" O ASP B 782 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 787 " --> pdb=" O ILE B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 798 Processing helix chain 'B' and resid 798 through 822 removed outlier: 3.948A pdb=" N ALA B 807 " --> pdb=" O ASP B 803 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 831 Processing helix chain 'B' and resid 831 through 853 Proline residue: B 840 - end of helix removed outlier: 3.821A pdb=" N LEU B 846 " --> pdb=" O TYR B 842 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN B 847 " --> pdb=" O VAL B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 904 Processing helix chain 'B' and resid 917 through 946 removed outlier: 4.195A pdb=" N TYR B 921 " --> pdb=" O ASN B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 954 removed outlier: 4.160A pdb=" N ASN B 951 " --> pdb=" O GLY B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 1002 removed outlier: 4.008A pdb=" N ASN B 961 " --> pdb=" O THR B 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.571A pdb=" N ARG A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 254 through 261 removed outlier: 3.749A pdb=" N PHE A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 299 through 304 removed outlier: 3.611A pdb=" N TYR A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 343 Processing helix chain 'A' and resid 352 through 355 removed outlier: 3.656A pdb=" N LYS A 355 " --> pdb=" O ASP A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 439 through 451 removed outlier: 3.835A pdb=" N ASN A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 451 " --> pdb=" O TRP A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 457 removed outlier: 3.563A pdb=" N VAL A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 485 removed outlier: 3.870A pdb=" N ASP A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 532 removed outlier: 4.791A pdb=" N LYS A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Proline residue: A 526 - end of helix Processing helix chain 'A' and resid 545 through 550 removed outlier: 3.573A pdb=" N LEU A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 550 " --> pdb=" O PHE A 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 545 through 550' Processing helix chain 'A' and resid 557 through 569 removed outlier: 4.043A pdb=" N GLY A 565 " --> pdb=" O LYS A 561 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU A 566 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 567 " --> pdb=" O PHE A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 590 Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 599 through 602 Processing helix chain 'A' and resid 603 through 613 removed outlier: 4.385A pdb=" N LEU A 607 " --> pdb=" O GLU A 603 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS A 608 " --> pdb=" O ASP A 604 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A 609 " --> pdb=" O ARG A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 661 removed outlier: 4.071A pdb=" N ARG A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP A 647 " --> pdb=" O GLN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 667 removed outlier: 3.519A pdb=" N VAL A 665 " --> pdb=" O PHE A 662 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A 667 " --> pdb=" O LYS A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 694 Processing helix chain 'A' and resid 694 through 710 removed outlier: 3.581A pdb=" N LEU A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 745 Processing helix chain 'A' and resid 750 through 787 removed outlier: 3.944A pdb=" N TYR A 754 " --> pdb=" O THR A 750 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY A 787 " --> pdb=" O ILE A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 798 Processing helix chain 'A' and resid 798 through 822 removed outlier: 3.948A pdb=" N ALA A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 831 Processing helix chain 'A' and resid 831 through 853 Proline residue: A 840 - end of helix removed outlier: 3.821A pdb=" N LEU A 846 " --> pdb=" O TYR A 842 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN A 847 " --> pdb=" O VAL A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 904 Processing helix chain 'A' and resid 917 through 946 removed outlier: 4.196A pdb=" N TYR A 921 " --> pdb=" O ASN A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 954 removed outlier: 4.159A pdb=" N ASN A 951 " --> pdb=" O GLY A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 1002 removed outlier: 4.008A pdb=" N ASN A 961 " --> pdb=" O THR A 957 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 239 through 240 removed outlier: 3.844A pdb=" N LYS A 874 " --> pdb=" O ASP A 882 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG B 391 " --> pdb=" O ALA A 873 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU A 875 " --> pdb=" O ARG B 391 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 248 through 252 removed outlier: 7.885A pdb=" N PHE B 279 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N THR B 405 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE B 357 " --> pdb=" O GLN B 429 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LEU B 431 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL B 359 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N CYS B 433 " --> pdb=" O VAL B 359 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 361 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LYS B 435 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N SER B 363 " --> pdb=" O LYS B 435 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET B 313 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU B 464 " --> pdb=" O MET B 313 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL B 315 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N PHE B 541 " --> pdb=" O GLY B 493 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY B 493 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ARG B 622 " --> pdb=" O ALA B 489 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA B 491 " --> pdb=" O ARG B 622 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N CYS B 624 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY B 493 " --> pdb=" O CYS B 624 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N SER B 626 " --> pdb=" O GLY B 493 " (cutoff:3.500A) removed outlier: 9.269A pdb=" N ILE B 495 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N ARG B 628 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 10.075A pdb=" N THR B 497 " --> pdb=" O ARG B 628 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLU B 630 " --> pdb=" O THR B 497 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 409 through 413 removed outlier: 7.174A pdb=" N LYS B 419 " --> pdb=" O SER B 411 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.844A pdb=" N LYS B 874 " --> pdb=" O ASP B 882 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 248 through 252 removed outlier: 7.885A pdb=" N PHE A 279 " --> pdb=" O THR A 405 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N THR A 405 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE A 357 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LEU A 431 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL A 359 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N CYS A 433 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE A 361 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LYS A 435 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N SER A 363 " --> pdb=" O LYS A 435 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET A 313 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU A 464 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 315 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N PHE A 541 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY A 493 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ARG A 622 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA A 491 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N CYS A 624 " --> pdb=" O ALA A 491 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY A 493 " --> pdb=" O CYS A 624 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N SER A 626 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 9.269A pdb=" N ILE A 495 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N ARG A 628 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 10.075A pdb=" N THR A 497 " --> pdb=" O ARG A 628 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLU A 630 " --> pdb=" O THR A 497 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 409 through 413 removed outlier: 7.173A pdb=" N LYS A 419 " --> pdb=" O SER A 411 " (cutoff:3.500A) 721 hydrogen bonds defined for protein. 2079 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: 6.02 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12244 1.03 - 1.22: 48 1.22 - 1.42: 5650 1.42 - 1.61: 7472 1.61 - 1.81: 104 Bond restraints: 25518 Sorted by residual: bond pdb=" C19 BJ9 B1204 " pdb=" N18 BJ9 B1204 " ideal model delta sigma weight residual 1.332 1.492 -0.160 2.00e-02 2.50e+03 6.43e+01 bond pdb=" C19 BJ9 A1205 " pdb=" N18 BJ9 A1205 " ideal model delta sigma weight residual 1.332 1.492 -0.160 2.00e-02 2.50e+03 6.42e+01 bond pdb=" C06 BJ9 A1205 " pdb=" N05 BJ9 A1205 " ideal model delta sigma weight residual 1.365 1.523 -0.158 2.00e-02 2.50e+03 6.27e+01 bond pdb=" C06 BJ9 B1204 " pdb=" N05 BJ9 B1204 " ideal model delta sigma weight residual 1.365 1.522 -0.157 2.00e-02 2.50e+03 6.20e+01 bond pdb=" C06 BJ9 B1204 " pdb=" N08 BJ9 B1204 " ideal model delta sigma weight residual 1.381 1.537 -0.156 2.00e-02 2.50e+03 6.10e+01 ... (remaining 25513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 45312 2.84 - 5.67: 291 5.67 - 8.51: 61 8.51 - 11.34: 16 11.34 - 14.18: 8 Bond angle restraints: 45688 Sorted by residual: angle pdb=" CA THR B 947 " pdb=" C THR B 947 " pdb=" O THR B 947 " ideal model delta sigma weight residual 120.24 114.36 5.88 1.11e+00 8.12e-01 2.81e+01 angle pdb=" CA THR A 947 " pdb=" C THR A 947 " pdb=" O THR A 947 " ideal model delta sigma weight residual 120.24 114.39 5.85 1.11e+00 8.12e-01 2.78e+01 angle pdb=" O12 3PE B1202 " pdb=" P 3PE B1202 " pdb=" O14 3PE B1202 " ideal model delta sigma weight residual 123.79 109.61 14.18 3.00e+00 1.11e-01 2.23e+01 angle pdb=" O12 3PE A1202 " pdb=" P 3PE A1202 " pdb=" O14 3PE A1202 " ideal model delta sigma weight residual 123.79 109.66 14.13 3.00e+00 1.11e-01 2.22e+01 angle pdb=" O12 3PE A1204 " pdb=" P 3PE A1204 " pdb=" O14 3PE A1204 " ideal model delta sigma weight residual 123.79 109.71 14.08 3.00e+00 1.11e-01 2.20e+01 ... (remaining 45683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 11594 17.78 - 35.56: 482 35.56 - 53.34: 178 53.34 - 71.12: 62 71.12 - 88.91: 10 Dihedral angle restraints: 12326 sinusoidal: 6564 harmonic: 5762 Sorted by residual: dihedral pdb=" O21 3PE B1202 " pdb=" C2 3PE B1202 " pdb=" C3 3PE B1202 " pdb=" O31 3PE B1202 " ideal model delta sinusoidal sigma weight residual 60.47 -23.68 84.15 1 3.00e+01 1.11e-03 9.58e+00 dihedral pdb=" O21 3PE A1202 " pdb=" C2 3PE A1202 " pdb=" C3 3PE A1202 " pdb=" O31 3PE A1202 " ideal model delta sinusoidal sigma weight residual 60.47 -23.65 84.12 1 3.00e+01 1.11e-03 9.57e+00 dihedral pdb=" O21 3PE B1201 " pdb=" C2 3PE B1201 " pdb=" C3 3PE B1201 " pdb=" O31 3PE B1201 " ideal model delta sinusoidal sigma weight residual 60.47 -23.12 83.59 1 3.00e+01 1.11e-03 9.48e+00 ... (remaining 12323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1742 0.062 - 0.125: 208 0.125 - 0.187: 16 0.187 - 0.250: 6 0.250 - 0.312: 2 Chirality restraints: 1974 Sorted by residual: chirality pdb=" C10 BJ9 B1204 " pdb=" C09 BJ9 B1204 " pdb=" C11 BJ9 B1204 " pdb=" O33 BJ9 B1204 " both_signs ideal model delta sigma weight residual False -2.47 -2.78 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C10 BJ9 A1205 " pdb=" C09 BJ9 A1205 " pdb=" C11 BJ9 A1205 " pdb=" O33 BJ9 A1205 " both_signs ideal model delta sigma weight residual False -2.47 -2.77 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA ILE B 790 " pdb=" N ILE B 790 " pdb=" C ILE B 790 " pdb=" CB ILE B 790 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 1971 not shown) Planarity restraints: 3742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 785 " -0.014 2.00e-02 2.50e+03 2.63e-02 6.93e+00 pdb=" N SER A 786 " 0.045 2.00e-02 2.50e+03 pdb=" CA SER A 786 " -0.012 2.00e-02 2.50e+03 pdb=" H SER A 786 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 785 " 0.014 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" N SER B 786 " -0.045 2.00e-02 2.50e+03 pdb=" CA SER B 786 " 0.012 2.00e-02 2.50e+03 pdb=" H SER B 786 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 788 " 0.011 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" N ARG B 789 " -0.034 2.00e-02 2.50e+03 pdb=" CA ARG B 789 " 0.009 2.00e-02 2.50e+03 pdb=" H ARG B 789 " 0.014 2.00e-02 2.50e+03 ... (remaining 3739 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 2891 2.27 - 2.85: 56098 2.85 - 3.43: 63297 3.43 - 4.02: 87202 4.02 - 4.60: 137107 Nonbonded interactions: 346595 Sorted by model distance: nonbonded pdb=" O TRP A 666 " pdb=" HZ3 LYS A 675 " model vdw 1.685 2.450 nonbonded pdb=" O TRP B 666 " pdb=" HZ3 LYS B 675 " model vdw 1.686 2.450 nonbonded pdb=" O GLU B 256 " pdb=" HG SER B 259 " model vdw 1.689 2.450 nonbonded pdb=" O GLU A 256 " pdb=" HG SER A 259 " model vdw 1.689 2.450 nonbonded pdb=" O GLY B 593 " pdb=" HG SER B 597 " model vdw 1.709 2.450 ... (remaining 346590 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 135 through 1203) selection = (chain 'B' and resid 135 through 1203) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.140 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.230 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.160 13250 Z= 0.349 Angle : 0.878 14.180 17906 Z= 0.390 Chirality : 0.043 0.312 1974 Planarity : 0.003 0.023 2218 Dihedral : 11.851 88.905 4944 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.15 % Allowed : 1.51 % Favored : 98.34 % 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: 1.91 (0.21), residues: 1564 helix: 2.70 (0.18), residues: 816 sheet: 0.98 (0.46), residues: 140 loop : -0.73 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 281 TYR 0.011 0.001 TYR B 517 PHE 0.019 0.001 PHE B 261 TRP 0.010 0.001 TRP A 933 HIS 0.004 0.001 HIS A 670 Details of bonding type rmsd covalent geometry : bond 0.00683 (13250) covalent geometry : angle 0.87821 (17906) hydrogen bonds : bond 0.14104 ( 721) hydrogen bonds : angle 5.14530 ( 2079) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.586 Fit side-chains REVERT: B 496 THR cc_start: 0.8567 (m) cc_final: 0.8359 (p) REVERT: B 699 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8245 (m-80) REVERT: A 496 THR cc_start: 0.8560 (m) cc_final: 0.8348 (p) REVERT: A 699 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.8248 (m-80) outliers start: 2 outliers final: 0 residues processed: 132 average time/residue: 0.2433 time to fit residues: 46.3402 Evaluate side-chains 73 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain A residue 699 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 598 ASN A 598 ASN ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.103849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.077312 restraints weight = 59294.045| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.03 r_work: 0.2907 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13250 Z= 0.150 Angle : 0.463 4.577 17906 Z= 0.251 Chirality : 0.038 0.153 1974 Planarity : 0.003 0.042 2218 Dihedral : 11.122 93.495 2126 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.45 % Allowed : 3.93 % Favored : 95.61 % 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: 1.93 (0.22), residues: 1564 helix: 2.62 (0.18), residues: 856 sheet: 0.90 (0.44), residues: 140 loop : -0.79 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 446 TYR 0.009 0.001 TYR B 511 PHE 0.010 0.001 PHE B 984 TRP 0.009 0.001 TRP A 933 HIS 0.004 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00339 (13250) covalent geometry : angle 0.46290 (17906) hydrogen bonds : bond 0.05891 ( 721) hydrogen bonds : angle 4.32400 ( 2079) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.493 Fit side-chains REVERT: B 420 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7158 (pp) REVERT: B 496 THR cc_start: 0.8844 (m) cc_final: 0.8562 (p) REVERT: B 699 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8584 (m-80) REVERT: A 420 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7185 (pp) REVERT: A 496 THR cc_start: 0.8850 (m) cc_final: 0.8559 (p) REVERT: A 699 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.8575 (m-80) outliers start: 6 outliers final: 2 residues processed: 71 average time/residue: 0.1783 time to fit residues: 20.7860 Evaluate side-chains 64 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 699 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 135 optimal weight: 4.9990 chunk 36 optimal weight: 0.0470 chunk 29 optimal weight: 7.9990 chunk 61 optimal weight: 0.0980 chunk 96 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.103724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.077031 restraints weight = 59339.172| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.03 r_work: 0.2888 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13250 Z= 0.103 Angle : 0.405 4.786 17906 Z= 0.216 Chirality : 0.037 0.143 1974 Planarity : 0.003 0.033 2218 Dihedral : 10.225 89.030 2126 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.61 % Allowed : 3.93 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.22), residues: 1564 helix: 2.71 (0.18), residues: 856 sheet: 1.07 (0.44), residues: 140 loop : -0.78 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 446 TYR 0.008 0.001 TYR B 511 PHE 0.008 0.001 PHE A 984 TRP 0.008 0.001 TRP B 933 HIS 0.006 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00227 (13250) covalent geometry : angle 0.40525 (17906) hydrogen bonds : bond 0.04879 ( 721) hydrogen bonds : angle 3.95757 ( 2079) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 420 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7373 (pp) REVERT: B 496 THR cc_start: 0.8910 (m) cc_final: 0.8705 (p) REVERT: A 420 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7347 (pp) REVERT: A 496 THR cc_start: 0.8913 (m) cc_final: 0.8706 (p) outliers start: 8 outliers final: 6 residues processed: 73 average time/residue: 0.1686 time to fit residues: 20.3170 Evaluate side-chains 68 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 989 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 989 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 827 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.097361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.071878 restraints weight = 59701.225| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.87 r_work: 0.2801 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13250 Z= 0.219 Angle : 0.501 5.183 17906 Z= 0.272 Chirality : 0.040 0.155 1974 Planarity : 0.003 0.030 2218 Dihedral : 10.996 86.859 2126 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.88 % Favored : 96.99 % Rotamer: Outliers : 0.68 % Allowed : 4.69 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.22), residues: 1564 helix: 2.42 (0.18), residues: 854 sheet: 0.57 (0.43), residues: 142 loop : -0.76 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 446 TYR 0.014 0.002 TYR B 511 PHE 0.016 0.002 PHE A 984 TRP 0.008 0.001 TRP A 933 HIS 0.007 0.002 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00527 (13250) covalent geometry : angle 0.50059 (17906) hydrogen bonds : bond 0.06311 ( 721) hydrogen bonds : angle 4.16511 ( 2079) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.491 Fit side-chains REVERT: B 420 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.7725 (pp) REVERT: B 699 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.8623 (m-80) REVERT: B 765 MET cc_start: 0.8809 (tpt) cc_final: 0.8533 (tpt) REVERT: A 420 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.7731 (pp) REVERT: A 699 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.8615 (m-80) outliers start: 9 outliers final: 5 residues processed: 66 average time/residue: 0.1846 time to fit residues: 20.2001 Evaluate side-chains 65 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 989 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 989 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 59 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 36 optimal weight: 0.0670 overall best weight: 1.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN A 827 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.099519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.073825 restraints weight = 59501.389| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.90 r_work: 0.2822 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13250 Z= 0.121 Angle : 0.415 5.135 17906 Z= 0.225 Chirality : 0.038 0.147 1974 Planarity : 0.003 0.028 2218 Dihedral : 10.431 88.849 2126 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.43 % Favored : 97.44 % Rotamer: Outliers : 0.61 % Allowed : 4.54 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.22), residues: 1564 helix: 2.64 (0.18), residues: 852 sheet: 0.63 (0.42), residues: 140 loop : -0.74 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 446 TYR 0.010 0.001 TYR B 511 PHE 0.010 0.001 PHE A 984 TRP 0.008 0.001 TRP B 976 HIS 0.005 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00279 (13250) covalent geometry : angle 0.41521 (17906) hydrogen bonds : bond 0.05344 ( 721) hydrogen bonds : angle 3.96794 ( 2079) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.595 Fit side-chains REVERT: B 420 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.7762 (pp) REVERT: B 699 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.8573 (m-80) REVERT: B 765 MET cc_start: 0.8830 (tpt) cc_final: 0.8577 (tpt) REVERT: A 420 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.7767 (pp) REVERT: A 699 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.8560 (m-80) outliers start: 8 outliers final: 4 residues processed: 67 average time/residue: 0.1681 time to fit residues: 18.9076 Evaluate side-chains 65 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 989 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 989 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 23 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.097160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.070668 restraints weight = 60227.111| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.00 r_work: 0.2770 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13250 Z= 0.196 Angle : 0.466 5.809 17906 Z= 0.253 Chirality : 0.039 0.152 1974 Planarity : 0.003 0.028 2218 Dihedral : 10.795 89.970 2126 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.64 % Favored : 96.23 % Rotamer: Outliers : 0.61 % Allowed : 4.77 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.22), residues: 1564 helix: 2.48 (0.18), residues: 862 sheet: 0.15 (0.43), residues: 146 loop : -0.67 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 446 TYR 0.012 0.001 TYR A 511 PHE 0.014 0.001 PHE B 984 TRP 0.009 0.001 TRP B 693 HIS 0.005 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00474 (13250) covalent geometry : angle 0.46600 (17906) hydrogen bonds : bond 0.06048 ( 721) hydrogen bonds : angle 4.05810 ( 2079) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.652 Fit side-chains REVERT: B 420 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7507 (pp) REVERT: B 699 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.8666 (m-80) REVERT: B 765 MET cc_start: 0.8775 (tpt) cc_final: 0.8502 (tpt) REVERT: A 420 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7500 (pp) REVERT: A 699 TYR cc_start: 0.9017 (OUTLIER) cc_final: 0.8658 (m-80) outliers start: 8 outliers final: 4 residues processed: 70 average time/residue: 0.1778 time to fit residues: 20.6997 Evaluate side-chains 67 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 989 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 989 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 137 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 69 optimal weight: 0.0970 chunk 66 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.097698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.072587 restraints weight = 59541.233| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.83 r_work: 0.2806 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13250 Z= 0.137 Angle : 0.421 5.843 17906 Z= 0.228 Chirality : 0.038 0.145 1974 Planarity : 0.003 0.027 2218 Dihedral : 10.587 90.471 2126 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.07 % Favored : 96.80 % Rotamer: Outliers : 0.61 % Allowed : 4.99 % Favored : 94.40 % 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: 1.87 (0.22), residues: 1564 helix: 2.57 (0.18), residues: 864 sheet: 0.17 (0.43), residues: 144 loop : -0.66 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 446 TYR 0.009 0.001 TYR A 511 PHE 0.010 0.001 PHE A 984 TRP 0.008 0.001 TRP B 933 HIS 0.005 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00321 (13250) covalent geometry : angle 0.42138 (17906) hydrogen bonds : bond 0.05451 ( 721) hydrogen bonds : angle 3.95365 ( 2079) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.662 Fit side-chains REVERT: B 420 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.7586 (pp) REVERT: B 699 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.8554 (m-80) REVERT: B 765 MET cc_start: 0.8821 (tpt) cc_final: 0.8581 (tpt) REVERT: A 420 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.7546 (pp) REVERT: A 699 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.8533 (m-80) outliers start: 8 outliers final: 4 residues processed: 63 average time/residue: 0.1775 time to fit residues: 18.6458 Evaluate side-chains 62 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 989 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 989 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 153 optimal weight: 5.9990 chunk 4 optimal weight: 0.3980 chunk 100 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 643 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.100665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.074805 restraints weight = 59663.465| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.93 r_work: 0.2858 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13250 Z= 0.086 Angle : 0.382 4.845 17906 Z= 0.205 Chirality : 0.037 0.139 1974 Planarity : 0.003 0.028 2218 Dihedral : 9.958 90.791 2126 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.52 % Favored : 96.36 % Rotamer: Outliers : 0.61 % Allowed : 4.69 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.22), residues: 1564 helix: 2.80 (0.18), residues: 858 sheet: 0.36 (0.43), residues: 144 loop : -0.74 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 281 TYR 0.007 0.001 TYR B 842 PHE 0.006 0.001 PHE B 938 TRP 0.009 0.001 TRP B 976 HIS 0.005 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00180 (13250) covalent geometry : angle 0.38183 (17906) hydrogen bonds : bond 0.04460 ( 721) hydrogen bonds : angle 3.71989 ( 2079) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.507 Fit side-chains REVERT: B 420 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7593 (pp) REVERT: B 765 MET cc_start: 0.8797 (tpt) cc_final: 0.8585 (tpt) REVERT: A 420 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7588 (pp) outliers start: 8 outliers final: 6 residues processed: 66 average time/residue: 0.1664 time to fit residues: 18.1829 Evaluate side-chains 64 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 989 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 989 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 154 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 643 GLN A 244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.098064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.071661 restraints weight = 60296.864| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.00 r_work: 0.2797 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13250 Z= 0.158 Angle : 0.431 5.228 17906 Z= 0.232 Chirality : 0.038 0.149 1974 Planarity : 0.003 0.026 2218 Dihedral : 10.258 90.097 2126 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.52 % Favored : 96.36 % Rotamer: Outliers : 0.68 % Allowed : 4.61 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.22), residues: 1564 helix: 2.71 (0.18), residues: 854 sheet: 0.26 (0.44), residues: 144 loop : -0.69 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 300 TYR 0.011 0.001 TYR B 511 PHE 0.010 0.001 PHE B 984 TRP 0.006 0.001 TRP B 933 HIS 0.006 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00377 (13250) covalent geometry : angle 0.43073 (17906) hydrogen bonds : bond 0.05338 ( 721) hydrogen bonds : angle 3.84911 ( 2079) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.631 Fit side-chains REVERT: B 420 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7505 (pp) REVERT: B 699 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8603 (m-80) REVERT: B 765 MET cc_start: 0.8760 (tpt) cc_final: 0.8513 (tpt) REVERT: A 420 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7486 (pp) REVERT: A 699 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.8591 (m-80) outliers start: 9 outliers final: 5 residues processed: 63 average time/residue: 0.1893 time to fit residues: 19.8180 Evaluate side-chains 64 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 989 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 989 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 32 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 149 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.099199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.073822 restraints weight = 59631.030| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.87 r_work: 0.2828 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13250 Z= 0.109 Angle : 0.398 5.119 17906 Z= 0.214 Chirality : 0.037 0.143 1974 Planarity : 0.003 0.026 2218 Dihedral : 10.050 90.687 2126 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.45 % Favored : 96.42 % Rotamer: Outliers : 0.61 % Allowed : 4.69 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.22), residues: 1564 helix: 2.74 (0.18), residues: 858 sheet: 0.31 (0.44), residues: 144 loop : -0.73 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 446 TYR 0.008 0.001 TYR A 511 PHE 0.009 0.001 PHE B 984 TRP 0.007 0.001 TRP B 976 HIS 0.004 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00247 (13250) covalent geometry : angle 0.39810 (17906) hydrogen bonds : bond 0.04884 ( 721) hydrogen bonds : angle 3.77980 ( 2079) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.651 Fit side-chains REVERT: B 420 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.7727 (pp) REVERT: B 765 MET cc_start: 0.8832 (tpt) cc_final: 0.8613 (tpt) REVERT: A 420 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.7722 (pp) outliers start: 8 outliers final: 4 residues processed: 63 average time/residue: 0.1676 time to fit residues: 17.5549 Evaluate side-chains 61 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 989 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 989 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 140 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 88 optimal weight: 0.2980 chunk 69 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.097750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.072292 restraints weight = 59943.372| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.88 r_work: 0.2795 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13250 Z= 0.152 Angle : 0.428 5.278 17906 Z= 0.231 Chirality : 0.038 0.149 1974 Planarity : 0.003 0.024 2218 Dihedral : 10.194 90.634 2122 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.90 % Favored : 95.97 % Rotamer: Outliers : 0.45 % Allowed : 4.84 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.22), residues: 1564 helix: 2.71 (0.18), residues: 852 sheet: 0.01 (0.44), residues: 146 loop : -0.69 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 446 TYR 0.011 0.001 TYR B 511 PHE 0.011 0.001 PHE B 984 TRP 0.007 0.001 TRP B 933 HIS 0.004 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00361 (13250) covalent geometry : angle 0.42834 (17906) hydrogen bonds : bond 0.05400 ( 721) hydrogen bonds : angle 3.87266 ( 2079) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5354.10 seconds wall clock time: 91 minutes 23.23 seconds (5483.23 seconds total)