Starting phenix.real_space_refine on Wed May 14 02:53:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3r_36857/05_2025/8k3r_36857.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3r_36857/05_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_36857/05_2025/8k3r_36857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3r_36857/05_2025/8k3r_36857.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3r_36857/05_2025/8k3r_36857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3r_36857/05_2025/8k3r_36857.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 5} 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: 10.96, per 1000 atoms: 0.99 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: 2.80 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.13 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: 3.51 Time building geometry restraints manager: 3.22 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 1125 or resid 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: 0.640 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.990 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.300 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.044 0.002 TRP A1103 HIS 0.006 0.002 HIS B 459 PHE 0.047 0.003 PHE B1015 TYR 0.024 0.003 TYR B 827 ARG 0.007 0.001 ARG B1040 Details of bonding type rmsd hydrogen bonds : bond 0.15429 ( 679) hydrogen bonds : angle 6.51589 ( 1947) covalent geometry : bond 0.00802 (11322) covalent geometry : angle 0.86405 (15352) *********************** 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 : 1.128 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: 0.2621 time to fit residues: 114.3930 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 : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 HIS B 548 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.167436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.132200 restraints weight = 18389.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.136474 restraints weight = 9189.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.139316 restraints weight = 6018.154| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11322 Z= 0.207 Angle : 0.622 8.584 15352 Z= 0.332 Chirality : 0.044 0.171 1750 Planarity : 0.004 0.045 1886 Dihedral : 9.828 115.234 1586 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.84 % Allowed : 12.60 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.22), residues: 1380 helix: 1.97 (0.18), residues: 764 sheet: -0.14 (0.43), residues: 136 loop : -0.86 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1047 HIS 0.012 0.002 HIS B 540 PHE 0.023 0.002 PHE A 911 TYR 0.024 0.002 TYR A 827 ARG 0.004 0.001 ARG B 594 Details of bonding type rmsd hydrogen bonds : bond 0.05172 ( 679) hydrogen bonds : angle 4.71055 ( 1947) covalent geometry : bond 0.00483 (11322) covalent geometry : angle 0.62180 (15352) *********************** 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 164 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 571 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8351 (tt) REVERT: A 601 LEU cc_start: 0.5873 (OUTLIER) cc_final: 0.5503 (mp) REVERT: A 653 GLU cc_start: 0.8671 (tt0) cc_final: 0.8469 (tt0) REVERT: A 876 MET cc_start: 0.8189 (tpp) cc_final: 0.7869 (tpp) REVERT: A 1070 MET cc_start: 0.5761 (mtm) cc_final: 0.5557 (mtm) REVERT: B 601 LEU cc_start: 0.5849 (OUTLIER) cc_final: 0.5513 (mp) REVERT: B 876 MET cc_start: 0.7867 (tpp) cc_final: 0.7655 (tpp) REVERT: B 1066 ASP cc_start: 0.6283 (t0) cc_final: 0.6017 (t0) REVERT: B 1070 MET cc_start: 0.5631 (mtm) cc_final: 0.5105 (mtm) outliers start: 21 outliers final: 12 residues processed: 161 average time/residue: 0.1945 time to fit residues: 47.8506 Evaluate side-chains 130 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 804 ILE 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 804 ILE 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 26 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 57 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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 A 650 GLN ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN B 650 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.162495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.126462 restraints weight = 18921.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.130576 restraints weight = 9667.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.133343 restraints weight = 6420.412| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11322 Z= 0.226 Angle : 0.612 6.722 15352 Z= 0.329 Chirality : 0.044 0.167 1750 Planarity : 0.004 0.044 1886 Dihedral : 9.441 98.021 1586 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.15 % Allowed : 12.60 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.22), residues: 1380 helix: 1.96 (0.18), residues: 782 sheet: -0.19 (0.43), residues: 136 loop : -1.05 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 806 HIS 0.008 0.002 HIS B 828 PHE 0.021 0.002 PHE B 378 TYR 0.020 0.002 TYR A 827 ARG 0.005 0.001 ARG B 594 Details of bonding type rmsd hydrogen bonds : bond 0.05120 ( 679) hydrogen bonds : angle 4.63836 ( 1947) covalent geometry : bond 0.00533 (11322) covalent geometry : angle 0.61177 (15352) *********************** 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 163 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.8045 (t80) cc_final: 0.7829 (t80) REVERT: A 601 LEU cc_start: 0.6118 (OUTLIER) cc_final: 0.5851 (mp) REVERT: A 760 TRP cc_start: 0.7941 (m-10) cc_final: 0.7591 (m-10) REVERT: A 876 MET cc_start: 0.8210 (tpp) cc_final: 0.7952 (tpp) REVERT: A 1005 TYR cc_start: 0.7068 (t80) cc_final: 0.6746 (t80) REVERT: A 1066 ASP cc_start: 0.6668 (t0) cc_final: 0.6299 (t0) REVERT: A 1070 MET cc_start: 0.5844 (mtm) cc_final: 0.5632 (mtm) REVERT: B 571 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8386 (tt) REVERT: B 601 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5919 (mp) REVERT: B 760 TRP cc_start: 0.7921 (m-10) cc_final: 0.7569 (m-10) REVERT: B 876 MET cc_start: 0.8109 (tpp) cc_final: 0.7852 (tpp) REVERT: B 1005 TYR cc_start: 0.7106 (t80) cc_final: 0.6776 (t80) REVERT: B 1066 ASP cc_start: 0.6342 (t0) cc_final: 0.5818 (t0) REVERT: B 1070 MET cc_start: 0.5533 (mtm) cc_final: 0.5307 (mtm) outliers start: 36 outliers final: 12 residues processed: 161 average time/residue: 0.2023 time to fit residues: 49.5492 Evaluate side-chains 126 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 384 ASN Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 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 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 53 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN ** 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 = 0.4270 r_free = 0.4270 target = 0.164177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.131645 restraints weight = 18763.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.135676 restraints weight = 9883.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.135807 restraints weight = 7315.751| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11322 Z= 0.147 Angle : 0.546 8.988 15352 Z= 0.285 Chirality : 0.041 0.157 1750 Planarity : 0.004 0.049 1886 Dihedral : 8.933 89.583 1586 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.36 % Allowed : 14.26 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.23), residues: 1380 helix: 2.28 (0.18), residues: 781 sheet: -0.14 (0.42), residues: 136 loop : -0.92 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 806 HIS 0.005 0.001 HIS A 828 PHE 0.025 0.001 PHE B 387 TYR 0.019 0.001 TYR B 827 ARG 0.005 0.000 ARG B 594 Details of bonding type rmsd hydrogen bonds : bond 0.04390 ( 679) hydrogen bonds : angle 4.36615 ( 1947) covalent geometry : bond 0.00337 (11322) covalent geometry : angle 0.54588 (15352) *********************** 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 157 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 571 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8448 (tt) REVERT: A 601 LEU cc_start: 0.6266 (OUTLIER) cc_final: 0.5825 (mp) REVERT: A 760 TRP cc_start: 0.7935 (m-10) cc_final: 0.7687 (m-10) REVERT: A 876 MET cc_start: 0.8147 (tpp) cc_final: 0.7879 (tpp) REVERT: A 886 MET cc_start: 0.7469 (mmm) cc_final: 0.6941 (mmm) REVERT: B 571 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8448 (tt) REVERT: B 601 LEU cc_start: 0.6346 (OUTLIER) cc_final: 0.5978 (mp) REVERT: B 760 TRP cc_start: 0.7914 (m-10) cc_final: 0.7614 (m-10) REVERT: B 876 MET cc_start: 0.8090 (tpp) cc_final: 0.7846 (tpp) REVERT: B 886 MET cc_start: 0.7566 (mmm) cc_final: 0.7120 (mmm) outliers start: 27 outliers final: 12 residues processed: 156 average time/residue: 0.2054 time to fit residues: 47.1766 Evaluate side-chains 127 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ASN 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 793 VAL 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 571 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 59 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 12 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 79 optimal weight: 0.0030 chunk 78 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 overall best weight: 1.7998 ------------------------------------------------------------------------------- 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 419 GLN B 472 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 = 0.4272 r_free = 0.4272 target = 0.164455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.131219 restraints weight = 18788.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.136352 restraints weight = 9920.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.136032 restraints weight = 6032.470| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11322 Z= 0.149 Angle : 0.550 8.275 15352 Z= 0.288 Chirality : 0.041 0.159 1750 Planarity : 0.004 0.049 1886 Dihedral : 8.790 89.194 1586 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.27 % Allowed : 15.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.23), residues: 1380 helix: 2.42 (0.18), residues: 782 sheet: -0.06 (0.42), residues: 136 loop : -0.94 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 806 HIS 0.005 0.001 HIS B 828 PHE 0.022 0.002 PHE A 387 TYR 0.017 0.001 TYR B 827 ARG 0.006 0.000 ARG A 594 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 679) hydrogen bonds : angle 4.29729 ( 1947) covalent geometry : bond 0.00344 (11322) covalent geometry : angle 0.54956 (15352) *********************** 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 154 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 583 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7714 (ttm-80) REVERT: A 601 LEU cc_start: 0.6260 (OUTLIER) cc_final: 0.5840 (mp) REVERT: A 760 TRP cc_start: 0.7965 (m-10) cc_final: 0.7727 (m-10) REVERT: A 876 MET cc_start: 0.8155 (tpp) cc_final: 0.7912 (tpp) REVERT: A 886 MET cc_start: 0.7639 (mmm) cc_final: 0.7327 (mmm) REVERT: B 475 TYR cc_start: 0.8499 (t80) cc_final: 0.8184 (t80) REVERT: B 571 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8468 (tt) REVERT: B 583 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7719 (ttm-80) REVERT: B 601 LEU cc_start: 0.6388 (OUTLIER) cc_final: 0.6131 (mp) REVERT: B 760 TRP cc_start: 0.7964 (m-10) cc_final: 0.7708 (m-10) REVERT: B 876 MET cc_start: 0.8048 (tpp) cc_final: 0.7813 (tpp) REVERT: B 886 MET cc_start: 0.7651 (mmm) cc_final: 0.7432 (mmt) REVERT: B 1005 TYR cc_start: 0.6886 (t80) cc_final: 0.6678 (t80) outliers start: 26 outliers final: 9 residues processed: 151 average time/residue: 0.2010 time to fit residues: 45.6349 Evaluate side-chains 130 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 810 SER Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain B residue 382 ASN 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 793 VAL Chi-restraints excluded: chain B residue 794 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 44 optimal weight: 0.0870 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 536 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.164521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.129019 restraints weight = 18879.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.133218 restraints weight = 9293.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.136081 restraints weight = 6050.293| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11322 Z= 0.138 Angle : 0.542 9.491 15352 Z= 0.281 Chirality : 0.041 0.216 1750 Planarity : 0.004 0.051 1886 Dihedral : 8.346 88.967 1586 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.92 % Allowed : 16.62 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.23), residues: 1380 helix: 2.48 (0.18), residues: 781 sheet: 0.07 (0.42), residues: 140 loop : -0.85 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 806 HIS 0.004 0.001 HIS A 828 PHE 0.026 0.001 PHE B 387 TYR 0.017 0.001 TYR A 827 ARG 0.006 0.000 ARG B 594 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 679) hydrogen bonds : angle 4.22226 ( 1947) covalent geometry : bond 0.00317 (11322) covalent geometry : angle 0.54196 (15352) *********************** 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 151 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.8009 (t80) cc_final: 0.7614 (t80) REVERT: A 475 TYR cc_start: 0.8497 (t80) cc_final: 0.8206 (t80) REVERT: A 583 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7806 (ttm-80) REVERT: A 601 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5764 (mp) REVERT: A 760 TRP cc_start: 0.7971 (m-10) cc_final: 0.7725 (m-10) REVERT: A 876 MET cc_start: 0.8160 (tpp) cc_final: 0.7927 (tpp) REVERT: B 475 TYR cc_start: 0.8424 (t80) cc_final: 0.8145 (t80) REVERT: B 583 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7809 (ttm-80) REVERT: B 601 LEU cc_start: 0.6294 (OUTLIER) cc_final: 0.5780 (mp) REVERT: B 760 TRP cc_start: 0.7947 (m-10) cc_final: 0.7710 (m-10) REVERT: B 876 MET cc_start: 0.8143 (tpp) cc_final: 0.7865 (tpp) outliers start: 22 outliers final: 12 residues processed: 146 average time/residue: 0.2013 time to fit residues: 43.9961 Evaluate side-chains 135 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 764 SER Chi-restraints excluded: chain A residue 793 VAL 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 583 ARG Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 129 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 65 optimal weight: 4.9990 chunk 29 optimal weight: 0.3980 chunk 58 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.162169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.126245 restraints weight = 19613.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.130135 restraints weight = 10048.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.132715 restraints weight = 6659.736| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11322 Z= 0.199 Angle : 0.609 12.010 15352 Z= 0.315 Chirality : 0.044 0.374 1750 Planarity : 0.004 0.050 1886 Dihedral : 8.708 88.419 1586 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.54 % Allowed : 16.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.23), residues: 1380 helix: 2.24 (0.18), residues: 782 sheet: -0.09 (0.42), residues: 140 loop : -0.95 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 806 HIS 0.005 0.001 HIS B 828 PHE 0.023 0.002 PHE B 800 TYR 0.015 0.002 TYR B 827 ARG 0.007 0.001 ARG B 594 Details of bonding type rmsd hydrogen bonds : bond 0.04668 ( 679) hydrogen bonds : angle 4.41923 ( 1947) covalent geometry : bond 0.00468 (11322) covalent geometry : angle 0.60906 (15352) *********************** 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 161 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.7994 (t80) cc_final: 0.7767 (t80) REVERT: A 523 PHE cc_start: 0.4835 (OUTLIER) cc_final: 0.3747 (p90) REVERT: A 583 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7824 (ttm-80) REVERT: A 601 LEU cc_start: 0.6191 (OUTLIER) cc_final: 0.5890 (mp) REVERT: A 656 MET cc_start: 0.7664 (mmm) cc_final: 0.7433 (ttp) REVERT: A 760 TRP cc_start: 0.8022 (m-10) cc_final: 0.7782 (m-10) REVERT: A 876 MET cc_start: 0.8116 (tpp) cc_final: 0.7896 (tpp) REVERT: B 523 PHE cc_start: 0.4863 (OUTLIER) cc_final: 0.3472 (p90) REVERT: B 583 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7832 (ttm-80) REVERT: B 656 MET cc_start: 0.7684 (mmm) cc_final: 0.7445 (ttp) REVERT: B 760 TRP cc_start: 0.8019 (m-10) cc_final: 0.7770 (m-10) REVERT: B 876 MET cc_start: 0.8025 (tpp) cc_final: 0.7821 (tpp) REVERT: B 886 MET cc_start: 0.7486 (mmt) cc_final: 0.7255 (mmm) REVERT: B 1028 TYR cc_start: 0.7502 (t80) cc_final: 0.7291 (t80) outliers start: 29 outliers final: 14 residues processed: 154 average time/residue: 0.2075 time to fit residues: 47.3986 Evaluate side-chains 135 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 793 VAL 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 523 PHE Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 17 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 130 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.163924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.128166 restraints weight = 19096.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.132352 restraints weight = 9458.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.135150 restraints weight = 6173.758| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11322 Z= 0.124 Angle : 0.553 10.404 15352 Z= 0.283 Chirality : 0.042 0.348 1750 Planarity : 0.004 0.044 1886 Dihedral : 8.195 89.885 1586 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.75 % Allowed : 18.29 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.23), residues: 1380 helix: 2.50 (0.18), residues: 780 sheet: -0.02 (0.42), residues: 140 loop : -0.83 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 806 HIS 0.003 0.001 HIS B 828 PHE 0.029 0.001 PHE B 387 TYR 0.015 0.001 TYR B 827 ARG 0.008 0.001 ARG A 594 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 679) hydrogen bonds : angle 4.19171 ( 1947) covalent geometry : bond 0.00277 (11322) covalent geometry : angle 0.55327 (15352) *********************** 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 138 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.8004 (t80) cc_final: 0.7432 (t80) REVERT: A 523 PHE cc_start: 0.4753 (OUTLIER) cc_final: 0.3922 (p90) REVERT: A 583 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7984 (ptm-80) REVERT: A 601 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5847 (mp) REVERT: A 656 MET cc_start: 0.7658 (mmm) cc_final: 0.7398 (ttp) REVERT: B 583 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7943 (ptm-80) REVERT: B 656 MET cc_start: 0.7675 (mmm) cc_final: 0.7407 (ttp) REVERT: B 760 TRP cc_start: 0.7917 (m-10) cc_final: 0.7702 (m-10) REVERT: B 876 MET cc_start: 0.8033 (tpp) cc_final: 0.7814 (tpp) REVERT: B 1028 TYR cc_start: 0.7346 (t80) cc_final: 0.7140 (t80) outliers start: 20 outliers final: 12 residues processed: 135 average time/residue: 0.1996 time to fit residues: 40.3453 Evaluate side-chains 132 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 810 SER Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 948 LEU 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 30 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 chunk 75 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.164249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.128564 restraints weight = 19201.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.132737 restraints weight = 9547.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.135147 restraints weight = 6235.474| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.5133 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= 0.123 Angle : 0.568 11.173 15352 Z= 0.285 Chirality : 0.041 0.351 1750 Planarity : 0.004 0.043 1886 Dihedral : 8.088 89.612 1586 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.01 % Allowed : 18.29 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.23), residues: 1380 helix: 2.59 (0.18), residues: 774 sheet: -0.02 (0.43), residues: 140 loop : -0.72 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 806 HIS 0.005 0.001 HIS B 828 PHE 0.013 0.001 PHE B 864 TYR 0.017 0.001 TYR B 827 ARG 0.009 0.000 ARG A 594 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 679) hydrogen bonds : angle 4.13285 ( 1947) covalent geometry : bond 0.00278 (11322) covalent geometry : angle 0.56789 (15352) *********************** 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 146 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.7965 (t80) cc_final: 0.7383 (t80) REVERT: A 523 PHE cc_start: 0.4742 (OUTLIER) cc_final: 0.4099 (p90) REVERT: A 583 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7812 (ttm-80) REVERT: A 601 LEU cc_start: 0.6231 (OUTLIER) cc_final: 0.5967 (mp) REVERT: A 656 MET cc_start: 0.7643 (mmm) cc_final: 0.7418 (ttp) REVERT: A 760 TRP cc_start: 0.7886 (m-10) cc_final: 0.7632 (m-10) REVERT: B 378 PHE cc_start: 0.3782 (m-80) cc_final: 0.3571 (m-10) REVERT: B 523 PHE cc_start: 0.4841 (OUTLIER) cc_final: 0.3835 (p90) REVERT: B 583 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7811 (ttm-80) REVERT: B 656 MET cc_start: 0.7678 (mmm) cc_final: 0.7441 (ttp) REVERT: B 760 TRP cc_start: 0.7912 (m-10) cc_final: 0.7697 (m-10) REVERT: B 1028 TYR cc_start: 0.7340 (t80) cc_final: 0.7121 (t80) outliers start: 23 outliers final: 11 residues processed: 143 average time/residue: 0.2103 time to fit residues: 45.7405 Evaluate side-chains 134 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 810 SER Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 583 ARG 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 948 LEU 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 101 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 91 optimal weight: 0.3980 chunk 126 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.166510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.133690 restraints weight = 19111.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.139134 restraints weight = 10002.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.138771 restraints weight = 6402.258| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.5242 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= 0.105 Angle : 0.556 11.714 15352 Z= 0.277 Chirality : 0.041 0.291 1750 Planarity : 0.004 0.044 1886 Dihedral : 7.797 85.371 1586 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.31 % Allowed : 19.16 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.23), residues: 1380 helix: 2.63 (0.18), residues: 780 sheet: 0.00 (0.42), residues: 140 loop : -0.72 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 760 HIS 0.004 0.001 HIS B 828 PHE 0.029 0.001 PHE A 800 TYR 0.020 0.001 TYR B 827 ARG 0.009 0.001 ARG B 594 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 679) hydrogen bonds : angle 4.00724 ( 1947) covalent geometry : bond 0.00226 (11322) covalent geometry : angle 0.55562 (15352) ********************** 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: 15 poor density : 123 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.7970 (t80) cc_final: 0.7502 (t80) REVERT: A 416 MET cc_start: 0.7523 (tmm) cc_final: 0.7250 (tmm) REVERT: A 583 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7805 (ttm-80) REVERT: A 601 LEU cc_start: 0.6410 (OUTLIER) cc_final: 0.5887 (mp) REVERT: B 583 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7798 (ttm-80) REVERT: B 656 MET cc_start: 0.7689 (mmm) cc_final: 0.7290 (ttp) REVERT: B 760 TRP cc_start: 0.7915 (m-10) cc_final: 0.7657 (m-10) REVERT: B 876 MET cc_start: 0.8003 (tpp) cc_final: 0.7499 (tpp) REVERT: B 886 MET cc_start: 0.8167 (mpp) cc_final: 0.7935 (mmt) REVERT: B 1028 TYR cc_start: 0.7344 (t80) cc_final: 0.7129 (t80) outliers start: 15 outliers final: 5 residues processed: 136 average time/residue: 0.2023 time to fit residues: 41.0871 Evaluate side-chains 121 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 793 VAL 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 96 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 58 optimal weight: 30.0000 chunk 36 optimal weight: 0.0770 chunk 75 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.167469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.134824 restraints weight = 19017.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.139625 restraints weight = 9932.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.139524 restraints weight = 6903.403| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11322 Z= 0.100 Angle : 0.543 10.608 15352 Z= 0.272 Chirality : 0.041 0.275 1750 Planarity : 0.004 0.044 1886 Dihedral : 7.564 80.677 1586 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.22 % Allowed : 19.77 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.23), residues: 1380 helix: 2.71 (0.18), residues: 780 sheet: 0.10 (0.42), residues: 140 loop : -0.66 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 760 HIS 0.003 0.001 HIS A 828 PHE 0.012 0.001 PHE B 864 TYR 0.017 0.001 TYR A 827 ARG 0.009 0.000 ARG A 594 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 679) hydrogen bonds : angle 3.94266 ( 1947) covalent geometry : bond 0.00212 (11322) covalent geometry : angle 0.54319 (15352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3294.97 seconds wall clock time: 58 minutes 39.72 seconds (3519.72 seconds total)