Starting phenix.real_space_refine on Sun Apr 5 19:54:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xjl_66939/04_2026/9xjl_66939.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xjl_66939/04_2026/9xjl_66939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xjl_66939/04_2026/9xjl_66939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xjl_66939/04_2026/9xjl_66939.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xjl_66939/04_2026/9xjl_66939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xjl_66939/04_2026/9xjl_66939.map" } resolution = 3.8 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= 0.001 sd= 0.015 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 8266 2.51 5 N 2066 2.21 5 O 2322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12734 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3179 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3188 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 15, 'TRANS': 392} Chain breaks: 1 Chain: "C" Number of atoms: 3179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3179 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3188 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 15, 'TRANS': 392} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASP A 592 " occ=0.60 ... (6 atoms not shown) pdb=" OD2 ASP A 592 " occ=0.60 residue: pdb=" N ASP C 592 " occ=0.60 ... (6 atoms not shown) pdb=" OD2 ASP C 592 " occ=0.60 Time building chain proxies: 2.54, per 1000 atoms: 0.20 Number of scatterers: 12734 At special positions: 0 Unit cell: (133.45, 101.15, 135.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2322 8.00 N 2066 7.00 C 8266 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 775 " distance=2.03 Simple disulfide: pdb=" SG CYS D 720 " - pdb=" SG CYS D 775 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 775 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 775 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 470.5 milliseconds 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2988 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 18 sheets defined 49.4% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 425 through 439 Processing helix chain 'A' and resid 457 through 460 removed outlier: 3.676A pdb=" N LYS A 460 " --> pdb=" O ALA A 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 460' Processing helix chain 'A' and resid 465 through 472 Processing helix chain 'A' and resid 484 through 489 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.709A pdb=" N LEU A 520 " --> pdb=" O PHE A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.569A pdb=" N TRP A 528 " --> pdb=" O ALA A 524 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET A 529 " --> pdb=" O TYR A 525 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N CYS A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL A 532 " --> pdb=" O TRP A 528 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE A 533 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 548 Processing helix chain 'A' and resid 577 through 585 removed outlier: 3.739A pdb=" N SER A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 626 removed outlier: 3.550A pdb=" N GLY A 605 " --> pdb=" O ARG A 601 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP A 607 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 609 " --> pdb=" O GLY A 605 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A 613 " --> pdb=" O PHE A 609 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 615 " --> pdb=" O THR A 611 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 619 " --> pdb=" O ILE A 615 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 623 " --> pdb=" O THR A 619 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 624 " --> pdb=" O ALA A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 644 removed outlier: 3.830A pdb=" N GLN A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 664 Processing helix chain 'A' and resid 666 through 678 removed outlier: 4.089A pdb=" N SER A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 698 removed outlier: 3.683A pdb=" N SER A 698 " --> pdb=" O ARG A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 716 removed outlier: 3.782A pdb=" N TYR A 713 " --> pdb=" O THR A 709 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 759 removed outlier: 3.720A pdb=" N LEU A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 770 removed outlier: 4.017A pdb=" N LYS A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 820 removed outlier: 3.528A pdb=" N TYR A 799 " --> pdb=" O ALA A 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 439 removed outlier: 3.547A pdb=" N ASP D 429 " --> pdb=" O GLY D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 471 removed outlier: 3.760A pdb=" N LEU D 469 " --> pdb=" O MET D 465 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL D 470 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR D 471 " --> pdb=" O GLY D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 489 Processing helix chain 'D' and resid 524 through 549 removed outlier: 3.508A pdb=" N TRP D 528 " --> pdb=" O ALA D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 587 Processing helix chain 'D' and resid 600 through 626 removed outlier: 3.690A pdb=" N ALA D 624 " --> pdb=" O ALA D 620 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE D 625 " --> pdb=" O ASN D 621 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 626 " --> pdb=" O LEU D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 643 removed outlier: 3.713A pdb=" N ALA D 642 " --> pdb=" O ALA D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 663 Processing helix chain 'D' and resid 666 through 679 removed outlier: 3.566A pdb=" N MET D 672 " --> pdb=" O VAL D 668 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER D 678 " --> pdb=" O THR D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 698 Processing helix chain 'D' and resid 708 through 716 removed outlier: 3.552A pdb=" N GLN D 716 " --> pdb=" O GLU D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 759 removed outlier: 3.657A pdb=" N GLY D 759 " --> pdb=" O LEU D 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 770 removed outlier: 4.127A pdb=" N LYS D 765 " --> pdb=" O LEU D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 823 removed outlier: 4.059A pdb=" N PHE D 798 " --> pdb=" O VAL D 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 421 No H-bonds generated for 'chain 'C' and resid 419 through 421' Processing helix chain 'C' and resid 425 through 439 Processing helix chain 'C' and resid 457 through 460 removed outlier: 3.676A pdb=" N LYS C 460 " --> pdb=" O ALA C 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 457 through 460' Processing helix chain 'C' and resid 465 through 472 Processing helix chain 'C' and resid 484 through 489 Processing helix chain 'C' and resid 517 through 521 removed outlier: 3.709A pdb=" N LEU C 520 " --> pdb=" O PHE C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 536 removed outlier: 3.568A pdb=" N TRP C 528 " --> pdb=" O ALA C 524 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET C 529 " --> pdb=" O TYR C 525 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N CYS C 530 " --> pdb=" O GLU C 526 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL C 532 " --> pdb=" O TRP C 528 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE C 533 " --> pdb=" O MET C 529 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 548 Processing helix chain 'C' and resid 577 through 585 removed outlier: 3.739A pdb=" N SER C 582 " --> pdb=" O SER C 578 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU C 583 " --> pdb=" O LEU C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 626 removed outlier: 3.551A pdb=" N GLY C 605 " --> pdb=" O ARG C 601 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP C 607 " --> pdb=" O VAL C 603 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE C 609 " --> pdb=" O GLY C 605 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE C 613 " --> pdb=" O PHE C 609 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE C 614 " --> pdb=" O PHE C 610 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE C 615 " --> pdb=" O THR C 611 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER C 616 " --> pdb=" O LEU C 612 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR C 619 " --> pdb=" O ILE C 615 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA C 623 " --> pdb=" O THR C 619 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA C 624 " --> pdb=" O ALA C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 644 removed outlier: 3.829A pdb=" N GLN C 644 " --> pdb=" O ASP C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 664 Processing helix chain 'C' and resid 666 through 678 removed outlier: 4.090A pdb=" N SER C 678 " --> pdb=" O THR C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 698 removed outlier: 3.682A pdb=" N SER C 698 " --> pdb=" O ARG C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 716 removed outlier: 3.782A pdb=" N TYR C 713 " --> pdb=" O THR C 709 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN C 716 " --> pdb=" O GLU C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 759 removed outlier: 3.720A pdb=" N LEU C 753 " --> pdb=" O ASN C 749 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS C 754 " --> pdb=" O LEU C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 770 removed outlier: 4.017A pdb=" N LYS C 765 " --> pdb=" O LEU C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 820 removed outlier: 3.528A pdb=" N TYR C 799 " --> pdb=" O ALA C 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 439 removed outlier: 3.547A pdb=" N ASP B 429 " --> pdb=" O GLY B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 removed outlier: 3.761A pdb=" N LEU B 469 " --> pdb=" O MET B 465 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL B 470 " --> pdb=" O VAL B 466 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR B 471 " --> pdb=" O GLY B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'B' and resid 524 through 549 removed outlier: 3.508A pdb=" N TRP B 528 " --> pdb=" O ALA B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 587 Processing helix chain 'B' and resid 600 through 626 removed outlier: 3.689A pdb=" N ALA B 624 " --> pdb=" O ALA B 620 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE B 625 " --> pdb=" O ASN B 621 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.713A pdb=" N ALA B 642 " --> pdb=" O ALA B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 663 Processing helix chain 'B' and resid 666 through 679 removed outlier: 3.566A pdb=" N MET B 672 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B 678 " --> pdb=" O THR B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 698 Processing helix chain 'B' and resid 708 through 716 removed outlier: 3.552A pdb=" N GLN B 716 " --> pdb=" O GLU B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 759 removed outlier: 3.657A pdb=" N GLY B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 770 removed outlier: 4.126A pdb=" N LYS B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 823 removed outlier: 4.059A pdb=" N PHE B 798 " --> pdb=" O VAL B 794 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 397 through 399 removed outlier: 6.440A pdb=" N VAL A 397 " --> pdb=" O LYS A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 409 through 410 removed outlier: 3.627A pdb=" N MET A 409 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 424 " --> pdb=" O MET A 409 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 455 Processing sheet with id=AA4, first strand: chain 'A' and resid 504 through 507 removed outlier: 3.767A pdb=" N ILE A 504 " --> pdb=" O VAL A 725 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 397 through 399 removed outlier: 6.114A pdb=" N VAL D 397 " --> pdb=" O LYS D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 409 through 410 Processing sheet with id=AA7, first strand: chain 'D' and resid 491 through 492 Processing sheet with id=AA8, first strand: chain 'D' and resid 498 through 500 removed outlier: 4.110A pdb=" N MET D 498 " --> pdb=" O TYR D 734 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS D 732 " --> pdb=" O LEU D 500 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 648 through 650 removed outlier: 6.925A pdb=" N ALA D 648 " --> pdb=" O ALA D 703 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N LEU D 705 " --> pdb=" O ALA D 648 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLY D 650 " --> pdb=" O LEU D 705 " (cutoff:3.500A) removed outlier: 9.510A pdb=" N GLU D 707 " --> pdb=" O GLY D 650 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N PHE D 702 " --> pdb=" O LYS D 507 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LYS D 507 " --> pdb=" O PHE D 702 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE D 504 " --> pdb=" O VAL D 725 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 397 through 399 removed outlier: 6.441A pdb=" N VAL C 397 " --> pdb=" O LYS C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 409 through 410 removed outlier: 3.627A pdb=" N MET C 409 " --> pdb=" O GLU C 424 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU C 424 " --> pdb=" O MET C 409 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 453 through 455 Processing sheet with id=AB4, first strand: chain 'C' and resid 504 through 507 removed outlier: 3.766A pdb=" N ILE C 504 " --> pdb=" O VAL C 725 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 397 through 399 removed outlier: 6.114A pdb=" N VAL B 397 " --> pdb=" O LYS B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 409 through 410 Processing sheet with id=AB7, first strand: chain 'B' and resid 491 through 492 Processing sheet with id=AB8, first strand: chain 'B' and resid 498 through 500 removed outlier: 4.109A pdb=" N MET B 498 " --> pdb=" O TYR B 734 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 732 " --> pdb=" O LEU B 500 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 648 through 650 removed outlier: 6.926A pdb=" N ALA B 648 " --> pdb=" O ALA B 703 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N LEU B 705 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLY B 650 " --> pdb=" O LEU B 705 " (cutoff:3.500A) removed outlier: 9.510A pdb=" N GLU B 707 " --> pdb=" O GLY B 650 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N PHE B 702 " --> pdb=" O LYS B 507 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LYS B 507 " --> pdb=" O PHE B 702 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE B 504 " --> pdb=" O VAL B 725 " (cutoff:3.500A) 504 hydrogen bonds defined for protein. 1494 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: 1.88 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3908 1.34 - 1.46: 3112 1.46 - 1.58: 5862 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 13018 Sorted by residual: bond pdb=" N GLU A 646 " pdb=" CA GLU A 646 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.10e+00 bond pdb=" N GLU C 646 " pdb=" CA GLU C 646 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.33e+00 bond pdb=" C ASP C 521 " pdb=" N PRO C 522 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.63e+00 bond pdb=" C ASP A 521 " pdb=" N PRO A 522 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.58e+00 bond pdb=" CA ASN C 413 " pdb=" CB ASN C 413 " ideal model delta sigma weight residual 1.527 1.548 -0.021 1.70e-02 3.46e+03 1.50e+00 ... (remaining 13013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 17303 2.14 - 4.28: 233 4.28 - 6.42: 26 6.42 - 8.57: 4 8.57 - 10.71: 2 Bond angle restraints: 17568 Sorted by residual: angle pdb=" N VAL A 628 " pdb=" CA VAL A 628 " pdb=" C VAL A 628 " ideal model delta sigma weight residual 112.98 108.92 4.06 1.25e+00 6.40e-01 1.05e+01 angle pdb=" N VAL C 628 " pdb=" CA VAL C 628 " pdb=" C VAL C 628 " ideal model delta sigma weight residual 112.98 108.93 4.05 1.25e+00 6.40e-01 1.05e+01 angle pdb=" CA LEU C 641 " pdb=" CB LEU C 641 " pdb=" CG LEU C 641 " ideal model delta sigma weight residual 116.30 127.01 -10.71 3.50e+00 8.16e-02 9.36e+00 angle pdb=" CA LEU A 641 " pdb=" CB LEU A 641 " pdb=" CG LEU A 641 " ideal model delta sigma weight residual 116.30 126.97 -10.67 3.50e+00 8.16e-02 9.30e+00 angle pdb=" CA GLU C 690 " pdb=" CB GLU C 690 " pdb=" CG GLU C 690 " ideal model delta sigma weight residual 114.10 120.17 -6.07 2.00e+00 2.50e-01 9.20e+00 ... (remaining 17563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 6552 17.34 - 34.68: 933 34.68 - 52.02: 216 52.02 - 69.35: 37 69.35 - 86.69: 22 Dihedral angle restraints: 7760 sinusoidal: 3078 harmonic: 4682 Sorted by residual: dihedral pdb=" CA GLY C 472 " pdb=" C GLY C 472 " pdb=" N LYS C 473 " pdb=" CA LYS C 473 " ideal model delta harmonic sigma weight residual 180.00 163.34 16.66 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA GLY A 472 " pdb=" C GLY A 472 " pdb=" N LYS A 473 " pdb=" CA LYS A 473 " ideal model delta harmonic sigma weight residual 180.00 163.40 16.60 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CB GLU C 774 " pdb=" CG GLU C 774 " pdb=" CD GLU C 774 " pdb=" OE1 GLU C 774 " ideal model delta sinusoidal sigma weight residual 0.00 86.69 -86.69 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 7757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1365 0.037 - 0.074: 423 0.074 - 0.111: 138 0.111 - 0.148: 28 0.148 - 0.185: 4 Chirality restraints: 1958 Sorted by residual: chirality pdb=" CB VAL C 545 " pdb=" CA VAL C 545 " pdb=" CG1 VAL C 545 " pdb=" CG2 VAL C 545 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CB VAL A 545 " pdb=" CA VAL A 545 " pdb=" CG1 VAL A 545 " pdb=" CG2 VAL A 545 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA ASN A 413 " pdb=" N ASN A 413 " pdb=" C ASN A 413 " pdb=" CB ASN A 413 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 1955 not shown) Planarity restraints: 2172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 420 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.52e+00 pdb=" C ASN B 420 " 0.037 2.00e-02 2.50e+03 pdb=" O ASN B 420 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP B 421 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 420 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C ASN D 420 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN D 420 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP D 421 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 447 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO A 448 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 448 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 448 " -0.028 5.00e-02 4.00e+02 ... (remaining 2169 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2681 2.77 - 3.31: 11659 3.31 - 3.84: 19448 3.84 - 4.37: 20542 4.37 - 4.90: 37974 Nonbonded interactions: 92304 Sorted by model distance: nonbonded pdb=" OD2 ASP B 456 " pdb=" OG1 THR B 459 " model vdw 2.242 3.040 nonbonded pdb=" OD2 ASP D 456 " pdb=" OG1 THR D 459 " model vdw 2.242 3.040 nonbonded pdb=" OD2 ASP A 730 " pdb=" NZ LYS A 732 " model vdw 2.294 3.120 nonbonded pdb=" OD2 ASP C 730 " pdb=" NZ LYS C 732 " model vdw 2.295 3.120 nonbonded pdb=" O ASP C 458 " pdb=" OG1 THR C 459 " model vdw 2.301 3.040 ... (remaining 92299 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.60 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.970 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.990 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 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 : 0.003 0.034 13022 Z= 0.145 Angle : 0.603 10.707 17576 Z= 0.327 Chirality : 0.041 0.185 1958 Planarity : 0.004 0.050 2172 Dihedral : 16.984 86.692 4760 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 28.82 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.21), residues: 1614 helix: 0.18 (0.20), residues: 782 sheet: -1.82 (0.40), residues: 162 loop : -2.97 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 677 TYR 0.013 0.001 TYR C 426 PHE 0.014 0.001 PHE D 417 TRP 0.012 0.001 TRP C 580 HIS 0.003 0.001 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00312 (13018) covalent geometry : angle 0.60307 (17568) SS BOND : bond 0.00144 ( 4) SS BOND : angle 0.28691 ( 8) hydrogen bonds : bond 0.17550 ( 504) hydrogen bonds : angle 6.16697 ( 1494) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 692 VAL cc_start: 0.7205 (t) cc_final: 0.6149 (t) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.1155 time to fit residues: 58.5998 Evaluate side-chains 183 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 414 HIS ** D 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 621 ASN B 414 HIS B 621 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.147019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.111713 restraints weight = 26609.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.114734 restraints weight = 15782.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.116732 restraints weight = 11789.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.117774 restraints weight = 9950.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.118622 restraints weight = 9059.200| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13022 Z= 0.120 Angle : 0.587 7.746 17576 Z= 0.304 Chirality : 0.041 0.152 1958 Planarity : 0.004 0.044 2172 Dihedral : 3.905 19.059 1758 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.06 % Allowed : 27.37 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.50 (0.21), residues: 1614 helix: 0.62 (0.20), residues: 792 sheet: -2.00 (0.39), residues: 174 loop : -2.83 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 663 TYR 0.012 0.001 TYR B 407 PHE 0.026 0.001 PHE A 519 TRP 0.030 0.001 TRP D 673 HIS 0.003 0.001 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00268 (13018) covalent geometry : angle 0.58702 (17568) SS BOND : bond 0.00557 ( 4) SS BOND : angle 1.22954 ( 8) hydrogen bonds : bond 0.04153 ( 504) hydrogen bonds : angle 4.26722 ( 1494) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 200 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 TYR cc_start: 0.6463 (m-10) cc_final: 0.6223 (m-10) REVERT: A 578 SER cc_start: 0.8526 (m) cc_final: 0.8270 (p) REVERT: A 659 GLU cc_start: 0.7935 (tp30) cc_final: 0.7087 (tp30) REVERT: A 663 ARG cc_start: 0.8314 (ttm110) cc_final: 0.7851 (ttm-80) REVERT: D 462 TRP cc_start: 0.7255 (m100) cc_final: 0.6765 (m100) REVERT: D 520 LEU cc_start: 0.8379 (mt) cc_final: 0.8068 (mp) REVERT: D 529 MET cc_start: 0.6706 (mmm) cc_final: 0.6473 (mmt) REVERT: D 587 MET cc_start: 0.6564 (mmt) cc_final: 0.6202 (mmt) REVERT: C 471 TYR cc_start: 0.6393 (m-10) cc_final: 0.6143 (m-10) REVERT: C 576 PHE cc_start: 0.7237 (t80) cc_final: 0.7015 (t80) REVERT: C 813 LEU cc_start: 0.8260 (mm) cc_final: 0.7867 (mt) REVERT: B 587 MET cc_start: 0.6825 (mmt) cc_final: 0.6453 (mmt) REVERT: B 641 LEU cc_start: 0.8699 (tt) cc_final: 0.8480 (tt) REVERT: B 645 THR cc_start: 0.7463 (m) cc_final: 0.7101 (p) outliers start: 42 outliers final: 16 residues processed: 236 average time/residue: 0.0951 time to fit residues: 33.3488 Evaluate side-chains 178 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 714 ILE Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 683 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 91 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 ASN C 711 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.130951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.094072 restraints weight = 26675.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.096802 restraints weight = 16658.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.098525 restraints weight = 12816.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.099606 restraints weight = 10987.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.100259 restraints weight = 10034.908| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 13022 Z= 0.335 Angle : 0.783 9.499 17576 Z= 0.412 Chirality : 0.050 0.215 1958 Planarity : 0.005 0.054 2172 Dihedral : 4.726 19.211 1758 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 6.48 % Allowed : 27.37 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.20), residues: 1614 helix: 0.03 (0.18), residues: 808 sheet: -1.47 (0.50), residues: 120 loop : -2.90 (0.20), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 663 TYR 0.020 0.002 TYR D 407 PHE 0.026 0.003 PHE D 684 TRP 0.066 0.003 TRP D 673 HIS 0.002 0.001 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00783 (13018) covalent geometry : angle 0.78297 (17568) SS BOND : bond 0.00438 ( 4) SS BOND : angle 1.00457 ( 8) hydrogen bonds : bond 0.06673 ( 504) hydrogen bonds : angle 5.06946 ( 1494) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 171 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.7447 (tpp) cc_final: 0.6805 (tpp) REVERT: A 489 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8293 (mt-10) REVERT: A 578 SER cc_start: 0.9032 (m) cc_final: 0.8736 (p) REVERT: A 659 GLU cc_start: 0.7962 (tp30) cc_final: 0.7336 (tp30) REVERT: A 663 ARG cc_start: 0.8315 (ttm110) cc_final: 0.8004 (ttm-80) REVERT: D 403 MET cc_start: 0.7767 (mmm) cc_final: 0.7510 (tpp) REVERT: D 601 ARG cc_start: 0.8650 (mtt-85) cc_final: 0.7905 (mtt-85) REVERT: D 821 ARG cc_start: 0.6411 (mtt180) cc_final: 0.5920 (ttp80) REVERT: C 403 MET cc_start: 0.7671 (tpp) cc_final: 0.7060 (tpp) REVERT: C 423 TYR cc_start: 0.7778 (m-80) cc_final: 0.7577 (m-10) REVERT: C 437 HIS cc_start: 0.7720 (OUTLIER) cc_final: 0.7072 (t-90) REVERT: C 481 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8189 (mp) REVERT: C 578 SER cc_start: 0.9104 (m) cc_final: 0.8779 (p) REVERT: B 587 MET cc_start: 0.8079 (mmt) cc_final: 0.7814 (mtt) outliers start: 89 outliers final: 55 residues processed: 251 average time/residue: 0.0864 time to fit residues: 33.3040 Evaluate side-chains 208 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 151 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 704 PHE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 494 SER Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 714 ILE Chi-restraints excluded: chain D residue 766 ASN Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain C residue 437 HIS Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 619 THR Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 661 PHE Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 704 PHE Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 814 ILE Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 813 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 5 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 HIS ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.135408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.099421 restraints weight = 26073.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.102380 restraints weight = 15978.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.104247 restraints weight = 12124.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.105383 restraints weight = 10315.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.106063 restraints weight = 9374.913| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13022 Z= 0.125 Angle : 0.588 8.433 17576 Z= 0.300 Chirality : 0.041 0.215 1958 Planarity : 0.004 0.042 2172 Dihedral : 4.003 17.506 1758 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.71 % Allowed : 30.06 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.23 (0.21), residues: 1614 helix: 0.72 (0.20), residues: 802 sheet: -1.44 (0.56), residues: 96 loop : -2.62 (0.20), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 663 TYR 0.012 0.001 TYR D 426 PHE 0.025 0.001 PHE C 519 TRP 0.032 0.001 TRP D 673 HIS 0.002 0.001 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00295 (13018) covalent geometry : angle 0.58680 (17568) SS BOND : bond 0.00945 ( 4) SS BOND : angle 1.51336 ( 8) hydrogen bonds : bond 0.03969 ( 504) hydrogen bonds : angle 4.26758 ( 1494) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 175 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.7846 (tpp) cc_final: 0.7405 (tpp) REVERT: A 578 SER cc_start: 0.8922 (m) cc_final: 0.8562 (p) REVERT: A 659 GLU cc_start: 0.7906 (tp30) cc_final: 0.7207 (tp30) REVERT: A 663 ARG cc_start: 0.8286 (ttm110) cc_final: 0.7969 (ttm-80) REVERT: D 576 PHE cc_start: 0.7571 (OUTLIER) cc_final: 0.7188 (t80) REVERT: D 750 LEU cc_start: 0.8392 (mt) cc_final: 0.8142 (mp) REVERT: C 437 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.7030 (t-90) REVERT: C 578 SER cc_start: 0.8947 (m) cc_final: 0.8542 (p) REVERT: B 576 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.7251 (t80) outliers start: 51 outliers final: 31 residues processed: 219 average time/residue: 0.0884 time to fit residues: 29.3398 Evaluate side-chains 191 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 704 PHE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 494 SER Chi-restraints excluded: chain D residue 576 PHE Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 704 PHE Chi-restraints excluded: chain D residue 714 ILE Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain C residue 437 HIS Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 704 PHE Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 704 PHE Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 813 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 9 optimal weight: 0.0770 chunk 98 optimal weight: 0.0870 chunk 159 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 153 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 132 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 HIS D 414 HIS D 437 HIS C 437 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.141162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.109418 restraints weight = 25982.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.109699 restraints weight = 19503.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.111098 restraints weight = 15167.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.111441 restraints weight = 12702.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.111713 restraints weight = 12031.244| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13022 Z= 0.103 Angle : 0.563 9.131 17576 Z= 0.282 Chirality : 0.041 0.242 1958 Planarity : 0.004 0.050 2172 Dihedral : 3.678 16.957 1758 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.08 % Allowed : 30.06 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.22), residues: 1614 helix: 0.93 (0.20), residues: 800 sheet: -0.96 (0.45), residues: 148 loop : -2.75 (0.21), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 677 TYR 0.009 0.001 TYR B 426 PHE 0.026 0.001 PHE C 519 TRP 0.038 0.001 TRP D 673 HIS 0.021 0.002 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00236 (13018) covalent geometry : angle 0.56220 (17568) SS BOND : bond 0.00383 ( 4) SS BOND : angle 1.07732 ( 8) hydrogen bonds : bond 0.03232 ( 504) hydrogen bonds : angle 4.06837 ( 1494) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 177 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.7731 (tpp) cc_final: 0.7339 (tpt) REVERT: A 410 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.7255 (t80) REVERT: A 471 TYR cc_start: 0.6281 (m-10) cc_final: 0.5908 (m-10) REVERT: A 578 SER cc_start: 0.8777 (m) cc_final: 0.8450 (p) REVERT: A 659 GLU cc_start: 0.7817 (tp30) cc_final: 0.7030 (tp30) REVERT: A 663 ARG cc_start: 0.8151 (ttm110) cc_final: 0.7782 (ttm-80) REVERT: D 576 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7298 (t80) REVERT: D 631 MET cc_start: 0.8375 (mmm) cc_final: 0.8121 (tmm) REVERT: D 719 PRO cc_start: 0.8334 (Cg_exo) cc_final: 0.8127 (Cg_endo) REVERT: C 576 PHE cc_start: 0.7244 (t80) cc_final: 0.7040 (t80) REVERT: C 578 SER cc_start: 0.8827 (m) cc_final: 0.8503 (p) REVERT: C 731 SER cc_start: 0.9300 (m) cc_final: 0.9088 (p) REVERT: C 813 LEU cc_start: 0.8320 (mm) cc_final: 0.8028 (mp) REVERT: B 576 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.7270 (t80) REVERT: B 817 CYS cc_start: 0.7361 (m) cc_final: 0.6815 (t) outliers start: 56 outliers final: 37 residues processed: 225 average time/residue: 0.0868 time to fit residues: 30.0379 Evaluate side-chains 205 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 704 PHE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain D residue 414 HIS Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 494 SER Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 576 PHE Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 704 PHE Chi-restraints excluded: chain D residue 766 ASN Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain C residue 437 HIS Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 704 PHE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 704 PHE Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 813 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 26 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 120 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 414 HIS B 414 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.140643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.109348 restraints weight = 27345.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.109390 restraints weight = 22513.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.110340 restraints weight = 17065.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.111290 restraints weight = 14385.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.111492 restraints weight = 13027.960| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13022 Z= 0.112 Angle : 0.582 12.005 17576 Z= 0.288 Chirality : 0.041 0.254 1958 Planarity : 0.004 0.044 2172 Dihedral : 3.593 16.893 1758 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.66 % Allowed : 28.75 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.22), residues: 1614 helix: 1.05 (0.20), residues: 794 sheet: -1.24 (0.43), residues: 162 loop : -2.65 (0.21), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 663 TYR 0.008 0.001 TYR D 407 PHE 0.021 0.001 PHE C 519 TRP 0.039 0.001 TRP D 673 HIS 0.014 0.002 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00263 (13018) covalent geometry : angle 0.58026 (17568) SS BOND : bond 0.00228 ( 4) SS BOND : angle 1.93651 ( 8) hydrogen bonds : bond 0.03303 ( 504) hydrogen bonds : angle 4.03703 ( 1494) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 174 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.7663 (tpp) cc_final: 0.7394 (tpt) REVERT: A 471 TYR cc_start: 0.6285 (m-10) cc_final: 0.5904 (m-10) REVERT: A 485 LEU cc_start: 0.9108 (tp) cc_final: 0.8805 (mm) REVERT: A 578 SER cc_start: 0.8710 (m) cc_final: 0.8421 (p) REVERT: A 659 GLU cc_start: 0.7948 (tp30) cc_final: 0.7008 (tp30) REVERT: A 663 ARG cc_start: 0.8166 (ttm110) cc_final: 0.7744 (ttm-80) REVERT: D 576 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.7345 (t80) REVERT: D 631 MET cc_start: 0.8373 (mmm) cc_final: 0.8112 (tmm) REVERT: D 719 PRO cc_start: 0.8352 (Cg_exo) cc_final: 0.8152 (Cg_endo) REVERT: C 437 HIS cc_start: 0.7404 (OUTLIER) cc_final: 0.7200 (t-90) REVERT: C 578 SER cc_start: 0.8801 (m) cc_final: 0.8471 (p) REVERT: C 731 SER cc_start: 0.9303 (m) cc_final: 0.9089 (p) REVERT: C 813 LEU cc_start: 0.8320 (mm) cc_final: 0.8007 (mp) REVERT: B 500 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8166 (pp) REVERT: B 576 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.7248 (t80) REVERT: B 817 CYS cc_start: 0.7280 (m) cc_final: 0.6731 (t) outliers start: 64 outliers final: 42 residues processed: 226 average time/residue: 0.0845 time to fit residues: 29.5759 Evaluate side-chains 207 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 576 PHE Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 704 PHE Chi-restraints excluded: chain D residue 714 ILE Chi-restraints excluded: chain D residue 766 ASN Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain C residue 437 HIS Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 704 PHE Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 813 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 112 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 156 optimal weight: 0.0570 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 414 HIS B 414 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.139814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.107958 restraints weight = 26092.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.107906 restraints weight = 24926.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.108922 restraints weight = 17276.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.109700 restraints weight = 14255.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.110017 restraints weight = 12991.024| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13022 Z= 0.121 Angle : 0.592 10.246 17576 Z= 0.292 Chirality : 0.042 0.268 1958 Planarity : 0.004 0.040 2172 Dihedral : 3.563 16.296 1758 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 5.09 % Allowed : 28.68 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.22), residues: 1614 helix: 1.13 (0.20), residues: 796 sheet: -1.17 (0.42), residues: 162 loop : -2.60 (0.21), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 663 TYR 0.008 0.001 TYR D 407 PHE 0.020 0.001 PHE C 519 TRP 0.045 0.001 TRP D 673 HIS 0.002 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00289 (13018) covalent geometry : angle 0.59081 (17568) SS BOND : bond 0.00425 ( 4) SS BOND : angle 1.72406 ( 8) hydrogen bonds : bond 0.03435 ( 504) hydrogen bonds : angle 4.06911 ( 1494) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 171 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 TYR cc_start: 0.6266 (m-10) cc_final: 0.5905 (m-10) REVERT: A 578 SER cc_start: 0.8719 (m) cc_final: 0.8444 (p) REVERT: A 659 GLU cc_start: 0.7987 (tp30) cc_final: 0.7057 (tp30) REVERT: A 663 ARG cc_start: 0.8176 (ttm110) cc_final: 0.7696 (ttm-80) REVERT: A 731 SER cc_start: 0.9326 (m) cc_final: 0.9036 (p) REVERT: D 576 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7338 (t80) REVERT: D 631 MET cc_start: 0.8335 (mmm) cc_final: 0.8108 (tmm) REVERT: D 791 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8544 (mt) REVERT: C 403 MET cc_start: 0.7873 (tpp) cc_final: 0.7249 (tpp) REVERT: C 578 SER cc_start: 0.8760 (m) cc_final: 0.8433 (p) REVERT: C 731 SER cc_start: 0.9292 (m) cc_final: 0.9070 (p) REVERT: B 500 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8144 (pp) REVERT: B 817 CYS cc_start: 0.7356 (m) cc_final: 0.6718 (t) outliers start: 70 outliers final: 50 residues processed: 229 average time/residue: 0.0867 time to fit residues: 30.6339 Evaluate side-chains 211 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 158 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 704 PHE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 437 HIS Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 576 PHE Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 704 PHE Chi-restraints excluded: chain D residue 714 ILE Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 766 ASN Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 704 PHE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 813 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 85 optimal weight: 9.9990 chunk 144 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 437 HIS B 414 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.135785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.100111 restraints weight = 26533.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.103061 restraints weight = 16199.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.104925 restraints weight = 12245.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.106051 restraints weight = 10422.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.106612 restraints weight = 9498.517| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13022 Z= 0.138 Angle : 0.620 15.095 17576 Z= 0.303 Chirality : 0.042 0.343 1958 Planarity : 0.004 0.040 2172 Dihedral : 3.622 15.666 1758 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.73 % Allowed : 29.18 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.22), residues: 1614 helix: 1.04 (0.20), residues: 804 sheet: -1.22 (0.42), residues: 162 loop : -2.67 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 662 TYR 0.009 0.001 TYR D 407 PHE 0.024 0.001 PHE C 576 TRP 0.048 0.001 TRP D 673 HIS 0.002 0.001 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00329 (13018) covalent geometry : angle 0.61981 (17568) SS BOND : bond 0.00307 ( 4) SS BOND : angle 1.24748 ( 8) hydrogen bonds : bond 0.03812 ( 504) hydrogen bonds : angle 4.16516 ( 1494) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 167 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.7336 (mmm) cc_final: 0.6945 (mtm) REVERT: A 471 TYR cc_start: 0.6398 (m-10) cc_final: 0.6019 (m-10) REVERT: A 578 SER cc_start: 0.8764 (m) cc_final: 0.8423 (p) REVERT: A 659 GLU cc_start: 0.8081 (tp30) cc_final: 0.7861 (tp30) REVERT: A 712 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: A 731 SER cc_start: 0.9382 (m) cc_final: 0.9077 (p) REVERT: D 576 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.7386 (t80) REVERT: D 601 ARG cc_start: 0.8145 (mtt-85) cc_final: 0.7521 (mtt-85) REVERT: D 631 MET cc_start: 0.8426 (mmm) cc_final: 0.8095 (tmm) REVERT: D 791 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8546 (mt) REVERT: C 403 MET cc_start: 0.7953 (tpp) cc_final: 0.7444 (tpp) REVERT: C 578 SER cc_start: 0.8860 (m) cc_final: 0.8456 (p) REVERT: C 731 SER cc_start: 0.9345 (m) cc_final: 0.9126 (p) REVERT: C 784 ASP cc_start: 0.8355 (t70) cc_final: 0.7916 (t0) REVERT: B 500 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8100 (pp) REVERT: B 601 ARG cc_start: 0.8038 (mtt-85) cc_final: 0.7001 (mtt-85) REVERT: B 817 CYS cc_start: 0.7372 (m) cc_final: 0.6876 (t) outliers start: 65 outliers final: 53 residues processed: 222 average time/residue: 0.0899 time to fit residues: 30.5369 Evaluate side-chains 213 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 156 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 704 PHE Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 494 SER Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 576 PHE Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 704 PHE Chi-restraints excluded: chain D residue 714 ILE Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 766 ASN Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 437 HIS Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 704 PHE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 704 PHE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 813 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 131 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 35 optimal weight: 0.0980 chunk 10 optimal weight: 0.0370 chunk 19 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 437 HIS B 414 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.137793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.102421 restraints weight = 26553.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.105377 restraints weight = 16021.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.107303 restraints weight = 12127.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.108284 restraints weight = 10286.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.109142 restraints weight = 9385.196| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13022 Z= 0.107 Angle : 0.607 14.044 17576 Z= 0.295 Chirality : 0.042 0.393 1958 Planarity : 0.004 0.042 2172 Dihedral : 3.533 16.708 1758 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.08 % Allowed : 29.62 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.22), residues: 1614 helix: 1.13 (0.20), residues: 804 sheet: -1.23 (0.46), residues: 140 loop : -2.56 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 662 TYR 0.015 0.001 TYR D 734 PHE 0.019 0.001 PHE C 519 TRP 0.054 0.001 TRP D 673 HIS 0.009 0.002 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00249 (13018) covalent geometry : angle 0.60703 (17568) SS BOND : bond 0.00248 ( 4) SS BOND : angle 0.97284 ( 8) hydrogen bonds : bond 0.03222 ( 504) hydrogen bonds : angle 4.02385 ( 1494) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 162 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 TYR cc_start: 0.6320 (m-10) cc_final: 0.5991 (m-10) REVERT: A 578 SER cc_start: 0.8705 (m) cc_final: 0.8348 (p) REVERT: A 659 GLU cc_start: 0.8060 (tp30) cc_final: 0.7608 (tp30) REVERT: A 731 SER cc_start: 0.9338 (m) cc_final: 0.9045 (p) REVERT: D 601 ARG cc_start: 0.7933 (mtt-85) cc_final: 0.7270 (mtt-85) REVERT: D 631 MET cc_start: 0.8342 (mmm) cc_final: 0.8104 (tmm) REVERT: D 791 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8483 (mt) REVERT: D 817 CYS cc_start: 0.7204 (m) cc_final: 0.6609 (t) REVERT: C 578 SER cc_start: 0.8768 (m) cc_final: 0.8404 (p) REVERT: C 731 SER cc_start: 0.9331 (m) cc_final: 0.9079 (p) REVERT: C 784 ASP cc_start: 0.8347 (t70) cc_final: 0.7917 (t0) REVERT: B 500 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8041 (pp) REVERT: B 596 ARG cc_start: 0.7232 (ttp80) cc_final: 0.6487 (mmm160) REVERT: B 817 CYS cc_start: 0.7379 (m) cc_final: 0.6782 (t) outliers start: 56 outliers final: 42 residues processed: 207 average time/residue: 0.0868 time to fit residues: 27.8911 Evaluate side-chains 203 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 704 PHE Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 704 PHE Chi-restraints excluded: chain D residue 766 ASN Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 437 HIS Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 704 PHE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 704 PHE Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 813 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 147 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 42 optimal weight: 0.0770 chunk 45 optimal weight: 0.0050 chunk 139 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 64 optimal weight: 0.0060 chunk 85 optimal weight: 8.9990 overall best weight: 0.9370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 437 HIS B 414 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.136490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.100697 restraints weight = 26758.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.103597 restraints weight = 16541.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.105476 restraints weight = 12648.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.106547 restraints weight = 10773.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.107078 restraints weight = 9854.762| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13022 Z= 0.122 Angle : 0.616 14.216 17576 Z= 0.299 Chirality : 0.042 0.390 1958 Planarity : 0.004 0.043 2172 Dihedral : 3.525 15.408 1758 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.64 % Allowed : 29.91 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.22), residues: 1614 helix: 1.17 (0.20), residues: 804 sheet: -1.28 (0.42), residues: 164 loop : -2.58 (0.21), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 662 TYR 0.014 0.001 TYR D 734 PHE 0.019 0.001 PHE D 816 TRP 0.014 0.001 TRP B 768 HIS 0.002 0.001 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00294 (13018) covalent geometry : angle 0.61585 (17568) SS BOND : bond 0.00250 ( 4) SS BOND : angle 0.92732 ( 8) hydrogen bonds : bond 0.03437 ( 504) hydrogen bonds : angle 4.07549 ( 1494) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 160 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 TYR cc_start: 0.6306 (m-10) cc_final: 0.5981 (m-10) REVERT: A 578 SER cc_start: 0.8714 (m) cc_final: 0.8343 (p) REVERT: A 659 GLU cc_start: 0.8047 (tp30) cc_final: 0.7595 (tp30) REVERT: A 731 SER cc_start: 0.9347 (m) cc_final: 0.9048 (p) REVERT: D 601 ARG cc_start: 0.7983 (mtt-85) cc_final: 0.7206 (mtt-85) REVERT: D 631 MET cc_start: 0.8417 (mmm) cc_final: 0.8086 (tmm) REVERT: D 791 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8482 (mt) REVERT: D 817 CYS cc_start: 0.7325 (m) cc_final: 0.6701 (t) REVERT: C 578 SER cc_start: 0.8785 (m) cc_final: 0.8410 (p) REVERT: C 731 SER cc_start: 0.9318 (m) cc_final: 0.9086 (p) REVERT: C 784 ASP cc_start: 0.8374 (t70) cc_final: 0.7942 (t0) REVERT: B 500 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8078 (pp) REVERT: B 817 CYS cc_start: 0.7435 (m) cc_final: 0.6784 (t) outliers start: 50 outliers final: 47 residues processed: 201 average time/residue: 0.0904 time to fit residues: 27.8431 Evaluate side-chains 205 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 156 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 704 PHE Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 704 PHE Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 766 ASN Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 437 HIS Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 704 PHE Chi-restraints excluded: chain C residue 712 GLU Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 704 PHE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 813 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 0.0570 chunk 96 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 0.0770 chunk 138 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 overall best weight: 0.8058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 437 HIS B 414 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.136599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.100875 restraints weight = 26664.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.103796 restraints weight = 16461.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.105689 restraints weight = 12525.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.106787 restraints weight = 10680.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.107501 restraints weight = 9747.078| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13022 Z= 0.115 Angle : 0.614 14.026 17576 Z= 0.295 Chirality : 0.042 0.364 1958 Planarity : 0.004 0.043 2172 Dihedral : 3.504 15.562 1758 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.78 % Allowed : 30.20 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.22), residues: 1614 helix: 1.23 (0.20), residues: 804 sheet: -1.28 (0.42), residues: 164 loop : -2.57 (0.21), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 662 TYR 0.013 0.001 TYR D 734 PHE 0.019 0.001 PHE D 816 TRP 0.014 0.001 TRP B 768 HIS 0.004 0.001 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00274 (13018) covalent geometry : angle 0.61434 (17568) SS BOND : bond 0.00239 ( 4) SS BOND : angle 0.88720 ( 8) hydrogen bonds : bond 0.03361 ( 504) hydrogen bonds : angle 4.09082 ( 1494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2209.66 seconds wall clock time: 38 minutes 54.26 seconds (2334.26 seconds total)