Starting phenix.real_space_refine on Wed Feb 4 14:24:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3r_36857/02_2026/8k3r_36857.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3r_36857/02_2026/8k3r_36857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k3r_36857/02_2026/8k3r_36857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3r_36857/02_2026/8k3r_36857.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3r_36857/02_2026/8k3r_36857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3r_36857/02_2026/8k3r_36857.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.060 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 66 5.16 5 C 7258 2.51 5 N 1781 2.21 5 O 1954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11061 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5482 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 20, 'TRANS': 681} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 6, 'GLU:plan': 9, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 5, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 139 Chain: "B" Number of atoms: 5483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5483 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 20, 'TRANS': 681} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 6, 'GLU:plan': 9, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 5, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 139 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 2.60, per 1000 atoms: 0.24 Number of scatterers: 11061 At special positions: 0 Unit cell: (119.78, 98.58, 113.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 2 15.00 O 1954 8.00 N 1781 7.00 C 7258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 483.0 milliseconds 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2678 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 8 sheets defined 64.5% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 392 through 401 removed outlier: 3.610A pdb=" N LEU A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 414 removed outlier: 4.100A pdb=" N LYS A 414 " --> pdb=" O PRO A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 414' Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.967A pdb=" N LEU A 428 " --> pdb=" O PRO A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 439 Processing helix chain 'A' and resid 458 through 478 Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 577 through 588 Processing helix chain 'A' and resid 588 through 594 removed outlier: 3.619A pdb=" N LEU A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 617 Processing helix chain 'A' and resid 618 through 621 removed outlier: 3.836A pdb=" N ASN A 621 " --> pdb=" O GLU A 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 618 through 621' Processing helix chain 'A' and resid 636 through 643 removed outlier: 3.550A pdb=" N PHE A 639 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N LYS A 641 " --> pdb=" O ARG A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 660 Processing helix chain 'A' and resid 660 through 669 removed outlier: 3.712A pdb=" N PHE A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 687 Processing helix chain 'A' and resid 688 through 696 Processing helix chain 'A' and resid 706 through 712 Processing helix chain 'A' and resid 713 through 716 removed outlier: 3.927A pdb=" N GLU A 716 " --> pdb=" O TYR A 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 713 through 716' Processing helix chain 'A' and resid 717 through 726 removed outlier: 3.681A pdb=" N CYS A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 774 removed outlier: 4.104A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.622A pdb=" N SER A 781 " --> pdb=" O VAL A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 807 removed outlier: 3.555A pdb=" N PHE A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 828 removed outlier: 3.662A pdb=" N PHE A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 856 Processing helix chain 'A' and resid 861 through 892 removed outlier: 3.906A pdb=" N TYR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 932 Processing helix chain 'A' and resid 936 through 941 Processing helix chain 'A' and resid 941 through 955 removed outlier: 3.558A pdb=" N TYR A 945 " --> pdb=" O SER A 941 " (cutoff:3.500A) Proline residue: A 950 - end of helix Processing helix chain 'A' and resid 955 through 963 Processing helix chain 'A' and resid 997 through 1012 removed outlier: 3.714A pdb=" N VAL A1011 " --> pdb=" O LYS A1007 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A1012 " --> pdb=" O TYR A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1060 removed outlier: 3.534A pdb=" N VAL A1043 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A1044 " --> pdb=" O ARG A1040 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A1054 " --> pdb=" O THR A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1075 Processing helix chain 'A' and resid 1091 through 1125 removed outlier: 4.101A pdb=" N SER A1095 " --> pdb=" O THR A1091 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A1102 " --> pdb=" O PHE A1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 401 removed outlier: 3.610A pdb=" N LEU B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR B 401 " --> pdb=" O ASP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 removed outlier: 4.098A pdb=" N LYS B 414 " --> pdb=" O PRO B 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 414' Processing helix chain 'B' and resid 424 through 428 removed outlier: 3.969A pdb=" N LEU B 428 " --> pdb=" O PRO B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 439 Processing helix chain 'B' and resid 458 through 478 Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 506 through 517 Processing helix chain 'B' and resid 577 through 588 Processing helix chain 'B' and resid 588 through 594 removed outlier: 3.620A pdb=" N LEU B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 617 Processing helix chain 'B' and resid 618 through 621 removed outlier: 3.837A pdb=" N ASN B 621 " --> pdb=" O GLU B 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 621' Processing helix chain 'B' and resid 636 through 643 removed outlier: 3.551A pdb=" N PHE B 639 " --> pdb=" O GLY B 636 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LYS B 641 " --> pdb=" O ARG B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 660 Processing helix chain 'B' and resid 660 through 669 removed outlier: 3.712A pdb=" N PHE B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 687 Processing helix chain 'B' and resid 688 through 696 Processing helix chain 'B' and resid 706 through 712 Processing helix chain 'B' and resid 713 through 716 removed outlier: 3.926A pdb=" N GLU B 716 " --> pdb=" O TYR B 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 713 through 716' Processing helix chain 'B' and resid 717 through 726 removed outlier: 3.681A pdb=" N CYS B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 774 removed outlier: 4.104A pdb=" N ARG B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.622A pdb=" N SER B 781 " --> pdb=" O VAL B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 807 removed outlier: 3.555A pdb=" N PHE B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 828 removed outlier: 3.663A pdb=" N PHE B 813 " --> pdb=" O LEU B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 856 Processing helix chain 'B' and resid 861 through 892 removed outlier: 3.907A pdb=" N TYR B 865 " --> pdb=" O THR B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 932 Processing helix chain 'B' and resid 936 through 941 Processing helix chain 'B' and resid 941 through 955 removed outlier: 3.557A pdb=" N TYR B 945 " --> pdb=" O SER B 941 " (cutoff:3.500A) Proline residue: B 950 - end of helix Processing helix chain 'B' and resid 955 through 963 Processing helix chain 'B' and resid 997 through 1012 removed outlier: 3.714A pdb=" N VAL B1011 " --> pdb=" O LYS B1007 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU B1012 " --> pdb=" O TYR B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1060 removed outlier: 3.532A pdb=" N VAL B1043 " --> pdb=" O VAL B1039 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B1044 " --> pdb=" O ARG B1040 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE B1054 " --> pdb=" O THR B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1075 Processing helix chain 'B' and resid 1091 through 1125 removed outlier: 4.100A pdb=" N SER B1095 " --> pdb=" O THR B1091 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B1102 " --> pdb=" O PHE B1098 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.799A pdb=" N ARG A 376 " --> pdb=" O MET B 992 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET B 992 " --> pdb=" O ARG A 376 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 386 through 390 removed outlier: 7.372A pdb=" N PHE A 415 " --> pdb=" O THR A 541 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N THR A 541 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS A 540 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLN A 566 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 448 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N CYS A 496 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU A 450 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE A 498 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 452 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLY A 625 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL A 624 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LYS A 735 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY A 626 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N CYS A 737 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS A 628 " --> pdb=" O CYS A 737 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N SER A 739 " --> pdb=" O CYS A 628 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLU A 630 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR A 741 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG A 632 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER A 743 " --> pdb=" O ARG A 632 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 531 through 532 removed outlier: 6.747A pdb=" N GLU A 527 " --> pdb=" O ILE B 982 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 549 removed outlier: 5.226A pdb=" N ILE A 546 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLU A 557 " --> pdb=" O ILE A 546 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 548 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 981 through 982 Processing sheet with id=AA6, first strand: chain 'A' and resid 991 through 992 removed outlier: 3.636A pdb=" N MET A 992 " --> pdb=" O ARG B 376 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 376 " --> pdb=" O MET A 992 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 386 through 390 removed outlier: 7.373A pdb=" N PHE B 415 " --> pdb=" O THR B 541 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N THR B 541 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS B 540 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLN B 566 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU B 448 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N CYS B 496 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU B 450 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE B 498 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL B 452 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY B 625 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL B 624 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LYS B 735 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY B 626 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N CYS B 737 " --> pdb=" O GLY B 626 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS B 628 " --> pdb=" O CYS B 737 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N SER B 739 " --> pdb=" O CYS B 628 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLU B 630 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR B 741 " --> pdb=" O GLU B 630 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG B 632 " --> pdb=" O TYR B 741 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER B 743 " --> pdb=" O ARG B 632 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 545 through 549 removed outlier: 5.226A pdb=" N ILE B 546 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLU B 557 " --> pdb=" O ILE B 546 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN B 548 " --> pdb=" O SER B 555 " (cutoff:3.500A) 679 hydrogen bonds defined for protein. 1947 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1686 1.31 - 1.43: 3265 1.43 - 1.56: 6244 1.56 - 1.68: 28 1.68 - 1.81: 100 Bond restraints: 11323 Sorted by residual: bond pdb=" C31 POV A1301 " pdb=" O31 POV A1301 " ideal model delta sigma weight residual 1.327 1.438 -0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C31 POV B1301 " pdb=" O31 POV B1301 " ideal model delta sigma weight residual 1.327 1.437 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C21 POV B1301 " pdb=" O21 POV B1301 " ideal model delta sigma weight residual 1.330 1.413 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C21 POV A1301 " pdb=" O21 POV A1301 " ideal model delta sigma weight residual 1.330 1.412 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb="C312 POV A1301 " pdb="C313 POV A1301 " ideal model delta sigma weight residual 1.523 1.599 -0.076 2.00e-02 2.50e+03 1.46e+01 ... (remaining 11318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 14966 2.40 - 4.80: 340 4.80 - 7.19: 36 7.19 - 9.59: 6 9.59 - 11.99: 6 Bond angle restraints: 15354 Sorted by residual: angle pdb=" N ARG B 508 " pdb=" CA ARG B 508 " pdb=" C ARG B 508 " ideal model delta sigma weight residual 112.89 107.62 5.27 1.24e+00 6.50e-01 1.81e+01 angle pdb=" N ARG A 508 " pdb=" CA ARG A 508 " pdb=" C ARG A 508 " ideal model delta sigma weight residual 112.89 107.65 5.24 1.24e+00 6.50e-01 1.78e+01 angle pdb=" CA VAL B 435 " pdb=" C VAL B 435 " pdb=" O VAL B 435 " ideal model delta sigma weight residual 121.67 117.30 4.37 1.05e+00 9.07e-01 1.73e+01 angle pdb=" CA VAL A 435 " pdb=" C VAL A 435 " pdb=" O VAL A 435 " ideal model delta sigma weight residual 121.67 117.32 4.35 1.05e+00 9.07e-01 1.72e+01 angle pdb=" O13 POV B1301 " pdb=" P POV B1301 " pdb=" O14 POV B1301 " ideal model delta sigma weight residual 121.11 109.12 11.99 3.00e+00 1.11e-01 1.60e+01 ... (remaining 15349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.62: 6309 25.62 - 51.25: 246 51.25 - 76.87: 58 76.87 - 102.50: 6 102.50 - 128.12: 2 Dihedral angle restraints: 6621 sinusoidal: 2481 harmonic: 4140 Sorted by residual: dihedral pdb=" CA ALA A 715 " pdb=" C ALA A 715 " pdb=" N GLU A 716 " pdb=" CA GLU A 716 " ideal model delta harmonic sigma weight residual -180.00 -152.34 -27.66 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA ALA B 715 " pdb=" C ALA B 715 " pdb=" N GLU B 716 " pdb=" CA GLU B 716 " ideal model delta harmonic sigma weight residual -180.00 -152.43 -27.57 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA TYR B 827 " pdb=" C TYR B 827 " pdb=" N HIS B 828 " pdb=" CA HIS B 828 " ideal model delta harmonic sigma weight residual 180.00 154.81 25.19 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 6618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1127 0.044 - 0.088: 479 0.088 - 0.132: 115 0.132 - 0.177: 23 0.177 - 0.221: 7 Chirality restraints: 1751 Sorted by residual: chirality pdb=" CA VAL B 435 " pdb=" N VAL B 435 " pdb=" C VAL B 435 " pdb=" CB VAL B 435 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA VAL A 435 " pdb=" N VAL A 435 " pdb=" C VAL A 435 " pdb=" CB VAL A 435 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C2 POV B1301 " pdb=" C1 POV B1301 " pdb=" C3 POV B1301 " pdb=" O21 POV B1301 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 1748 not shown) Planarity restraints: 1886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 504 " -0.017 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C LYS A 504 " 0.056 2.00e-02 2.50e+03 pdb=" O LYS A 504 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE A 505 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 504 " 0.017 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C LYS B 504 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS B 504 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE B 505 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1015 " -0.025 2.00e-02 2.50e+03 2.09e-02 7.65e+00 pdb=" CG PHE A1015 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A1015 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A1015 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A1015 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A1015 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A1015 " -0.010 2.00e-02 2.50e+03 ... (remaining 1883 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2642 2.79 - 3.32: 10382 3.32 - 3.84: 17977 3.84 - 4.37: 21459 4.37 - 4.90: 37428 Nonbonded interactions: 89888 Sorted by model distance: nonbonded pdb=" NH1 ARG B 817 " pdb=" O13 POV B1301 " model vdw 2.259 3.120 nonbonded pdb=" NH1 ARG A 817 " pdb=" O13 POV A1301 " model vdw 2.260 3.120 nonbonded pdb=" OG1 THR A 394 " pdb=" NE2 GLN B1002 " model vdw 2.273 3.120 nonbonded pdb=" NE2 GLN A1002 " pdb=" OG1 THR B 394 " model vdw 2.311 3.120 nonbonded pdb=" OG SER B 611 " pdb=" O TYR B 741 " model vdw 2.318 3.040 ... (remaining 89883 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and ((resid 375 and (name CA or name C or name O or name CB or name C \ G1 or name CG2 or name CD1)) or resid 376 through 1301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.830 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 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 : 0.008 0.111 11323 Z= 0.378 Angle : 0.864 11.988 15354 Z= 0.479 Chirality : 0.052 0.221 1751 Planarity : 0.005 0.057 1886 Dihedral : 14.850 128.121 3943 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.92 % Allowed : 0.52 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.23), residues: 1380 helix: 1.35 (0.19), residues: 752 sheet: -0.22 (0.39), residues: 166 loop : -1.05 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1040 TYR 0.024 0.003 TYR B 827 PHE 0.047 0.003 PHE B1015 TRP 0.044 0.002 TRP A1103 HIS 0.006 0.002 HIS B 459 Details of bonding type rmsd covalent geometry : bond 0.00802 (11323) covalent geometry : angle 0.86399 (15354) hydrogen bonds : bond 0.15429 ( 679) hydrogen bonds : angle 6.51589 ( 1947) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 310 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 799 PHE cc_start: 0.8588 (t80) cc_final: 0.8366 (t80) REVERT: B 799 PHE cc_start: 0.8604 (t80) cc_final: 0.8401 (t80) outliers start: 22 outliers final: 0 residues processed: 324 average time/residue: 0.1171 time to fit residues: 51.3604 Evaluate side-chains 121 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN A 540 HIS A 548 ASN B 472 ASN B 540 HIS B 548 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.172670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.137866 restraints weight = 18264.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.142418 restraints weight = 9012.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.145335 restraints weight = 5813.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.147271 restraints weight = 4460.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.148229 restraints weight = 3762.402| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11323 Z= 0.147 Angle : 0.573 8.481 15354 Z= 0.303 Chirality : 0.042 0.167 1751 Planarity : 0.004 0.050 1886 Dihedral : 9.652 115.058 1586 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.01 % Allowed : 11.72 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.22), residues: 1380 helix: 2.09 (0.18), residues: 752 sheet: -0.09 (0.43), residues: 136 loop : -0.74 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 687 TYR 0.026 0.001 TYR A 827 PHE 0.021 0.002 PHE A 911 TRP 0.014 0.002 TRP B1047 HIS 0.011 0.002 HIS B 540 Details of bonding type rmsd covalent geometry : bond 0.00330 (11323) covalent geometry : angle 0.57301 (15354) hydrogen bonds : bond 0.04755 ( 679) hydrogen bonds : angle 4.57511 ( 1947) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 454 MET cc_start: 0.7314 (mtp) cc_final: 0.6917 (mtt) REVERT: A 601 LEU cc_start: 0.5651 (OUTLIER) cc_final: 0.5274 (mp) REVERT: A 653 GLU cc_start: 0.8646 (tt0) cc_final: 0.8421 (tt0) REVERT: A 876 MET cc_start: 0.8133 (tpp) cc_final: 0.7827 (tpp) REVERT: B 601 LEU cc_start: 0.5649 (OUTLIER) cc_final: 0.5295 (mp) REVERT: B 653 GLU cc_start: 0.8645 (tt0) cc_final: 0.8408 (tt0) REVERT: B 875 MET cc_start: 0.8843 (mtp) cc_final: 0.8642 (mtm) REVERT: B 876 MET cc_start: 0.7715 (tpp) cc_final: 0.7366 (tpt) REVERT: B 1066 ASP cc_start: 0.6413 (t0) cc_final: 0.6066 (t0) REVERT: B 1070 MET cc_start: 0.5396 (mtm) cc_final: 0.4950 (mtm) outliers start: 23 outliers final: 10 residues processed: 166 average time/residue: 0.0746 time to fit residues: 19.2974 Evaluate side-chains 124 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain B residue 1114 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 128 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN A 650 GLN ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN B 548 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 828 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.165489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.131935 restraints weight = 18889.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.136077 restraints weight = 10411.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.136146 restraints weight = 7318.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.136699 restraints weight = 6280.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.136821 restraints weight = 5843.206| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11323 Z= 0.200 Angle : 0.587 6.654 15354 Z= 0.316 Chirality : 0.043 0.165 1751 Planarity : 0.004 0.041 1886 Dihedral : 8.850 97.459 1586 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.01 % Allowed : 13.74 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.22), residues: 1380 helix: 2.00 (0.18), residues: 782 sheet: 0.03 (0.44), residues: 136 loop : -0.97 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 594 TYR 0.022 0.002 TYR A 827 PHE 0.024 0.002 PHE A 799 TRP 0.013 0.001 TRP B 806 HIS 0.010 0.002 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00459 (11323) covalent geometry : angle 0.58660 (15354) hydrogen bonds : bond 0.04947 ( 679) hydrogen bonds : angle 4.54531 ( 1947) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.5914 (mp) REVERT: A 610 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8423 (m-30) REVERT: A 760 TRP cc_start: 0.7906 (m-10) cc_final: 0.7504 (m-10) REVERT: A 876 MET cc_start: 0.8191 (tpp) cc_final: 0.7893 (tpp) REVERT: B 571 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8437 (tt) REVERT: B 601 LEU cc_start: 0.6273 (OUTLIER) cc_final: 0.5752 (mp) REVERT: B 610 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8376 (m-30) REVERT: B 760 TRP cc_start: 0.7901 (m-10) cc_final: 0.7491 (m-10) REVERT: B 876 MET cc_start: 0.8057 (tpp) cc_final: 0.7805 (tpp) outliers start: 23 outliers final: 9 residues processed: 140 average time/residue: 0.0765 time to fit residues: 16.6568 Evaluate side-chains 123 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 47 optimal weight: 0.0570 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 ASN B 650 GLN B 828 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.163262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.127331 restraints weight = 19008.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.131509 restraints weight = 9732.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.134270 restraints weight = 6421.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.135977 restraints weight = 4971.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.136947 restraints weight = 4251.814| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11323 Z= 0.192 Angle : 0.570 6.045 15354 Z= 0.304 Chirality : 0.043 0.159 1751 Planarity : 0.004 0.046 1886 Dihedral : 8.667 90.952 1586 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.89 % Allowed : 13.65 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.22), residues: 1380 helix: 2.15 (0.18), residues: 782 sheet: -0.21 (0.41), residues: 136 loop : -0.96 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 594 TYR 0.018 0.002 TYR B 827 PHE 0.023 0.002 PHE B 387 TRP 0.013 0.001 TRP A 806 HIS 0.011 0.002 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00450 (11323) covalent geometry : angle 0.57037 (15354) hydrogen bonds : bond 0.04700 ( 679) hydrogen bonds : angle 4.46481 ( 1947) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 LEU cc_start: 0.5996 (OUTLIER) cc_final: 0.5690 (mp) REVERT: A 610 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8312 (m-30) REVERT: A 656 MET cc_start: 0.7779 (mmm) cc_final: 0.7393 (ttp) REVERT: A 760 TRP cc_start: 0.7945 (m-10) cc_final: 0.7684 (m-10) REVERT: A 876 MET cc_start: 0.8189 (tpp) cc_final: 0.7926 (tpp) REVERT: B 571 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8297 (tt) REVERT: B 601 LEU cc_start: 0.6050 (OUTLIER) cc_final: 0.5746 (mp) REVERT: B 610 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8302 (m-30) REVERT: B 656 MET cc_start: 0.7782 (mmm) cc_final: 0.7433 (ttp) REVERT: B 760 TRP cc_start: 0.7937 (m-10) cc_final: 0.7668 (m-10) REVERT: B 876 MET cc_start: 0.8175 (tpp) cc_final: 0.7893 (tpp) REVERT: B 886 MET cc_start: 0.7483 (mmm) cc_final: 0.6995 (mmm) outliers start: 33 outliers final: 14 residues processed: 163 average time/residue: 0.0804 time to fit residues: 19.9579 Evaluate side-chains 132 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1040 ARG Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 6 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 97 optimal weight: 0.3980 chunk 122 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 472 ASN A 545 ASN A 548 ASN B 419 GLN B 472 ASN B 548 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.165991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.130657 restraints weight = 18709.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.134886 restraints weight = 9547.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.137736 restraints weight = 6260.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.139503 restraints weight = 4800.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.140412 restraints weight = 4075.150| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11323 Z= 0.129 Angle : 0.534 9.374 15354 Z= 0.276 Chirality : 0.041 0.153 1751 Planarity : 0.004 0.048 1886 Dihedral : 8.009 84.499 1586 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.45 % Allowed : 15.66 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.23), residues: 1380 helix: 2.41 (0.18), residues: 781 sheet: -0.09 (0.42), residues: 136 loop : -0.87 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 594 TYR 0.019 0.001 TYR B 827 PHE 0.015 0.001 PHE B 864 TRP 0.010 0.001 TRP B 806 HIS 0.004 0.001 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00291 (11323) covalent geometry : angle 0.53365 (15354) hydrogen bonds : bond 0.04147 ( 679) hydrogen bonds : angle 4.27507 ( 1947) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.297 Fit side-chains REVERT: A 583 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7699 (ttm-80) REVERT: A 601 LEU cc_start: 0.5960 (OUTLIER) cc_final: 0.5726 (mp) REVERT: A 610 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8300 (m-30) REVERT: A 653 GLU cc_start: 0.8725 (tt0) cc_final: 0.8459 (tt0) REVERT: A 656 MET cc_start: 0.7695 (mmm) cc_final: 0.7440 (ttp) REVERT: A 760 TRP cc_start: 0.7920 (m-10) cc_final: 0.7684 (m-10) REVERT: A 876 MET cc_start: 0.8193 (tpp) cc_final: 0.7948 (tpp) REVERT: A 886 MET cc_start: 0.7523 (mmm) cc_final: 0.6885 (mmm) REVERT: B 583 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7703 (ttm-80) REVERT: B 601 LEU cc_start: 0.6058 (OUTLIER) cc_final: 0.5658 (mp) REVERT: B 610 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8318 (m-30) REVERT: B 653 GLU cc_start: 0.8730 (tt0) cc_final: 0.8475 (tt0) REVERT: B 656 MET cc_start: 0.7680 (mmm) cc_final: 0.7442 (ttp) REVERT: B 760 TRP cc_start: 0.7911 (m-10) cc_final: 0.7677 (m-10) REVERT: B 876 MET cc_start: 0.8125 (tpp) cc_final: 0.7883 (tpp) REVERT: B 1005 TYR cc_start: 0.6806 (t80) cc_final: 0.6536 (t80) outliers start: 28 outliers final: 11 residues processed: 159 average time/residue: 0.0775 time to fit residues: 18.5027 Evaluate side-chains 141 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 12 optimal weight: 0.4980 chunk 65 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 104 optimal weight: 0.0370 chunk 5 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 overall best weight: 1.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 HIS A 548 ASN B 536 HIS B 548 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.165621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.129792 restraints weight = 18871.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.134151 restraints weight = 9384.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.137050 restraints weight = 6073.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.138790 restraints weight = 4651.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.139925 restraints weight = 3945.936| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11323 Z= 0.139 Angle : 0.542 8.016 15354 Z= 0.282 Chirality : 0.041 0.156 1751 Planarity : 0.004 0.050 1886 Dihedral : 7.882 83.783 1586 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.19 % Allowed : 16.45 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.23), residues: 1380 helix: 2.45 (0.18), residues: 782 sheet: 0.09 (0.42), residues: 140 loop : -0.88 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 594 TYR 0.017 0.001 TYR B 827 PHE 0.027 0.002 PHE B 387 TRP 0.010 0.001 TRP A 806 HIS 0.003 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00319 (11323) covalent geometry : angle 0.54215 (15354) hydrogen bonds : bond 0.04119 ( 679) hydrogen bonds : angle 4.26065 ( 1947) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7727 (ttm-80) REVERT: A 601 LEU cc_start: 0.6014 (OUTLIER) cc_final: 0.5610 (mp) REVERT: A 760 TRP cc_start: 0.7938 (m-10) cc_final: 0.7700 (m-10) REVERT: A 876 MET cc_start: 0.8157 (tpp) cc_final: 0.7904 (tpp) REVERT: B 583 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7742 (ttm-80) REVERT: B 601 LEU cc_start: 0.6138 (OUTLIER) cc_final: 0.5627 (mp) REVERT: B 656 MET cc_start: 0.7685 (mmm) cc_final: 0.7445 (ttp) REVERT: B 760 TRP cc_start: 0.7933 (m-10) cc_final: 0.7697 (m-10) REVERT: B 876 MET cc_start: 0.8052 (tpp) cc_final: 0.7830 (tpp) REVERT: B 886 MET cc_start: 0.7620 (mmm) cc_final: 0.7379 (mmm) REVERT: B 1005 TYR cc_start: 0.6840 (t80) cc_final: 0.6638 (t80) REVERT: B 1066 ASP cc_start: 0.6784 (t0) cc_final: 0.6385 (t0) outliers start: 25 outliers final: 12 residues processed: 156 average time/residue: 0.0804 time to fit residues: 18.6464 Evaluate side-chains 139 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 8 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN B 548 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.159126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.122582 restraints weight = 19413.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.126647 restraints weight = 9847.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.129276 restraints weight = 6495.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.131007 restraints weight = 5040.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.131879 restraints weight = 4312.837| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 11323 Z= 0.283 Angle : 0.684 9.854 15354 Z= 0.359 Chirality : 0.047 0.348 1751 Planarity : 0.004 0.049 1886 Dihedral : 9.142 104.409 1586 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.45 % Allowed : 16.71 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.23), residues: 1380 helix: 1.95 (0.18), residues: 782 sheet: -0.28 (0.44), residues: 138 loop : -1.09 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 594 TYR 0.016 0.002 TYR B1028 PHE 0.022 0.002 PHE A1052 TRP 0.017 0.002 TRP B 806 HIS 0.006 0.002 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00669 (11323) covalent geometry : angle 0.68401 (15354) hydrogen bonds : bond 0.05267 ( 679) hydrogen bonds : angle 4.72950 ( 1947) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 523 PHE cc_start: 0.4871 (OUTLIER) cc_final: 0.3534 (p90) REVERT: A 601 LEU cc_start: 0.6099 (OUTLIER) cc_final: 0.5774 (mp) REVERT: A 760 TRP cc_start: 0.8094 (m-10) cc_final: 0.7843 (m-10) REVERT: B 475 TYR cc_start: 0.8422 (t80) cc_final: 0.8173 (t80) REVERT: B 523 PHE cc_start: 0.4939 (OUTLIER) cc_final: 0.3692 (p90) REVERT: B 601 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5971 (mp) REVERT: B 610 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8288 (t0) REVERT: B 760 TRP cc_start: 0.8075 (m-10) cc_final: 0.7831 (m-10) outliers start: 28 outliers final: 13 residues processed: 151 average time/residue: 0.0745 time to fit residues: 18.1557 Evaluate side-chains 135 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 75 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.156875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.123395 restraints weight = 18889.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.127125 restraints weight = 9690.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.129596 restraints weight = 6469.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.130849 restraints weight = 5064.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.131971 restraints weight = 4430.286| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11323 Z= 0.167 Angle : 0.599 10.046 15354 Z= 0.310 Chirality : 0.043 0.331 1751 Planarity : 0.004 0.043 1886 Dihedral : 8.631 89.362 1586 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.92 % Allowed : 18.20 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.23), residues: 1380 helix: 2.18 (0.18), residues: 782 sheet: -0.18 (0.43), residues: 139 loop : -1.00 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 594 TYR 0.018 0.001 TYR A 475 PHE 0.028 0.002 PHE B 387 TRP 0.012 0.001 TRP B 806 HIS 0.004 0.001 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00387 (11323) covalent geometry : angle 0.59907 (15354) hydrogen bonds : bond 0.04497 ( 679) hydrogen bonds : angle 4.47180 ( 1947) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 523 PHE cc_start: 0.4879 (OUTLIER) cc_final: 0.3899 (p90) REVERT: A 583 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7918 (ttm-80) REVERT: A 601 LEU cc_start: 0.6031 (OUTLIER) cc_final: 0.5784 (mp) REVERT: A 876 MET cc_start: 0.8048 (tpp) cc_final: 0.7781 (tpp) REVERT: A 945 TYR cc_start: 0.8916 (t80) cc_final: 0.8682 (t80) REVERT: B 475 TYR cc_start: 0.8466 (t80) cc_final: 0.8165 (t80) REVERT: B 523 PHE cc_start: 0.4883 (OUTLIER) cc_final: 0.3896 (p90) REVERT: B 583 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7899 (ttm-80) REVERT: B 601 LEU cc_start: 0.6272 (OUTLIER) cc_final: 0.6058 (mp) REVERT: B 886 MET cc_start: 0.7247 (mmt) cc_final: 0.6882 (mmm) outliers start: 22 outliers final: 11 residues processed: 145 average time/residue: 0.0821 time to fit residues: 17.9902 Evaluate side-chains 136 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 27 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 12 optimal weight: 30.0000 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 937 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.153806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.121074 restraints weight = 19035.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.124544 restraints weight = 9920.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.126851 restraints weight = 6711.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.128294 restraints weight = 5295.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.128985 restraints weight = 4593.861| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11323 Z= 0.265 Angle : 0.673 9.223 15354 Z= 0.351 Chirality : 0.045 0.298 1751 Planarity : 0.004 0.042 1886 Dihedral : 9.097 98.758 1586 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.54 % Allowed : 18.11 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.23), residues: 1380 helix: 1.89 (0.18), residues: 789 sheet: -0.39 (0.43), residues: 138 loop : -1.15 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 594 TYR 0.018 0.002 TYR B1028 PHE 0.030 0.002 PHE A 800 TRP 0.017 0.002 TRP B 806 HIS 0.005 0.001 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00628 (11323) covalent geometry : angle 0.67294 (15354) hydrogen bonds : bond 0.05007 ( 679) hydrogen bonds : angle 4.67454 ( 1947) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 523 PHE cc_start: 0.5038 (OUTLIER) cc_final: 0.4339 (p90) REVERT: A 583 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7878 (ttm-80) REVERT: A 601 LEU cc_start: 0.6130 (OUTLIER) cc_final: 0.5808 (mp) REVERT: A 945 TYR cc_start: 0.8967 (t80) cc_final: 0.8724 (t80) REVERT: B 475 TYR cc_start: 0.8427 (t80) cc_final: 0.8123 (t80) REVERT: B 523 PHE cc_start: 0.4303 (OUTLIER) cc_final: 0.3736 (p90) REVERT: B 583 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7876 (ttm-80) REVERT: B 601 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.6099 (mp) REVERT: B 886 MET cc_start: 0.7508 (mmt) cc_final: 0.7271 (mmm) outliers start: 29 outliers final: 16 residues processed: 143 average time/residue: 0.0740 time to fit residues: 16.8224 Evaluate side-chains 137 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 102 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN B 756 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.162326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.126252 restraints weight = 19322.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.130400 restraints weight = 9665.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.133194 restraints weight = 6351.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.134862 restraints weight = 4909.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.135772 restraints weight = 4201.196| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11323 Z= 0.129 Angle : 0.573 11.004 15354 Z= 0.295 Chirality : 0.042 0.297 1751 Planarity : 0.004 0.043 1886 Dihedral : 8.353 89.250 1586 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.84 % Allowed : 18.90 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.23), residues: 1380 helix: 2.29 (0.18), residues: 780 sheet: -0.28 (0.44), residues: 139 loop : -0.97 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 594 TYR 0.018 0.001 TYR A1028 PHE 0.027 0.002 PHE B 800 TRP 0.010 0.001 TRP B 806 HIS 0.002 0.001 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00285 (11323) covalent geometry : angle 0.57259 (15354) hydrogen bonds : bond 0.04191 ( 679) hydrogen bonds : angle 4.33908 ( 1947) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 416 MET cc_start: 0.7398 (tmm) cc_final: 0.7107 (tmm) REVERT: A 583 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7942 (ttm-80) REVERT: A 601 LEU cc_start: 0.6079 (OUTLIER) cc_final: 0.5842 (mp) REVERT: A 876 MET cc_start: 0.8036 (tpp) cc_final: 0.7460 (tpp) REVERT: A 945 TYR cc_start: 0.8905 (t80) cc_final: 0.8647 (t80) REVERT: A 1103 TRP cc_start: 0.7870 (m100) cc_final: 0.7644 (m100) REVERT: B 416 MET cc_start: 0.7390 (tmm) cc_final: 0.7089 (tmm) REVERT: B 475 TYR cc_start: 0.8508 (t80) cc_final: 0.8196 (t80) REVERT: B 523 PHE cc_start: 0.4504 (OUTLIER) cc_final: 0.3881 (p90) REVERT: B 583 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7906 (ttm-80) REVERT: B 876 MET cc_start: 0.7894 (tpp) cc_final: 0.7595 (tpp) REVERT: B 1090 MET cc_start: 0.2846 (ttp) cc_final: 0.2223 (ttp) REVERT: B 1103 TRP cc_start: 0.7879 (m100) cc_final: 0.7654 (m100) outliers start: 21 outliers final: 14 residues processed: 138 average time/residue: 0.0870 time to fit residues: 17.9360 Evaluate side-chains 137 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 104 optimal weight: 0.6980 chunk 10 optimal weight: 0.0770 chunk 82 optimal weight: 20.0000 chunk 92 optimal weight: 0.0770 chunk 50 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 89 optimal weight: 0.0010 chunk 85 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 30.0000 overall best weight: 0.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.166335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.131273 restraints weight = 19229.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.135639 restraints weight = 9525.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.138422 restraints weight = 6196.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.140270 restraints weight = 4759.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.141313 restraints weight = 4017.751| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.5374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11323 Z= 0.100 Angle : 0.561 10.331 15354 Z= 0.283 Chirality : 0.041 0.280 1751 Planarity : 0.004 0.057 1886 Dihedral : 7.770 84.755 1586 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.14 % Allowed : 19.42 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.23), residues: 1380 helix: 2.54 (0.18), residues: 780 sheet: -0.13 (0.43), residues: 140 loop : -0.89 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 594 TYR 0.021 0.001 TYR B 827 PHE 0.016 0.001 PHE B 799 TRP 0.007 0.001 TRP B 806 HIS 0.003 0.000 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00207 (11323) covalent geometry : angle 0.56051 (15354) hydrogen bonds : bond 0.03566 ( 679) hydrogen bonds : angle 4.04958 ( 1947) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1640.95 seconds wall clock time: 29 minutes 4.51 seconds (1744.51 seconds total)