Starting phenix.real_space_refine on Sat Aug 23 09:53:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3r_36857/08_2025/8k3r_36857.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3r_36857/08_2025/8k3r_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_36857/08_2025/8k3r_36857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3r_36857/08_2025/8k3r_36857.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3r_36857/08_2025/8k3r_36857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3r_36857/08_2025/8k3r_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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11061 Number of models: 1 Model: "" Number of chains: 3 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 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 Restraints were copied for chains: B Time building chain proxies: 4.97, per 1000 atoms: 0.45 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: 1.03 Conformation dependent library (CDL) restraints added in 642.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.45 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: 2.48 Time building geometry restraints manager: 1.35 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: 6243 1.56 - 1.68: 28 1.68 - 1.81: 100 Bond restraints: 11322 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 11317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 14964 2.40 - 4.80: 340 4.80 - 7.19: 36 7.19 - 9.59: 6 9.59 - 11.99: 6 Bond angle restraints: 15352 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 15347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.62: 6308 25.62 - 51.25: 246 51.25 - 76.87: 58 76.87 - 102.50: 6 102.50 - 128.12: 2 Dihedral angle restraints: 6620 sinusoidal: 2480 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 6617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1126 0.044 - 0.088: 479 0.088 - 0.132: 115 0.132 - 0.177: 23 0.177 - 0.221: 7 Chirality restraints: 1750 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 1747 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: 1.46 - 2.15: 1 2.15 - 2.84: 3631 2.84 - 3.52: 14988 3.52 - 4.21: 25209 4.21 - 4.90: 46062 Nonbonded interactions: 89891 Sorted by model distance: nonbonded pdb=" N ILE B 375 " pdb=" CA ILE B 375 " model vdw 1.459 3.550 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 ... (remaining 89886 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.200 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.740 ------------------------------------------------------------------------------- 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 11322 Z= 0.378 Angle : 0.864 11.988 15352 Z= 0.479 Chirality : 0.052 0.221 1750 Planarity : 0.005 0.057 1886 Dihedral : 14.851 128.121 3942 Min Nonbonded Distance : 1.459 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 aren 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 (11322) covalent geometry : angle 0.86405 (15352) 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 : 0.417 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: 0.1289 time to fit residues: 56.5965 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 : 0.445 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 HIS A 548 ASN B 472 ASN B 540 HIS B 548 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.172893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.138045 restraints weight = 18224.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.142620 restraints weight = 8876.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.145747 restraints weight = 5713.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.147590 restraints weight = 4314.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.148786 restraints weight = 3651.474| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11322 Z= 0.147 Angle : 0.572 8.266 15352 Z= 0.304 Chirality : 0.042 0.168 1750 Planarity : 0.004 0.051 1886 Dihedral : 9.781 117.388 1586 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.92 % Allowed : 11.64 % Favored : 86.44 % 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 aren not related in a simple way. whole: 1.32 (0.22), residues: 1380 helix: 2.05 (0.18), residues: 770 sheet: 0.04 (0.40), residues: 156 loop : -0.89 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 594 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 0.00328 (11322) covalent geometry : angle 0.57248 (15352) hydrogen bonds : bond 0.04894 ( 679) hydrogen bonds : angle 4.62520 ( 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 170 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 454 MET cc_start: 0.7368 (mtp) cc_final: 0.6997 (mtm) REVERT: A 601 LEU cc_start: 0.5595 (OUTLIER) cc_final: 0.5280 (mp) REVERT: A 653 GLU cc_start: 0.8636 (tt0) cc_final: 0.8414 (tt0) REVERT: A 876 MET cc_start: 0.8132 (tpp) cc_final: 0.7815 (tpp) REVERT: B 454 MET cc_start: 0.7395 (mtp) cc_final: 0.7033 (mtm) REVERT: B 601 LEU cc_start: 0.5654 (OUTLIER) cc_final: 0.5361 (mp) REVERT: B 653 GLU cc_start: 0.8636 (tt0) cc_final: 0.8400 (tt0) REVERT: B 876 MET cc_start: 0.7679 (tpp) cc_final: 0.7366 (tpt) REVERT: B 1066 ASP cc_start: 0.6427 (t0) cc_final: 0.6089 (t0) REVERT: B 1070 MET cc_start: 0.5402 (mtm) cc_final: 0.4946 (mtm) outliers start: 22 outliers final: 11 residues processed: 165 average time/residue: 0.0871 time to fit residues: 22.1963 Evaluate side-chains 131 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 571 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 A residue 1114 ILE 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 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: 6.9990 chunk 38 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 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: 3.1988 ------------------------------------------------------------------------------- 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 650 GLN ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN ** B 828 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.163348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.126551 restraints weight = 19082.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.130835 restraints weight = 9531.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.133724 restraints weight = 6255.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.135249 restraints weight = 4816.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.136409 restraints weight = 4166.648| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11322 Z= 0.237 Angle : 0.640 6.616 15352 Z= 0.343 Chirality : 0.045 0.170 1750 Planarity : 0.004 0.046 1886 Dihedral : 9.166 100.277 1586 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.92 % Allowed : 12.95 % Favored : 85.13 % 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 aren not related in a simple way. whole: 1.11 (0.22), residues: 1380 helix: 1.89 (0.18), residues: 782 sheet: -0.09 (0.43), residues: 136 loop : -1.01 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 594 TYR 0.020 0.002 TYR A 827 PHE 0.021 0.002 PHE B 639 TRP 0.014 0.002 TRP A 806 HIS 0.010 0.002 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00553 (11322) covalent geometry : angle 0.63988 (15352) hydrogen bonds : bond 0.05207 ( 679) hydrogen bonds : angle 4.68576 ( 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 158 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LEU cc_start: 0.5980 (OUTLIER) cc_final: 0.5658 (mp) REVERT: A 610 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8329 (m-30) REVERT: A 760 TRP cc_start: 0.7966 (m-10) cc_final: 0.7586 (m-10) REVERT: A 876 MET cc_start: 0.8168 (tpp) cc_final: 0.7883 (tpp) REVERT: B 601 LEU cc_start: 0.6079 (OUTLIER) cc_final: 0.5772 (mp) REVERT: B 610 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8325 (m-30) REVERT: B 760 TRP cc_start: 0.7939 (m-10) cc_final: 0.7557 (m-10) REVERT: B 876 MET cc_start: 0.8128 (tpp) cc_final: 0.7840 (tpp) outliers start: 22 outliers final: 9 residues processed: 155 average time/residue: 0.0852 time to fit residues: 20.5644 Evaluate side-chains 126 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 542 THR 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 814 LEU Chi-restraints excluded: chain B residue 825 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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** ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 828 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.165076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.132109 restraints weight = 18859.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.136414 restraints weight = 10242.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.136519 restraints weight = 6914.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.137059 restraints weight = 6163.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.137148 restraints weight = 5669.596| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11322 Z= 0.143 Angle : 0.549 9.142 15352 Z= 0.288 Chirality : 0.042 0.159 1750 Planarity : 0.004 0.048 1886 Dihedral : 8.636 86.464 1586 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.10 % Allowed : 14.00 % Favored : 83.90 % 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 aren not related in a simple way. whole: 1.50 (0.22), residues: 1380 helix: 2.24 (0.18), residues: 782 sheet: -0.10 (0.43), residues: 136 loop : -0.87 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 594 TYR 0.020 0.001 TYR B 827 PHE 0.024 0.002 PHE A 387 TRP 0.010 0.001 TRP B 806 HIS 0.012 0.001 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00325 (11322) covalent geometry : angle 0.54908 (15352) hydrogen bonds : bond 0.04461 ( 679) hydrogen bonds : angle 4.36214 ( 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 151 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 571 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8452 (tt) REVERT: A 601 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5943 (mp) REVERT: A 610 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8351 (m-30) REVERT: A 656 MET cc_start: 0.7750 (mmm) cc_final: 0.7410 (ttp) REVERT: A 760 TRP cc_start: 0.7887 (m-10) cc_final: 0.7583 (m-10) REVERT: A 876 MET cc_start: 0.8200 (tpp) cc_final: 0.7935 (tpp) REVERT: A 886 MET cc_start: 0.7500 (mmm) cc_final: 0.6986 (mmm) REVERT: B 571 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8395 (tt) REVERT: B 601 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5982 (mp) REVERT: B 610 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8346 (m-30) REVERT: B 656 MET cc_start: 0.7740 (mmm) cc_final: 0.7417 (ttp) REVERT: B 760 TRP cc_start: 0.7883 (m-10) cc_final: 0.7576 (m-10) REVERT: B 876 MET cc_start: 0.8142 (tpp) cc_final: 0.7892 (tpp) REVERT: B 886 MET cc_start: 0.7507 (mmm) cc_final: 0.7023 (mmm) outliers start: 24 outliers final: 7 residues processed: 149 average time/residue: 0.0861 time to fit residues: 20.1158 Evaluate side-chains 125 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 804 ILE 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 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 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: 7.9990 chunk 132 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 545 ASN ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 828 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.162619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.126819 restraints weight = 18927.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.131068 restraints weight = 9374.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.133908 restraints weight = 6076.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.135677 restraints weight = 4657.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.136438 restraints weight = 3950.980| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11322 Z= 0.186 Angle : 0.589 8.426 15352 Z= 0.310 Chirality : 0.043 0.159 1750 Planarity : 0.004 0.050 1886 Dihedral : 8.857 89.298 1586 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.45 % Allowed : 14.79 % Favored : 82.76 % 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 aren not related in a simple way. whole: 1.46 (0.23), residues: 1380 helix: 2.23 (0.18), residues: 782 sheet: -0.15 (0.43), residues: 136 loop : -0.93 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 594 TYR 0.017 0.002 TYR B1028 PHE 0.016 0.002 PHE A1052 TRP 0.013 0.001 TRP A 806 HIS 0.009 0.002 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00436 (11322) covalent geometry : angle 0.58907 (15352) hydrogen bonds : bond 0.04661 ( 679) hydrogen bonds : angle 4.43602 ( 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 151 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 583 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7659 (ttm-80) REVERT: A 601 LEU cc_start: 0.6054 (OUTLIER) cc_final: 0.5765 (mp) REVERT: A 610 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8338 (m-30) REVERT: A 760 TRP cc_start: 0.7976 (m-10) cc_final: 0.7729 (m-10) REVERT: A 876 MET cc_start: 0.8187 (tpp) cc_final: 0.7919 (tpp) REVERT: A 886 MET cc_start: 0.7639 (mmm) cc_final: 0.7437 (mmt) REVERT: B 571 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8297 (tt) REVERT: B 583 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7656 (ttm-80) REVERT: B 601 LEU cc_start: 0.6137 (OUTLIER) cc_final: 0.5871 (mp) REVERT: B 610 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8391 (m-30) REVERT: B 760 TRP cc_start: 0.7975 (m-10) cc_final: 0.7723 (m-10) REVERT: B 876 MET cc_start: 0.8100 (tpp) cc_final: 0.7864 (tpp) REVERT: B 1005 TYR cc_start: 0.6884 (t80) cc_final: 0.6670 (t80) REVERT: B 1040 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8160 (ttt180) outliers start: 28 outliers final: 12 residues processed: 147 average time/residue: 0.0896 time to fit residues: 20.3909 Evaluate side-chains 136 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ASN 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 793 VAL Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 1040 ARG 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 583 ARG 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 810 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 12 optimal weight: 30.0000 chunk 65 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 B 419 GLN B 472 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.163833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.130439 restraints weight = 18965.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.134619 restraints weight = 10627.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.134581 restraints weight = 7273.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.135146 restraints weight = 6513.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.135229 restraints weight = 5996.076| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11322 Z= 0.152 Angle : 0.549 9.345 15352 Z= 0.286 Chirality : 0.041 0.150 1750 Planarity : 0.004 0.052 1886 Dihedral : 8.597 89.886 1586 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.36 % Allowed : 15.66 % Favored : 81.98 % 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 aren not related in a simple way. whole: 1.67 (0.23), residues: 1380 helix: 2.40 (0.18), residues: 782 sheet: -0.01 (0.42), residues: 138 loop : -0.86 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 594 TYR 0.017 0.001 TYR B1028 PHE 0.027 0.002 PHE B 387 TRP 0.011 0.001 TRP A 806 HIS 0.004 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00353 (11322) covalent geometry : angle 0.54901 (15352) hydrogen bonds : bond 0.04237 ( 679) hydrogen bonds : angle 4.30402 ( 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 157 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 448 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8731 (mp) REVERT: A 475 TYR cc_start: 0.8424 (t80) cc_final: 0.8198 (t80) REVERT: A 583 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7824 (ttm-80) REVERT: A 601 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.5889 (mp) REVERT: A 760 TRP cc_start: 0.7920 (m-10) cc_final: 0.7714 (m-10) REVERT: A 876 MET cc_start: 0.8084 (tpp) cc_final: 0.7844 (tpp) REVERT: A 886 MET cc_start: 0.7636 (mmm) cc_final: 0.7434 (mmt) REVERT: B 583 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7825 (ttm-80) REVERT: B 601 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.6178 (mp) REVERT: B 610 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8455 (m-30) REVERT: B 760 TRP cc_start: 0.7923 (m-10) cc_final: 0.7713 (m-10) REVERT: B 876 MET cc_start: 0.8021 (tpp) cc_final: 0.7805 (tpp) outliers start: 27 outliers final: 14 residues processed: 151 average time/residue: 0.0917 time to fit residues: 21.0262 Evaluate side-chains 139 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 448 LEU 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 804 ILE Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain B residue 382 ASN 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 821 VAL 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: 7.9990 chunk 86 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 HIS A 937 HIS B 536 HIS B 545 ASN B 937 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.158081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.121393 restraints weight = 19678.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.125252 restraints weight = 9991.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.127759 restraints weight = 6644.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.129303 restraints weight = 5194.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.130098 restraints weight = 4477.103| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 11322 Z= 0.322 Angle : 0.715 9.687 15352 Z= 0.377 Chirality : 0.047 0.167 1750 Planarity : 0.005 0.051 1886 Dihedral : 9.850 107.952 1586 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.97 % Allowed : 15.75 % Favored : 81.28 % 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 aren not related in a simple way. whole: 0.96 (0.23), residues: 1380 helix: 1.84 (0.18), residues: 782 sheet: -0.36 (0.44), residues: 136 loop : -1.17 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 594 TYR 0.018 0.002 TYR B1028 PHE 0.023 0.002 PHE A1052 TRP 0.020 0.002 TRP B 806 HIS 0.006 0.002 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00764 (11322) covalent geometry : angle 0.71515 (15352) hydrogen bonds : bond 0.05436 ( 679) hydrogen bonds : angle 4.79197 ( 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 158 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 448 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8714 (mp) REVERT: A 523 PHE cc_start: 0.4876 (OUTLIER) cc_final: 0.3892 (p90) REVERT: A 601 LEU cc_start: 0.6306 (OUTLIER) cc_final: 0.6035 (mp) REVERT: A 610 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8310 (t0) REVERT: A 760 TRP cc_start: 0.8075 (m-10) cc_final: 0.7825 (m-10) REVERT: B 523 PHE cc_start: 0.4850 (OUTLIER) cc_final: 0.3769 (p90) REVERT: B 601 LEU cc_start: 0.6299 (OUTLIER) cc_final: 0.6041 (mp) REVERT: B 610 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8412 (t0) REVERT: B 760 TRP cc_start: 0.8074 (m-10) cc_final: 0.7820 (m-10) REVERT: B 876 MET cc_start: 0.8090 (tpp) cc_final: 0.7878 (tpp) REVERT: B 1066 ASP cc_start: 0.6726 (t0) cc_final: 0.6182 (t0) outliers start: 34 outliers final: 16 residues processed: 151 average time/residue: 0.0862 time to fit residues: 20.7130 Evaluate side-chains 140 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 499 SER 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 610 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 810 SER 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 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 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: 8.9990 chunk 89 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.156111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.123015 restraints weight = 18931.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.126638 restraints weight = 9992.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.128899 restraints weight = 6775.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.130368 restraints weight = 5385.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.131112 restraints weight = 4675.643| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11322 Z= 0.165 Angle : 0.584 9.460 15352 Z= 0.304 Chirality : 0.042 0.167 1750 Planarity : 0.004 0.044 1886 Dihedral : 9.240 92.668 1586 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.27 % Allowed : 17.94 % Favored : 79.79 % 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 aren not related in a simple way. whole: 1.36 (0.23), residues: 1380 helix: 2.17 (0.18), residues: 782 sheet: -0.18 (0.44), residues: 138 loop : -1.01 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 594 TYR 0.017 0.001 TYR B1028 PHE 0.029 0.002 PHE B 387 TRP 0.013 0.001 TRP A 806 HIS 0.005 0.001 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00384 (11322) covalent geometry : angle 0.58430 (15352) hydrogen bonds : bond 0.04571 ( 679) hydrogen bonds : angle 4.46103 ( 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 158 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8623 (mp) REVERT: A 523 PHE cc_start: 0.5000 (OUTLIER) cc_final: 0.4294 (p90) REVERT: A 583 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7920 (ttm-80) REVERT: A 601 LEU cc_start: 0.6115 (OUTLIER) cc_final: 0.5872 (mp) REVERT: A 876 MET cc_start: 0.8052 (tpp) cc_final: 0.7794 (tpp) REVERT: A 1103 TRP cc_start: 0.7863 (m100) cc_final: 0.7636 (m100) REVERT: B 523 PHE cc_start: 0.4841 (OUTLIER) cc_final: 0.4055 (p90) REVERT: B 583 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7899 (ttm-80) REVERT: B 601 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.6108 (mp) REVERT: B 876 MET cc_start: 0.8050 (tpp) cc_final: 0.7831 (tpp) outliers start: 26 outliers final: 13 residues processed: 152 average time/residue: 0.0956 time to fit residues: 22.1605 Evaluate side-chains 140 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 448 LEU 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 764 SER Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 810 SER 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 27 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 71 optimal weight: 30.0000 chunk 51 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 138 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 HIS ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.156716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.120696 restraints weight = 19425.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.124549 restraints weight = 9920.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.127057 restraints weight = 6623.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.128666 restraints weight = 5183.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.129487 restraints weight = 4466.315| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 11322 Z= 0.283 Angle : 0.697 9.731 15352 Z= 0.363 Chirality : 0.046 0.155 1750 Planarity : 0.004 0.043 1886 Dihedral : 9.726 101.976 1586 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.45 % Allowed : 18.29 % 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 aren not related in a simple way. whole: 0.87 (0.23), residues: 1380 helix: 1.72 (0.18), residues: 796 sheet: -0.35 (0.43), residues: 136 loop : -1.21 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 594 TYR 0.018 0.002 TYR B1028 PHE 0.026 0.002 PHE B 800 TRP 0.018 0.002 TRP A 806 HIS 0.007 0.001 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00673 (11322) covalent geometry : angle 0.69700 (15352) hydrogen bonds : bond 0.05228 ( 679) hydrogen bonds : angle 4.73049 ( 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: 28 poor density : 120 time to evaluate : 0.462 Fit side-chains REVERT: A 448 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8753 (mp) REVERT: A 523 PHE cc_start: 0.4444 (OUTLIER) cc_final: 0.4056 (p90) REVERT: A 583 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7863 (ttm-80) REVERT: A 601 LEU cc_start: 0.6339 (OUTLIER) cc_final: 0.6077 (mp) REVERT: A 876 MET cc_start: 0.8026 (tpp) cc_final: 0.7825 (tpp) REVERT: B 523 PHE cc_start: 0.4130 (OUTLIER) cc_final: 0.3680 (p90) REVERT: B 583 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7864 (ttm-80) REVERT: B 601 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.6085 (mp) REVERT: B 876 MET cc_start: 0.8074 (tpp) cc_final: 0.7863 (tpp) REVERT: B 1090 MET cc_start: 0.2763 (ttp) cc_final: 0.2139 (ttp) outliers start: 28 outliers final: 16 residues processed: 141 average time/residue: 0.0921 time to fit residues: 20.1132 Evaluate side-chains 141 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 448 LEU 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 804 ILE Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 494 VAL 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 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 Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 102 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 14 optimal weight: 0.2980 chunk 26 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 756 GLN ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.162830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.127698 restraints weight = 19312.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.131912 restraints weight = 9555.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.134709 restraints weight = 6216.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.136186 restraints weight = 4777.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.137455 restraints weight = 4119.989| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.5412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11322 Z= 0.110 Angle : 0.557 9.818 15352 Z= 0.288 Chirality : 0.041 0.153 1750 Planarity : 0.004 0.045 1886 Dihedral : 8.608 88.835 1586 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.49 % Allowed : 19.16 % 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 aren not related in a simple way. whole: 1.42 (0.23), residues: 1380 helix: 2.20 (0.18), residues: 793 sheet: -0.18 (0.44), residues: 139 loop : -1.02 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 594 TYR 0.018 0.001 TYR A1028 PHE 0.029 0.001 PHE B 387 TRP 0.010 0.001 TRP A 779 HIS 0.003 0.001 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00228 (11322) covalent geometry : angle 0.55709 (15352) hydrogen bonds : bond 0.04032 ( 679) hydrogen bonds : angle 4.22668 ( 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 138 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.360 Fit side-chains REVERT: A 416 MET cc_start: 0.7363 (tmm) cc_final: 0.7156 (tmm) REVERT: A 583 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7920 (ttm-80) REVERT: A 876 MET cc_start: 0.8085 (tpp) cc_final: 0.7854 (tpp) REVERT: A 1103 TRP cc_start: 0.7877 (m100) cc_final: 0.7674 (m100) REVERT: B 416 MET cc_start: 0.7350 (tmm) cc_final: 0.7142 (tmm) REVERT: B 583 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7917 (ttm-80) REVERT: B 618 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: B 1090 MET cc_start: 0.2787 (ttp) cc_final: 0.2185 (ttp) REVERT: B 1103 TRP cc_start: 0.7888 (m100) cc_final: 0.7677 (m100) outliers start: 17 outliers final: 9 residues processed: 134 average time/residue: 0.0820 time to fit residues: 17.1180 Evaluate side-chains 125 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 823 ILE 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: 0.0870 chunk 10 optimal weight: 0.6980 chunk 82 optimal weight: 30.0000 chunk 92 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 30.0000 overall best weight: 1.1564 ------------------------------------------------------------------------------- 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 574 GLN ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.163036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.127708 restraints weight = 19376.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.131894 restraints weight = 9616.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.134606 restraints weight = 6276.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.136354 restraints weight = 4832.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.137358 restraints weight = 4110.228| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11322 Z= 0.121 Angle : 0.572 11.358 15352 Z= 0.291 Chirality : 0.041 0.199 1750 Planarity : 0.004 0.045 1886 Dihedral : 8.437 89.870 1586 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.57 % Allowed : 19.25 % Favored : 79.18 % 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 aren not related in a simple way. whole: 1.44 (0.23), residues: 1380 helix: 2.21 (0.18), residues: 799 sheet: -0.10 (0.44), residues: 140 loop : -1.06 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 594 TYR 0.018 0.001 TYR B1028 PHE 0.030 0.001 PHE B 800 TRP 0.016 0.001 TRP B 760 HIS 0.004 0.001 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00270 (11322) covalent geometry : angle 0.57179 (15352) hydrogen bonds : bond 0.03998 ( 679) hydrogen bonds : angle 4.20267 ( 1947) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1888.65 seconds wall clock time: 33 minutes 35.46 seconds (2015.46 seconds total)