Starting phenix.real_space_refine on Fri Jul 3 01:05:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8k3r_36857/07_2026/8k3r_36857.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3r_36857/07_2026/8k3r_36857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8k3r_36857/07_2026/8k3r_36857.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8k3r_36857/07_2026/8k3r_36857.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k3r_36857/07_2026/8k3r_36857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3r_36857/07_2026/8k3r_36857.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3r_36857/07_2026/8k3r_36857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3r_36857/07_2026/8k3r_36857.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 66 5.16 5 C 7258 2.51 5 N 1781 2.21 5 O 1954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11061 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5482 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 20, 'TRANS': 681} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 6, 'GLU:plan': 9, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 5, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 139 Chain: "B" Number of atoms: 5483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5483 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 20, 'TRANS': 681} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 6, 'GLU:plan': 9, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 5, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 139 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 2.84, per 1000 atoms: 0.26 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: 1.01 Conformation dependent library (CDL) restraints added in 623.8 milliseconds 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2678 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 8 sheets defined 64.5% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 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: 2.47 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1686 1.31 - 1.43: 3265 1.43 - 1.56: 6244 1.56 - 1.68: 28 1.68 - 1.81: 100 Bond restraints: 11323 Sorted by residual: bond pdb=" C31 POV A1301 " pdb=" O31 POV A1301 " ideal model delta sigma weight residual 1.327 1.438 -0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C31 POV B1301 " pdb=" O31 POV B1301 " ideal model delta sigma weight residual 1.327 1.437 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C21 POV B1301 " pdb=" O21 POV B1301 " ideal model delta sigma weight residual 1.330 1.413 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C21 POV A1301 " pdb=" O21 POV A1301 " ideal model delta sigma weight residual 1.330 1.412 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb="C312 POV A1301 " pdb="C313 POV A1301 " ideal model delta sigma weight residual 1.523 1.599 -0.076 2.00e-02 2.50e+03 1.46e+01 ... (remaining 11318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 14966 2.40 - 4.80: 340 4.80 - 7.19: 36 7.19 - 9.59: 6 9.59 - 11.99: 6 Bond angle restraints: 15354 Sorted by residual: angle pdb=" N ARG B 508 " pdb=" CA ARG B 508 " pdb=" C ARG B 508 " ideal model delta sigma weight residual 112.89 107.62 5.27 1.24e+00 6.50e-01 1.81e+01 angle pdb=" N ARG A 508 " pdb=" CA ARG A 508 " pdb=" C ARG A 508 " ideal model delta sigma weight residual 112.89 107.65 5.24 1.24e+00 6.50e-01 1.78e+01 angle pdb=" CA VAL B 435 " pdb=" C VAL B 435 " pdb=" O VAL B 435 " ideal model delta sigma weight residual 121.67 117.30 4.37 1.05e+00 9.07e-01 1.73e+01 angle pdb=" CA VAL A 435 " pdb=" C VAL A 435 " pdb=" O VAL A 435 " ideal model delta sigma weight residual 121.67 117.32 4.35 1.05e+00 9.07e-01 1.72e+01 angle pdb=" O13 POV B1301 " pdb=" P POV B1301 " pdb=" O14 POV B1301 " ideal model delta sigma weight residual 121.11 109.12 11.99 3.00e+00 1.11e-01 1.60e+01 ... (remaining 15349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.62: 6299 25.62 - 51.25: 244 51.25 - 76.87: 58 76.87 - 102.50: 6 102.50 - 128.12: 2 Dihedral angle restraints: 6609 sinusoidal: 2469 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 6606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1127 0.044 - 0.088: 479 0.088 - 0.132: 115 0.132 - 0.177: 23 0.177 - 0.221: 7 Chirality restraints: 1751 Sorted by residual: chirality pdb=" CA VAL B 435 " pdb=" N VAL B 435 " pdb=" C VAL B 435 " pdb=" CB VAL B 435 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA VAL A 435 " pdb=" N VAL A 435 " pdb=" C VAL A 435 " pdb=" CB VAL A 435 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C2 POV B1301 " pdb=" C1 POV B1301 " pdb=" C3 POV B1301 " pdb=" O21 POV B1301 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 1748 not shown) Planarity restraints: 1886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 504 " -0.017 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C LYS A 504 " 0.056 2.00e-02 2.50e+03 pdb=" O LYS A 504 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE A 505 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 504 " 0.017 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C LYS B 504 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS B 504 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE B 505 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1015 " -0.025 2.00e-02 2.50e+03 2.09e-02 7.65e+00 pdb=" CG PHE A1015 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A1015 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A1015 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A1015 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A1015 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A1015 " -0.010 2.00e-02 2.50e+03 ... (remaining 1883 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2642 2.79 - 3.32: 10382 3.32 - 3.84: 17977 3.84 - 4.37: 21459 4.37 - 4.90: 37428 Nonbonded interactions: 89888 Sorted by model distance: nonbonded pdb=" NH1 ARG B 817 " pdb=" O13 POV B1301 " model vdw 2.259 3.120 nonbonded pdb=" NH1 ARG A 817 " pdb=" O13 POV A1301 " model vdw 2.260 3.120 nonbonded pdb=" OG1 THR A 394 " pdb=" NE2 GLN B1002 " model vdw 2.273 3.120 nonbonded pdb=" NE2 GLN A1002 " pdb=" OG1 THR B 394 " model vdw 2.311 3.120 nonbonded pdb=" OG SER B 611 " pdb=" O TYR B 741 " model vdw 2.318 3.040 ... (remaining 89883 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and ((resid 375 and (name CA or name C or name O or name CB or name C \ G1 or name CG2 or name CD1)) or resid 376 through 1301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.220 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.111 11323 Z= 0.378 Angle : 0.864 11.988 15354 Z= 0.479 Chirality : 0.052 0.221 1751 Planarity : 0.005 0.057 1886 Dihedral : 14.819 128.121 3931 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.92 % Allowed : 0.52 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.23), residues: 1380 helix: 1.35 (0.19), residues: 752 sheet: -0.22 (0.39), residues: 166 loop : -1.05 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1040 TYR 0.024 0.003 TYR B 827 PHE 0.047 0.003 PHE B1015 TRP 0.044 0.002 TRP A1103 HIS 0.006 0.002 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00802 / 0.38 (11323) covalent geometry : angle 0.86399 / 0.48 (15354) hydrogen bonds : bond 0.15429 / 10.53 ( 679) hydrogen bonds : angle 6.51589 / 4.48 ( 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 : 0.413 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: 0.1098 time to fit residues: 48.7022 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 : 0.410 ------------------------------------------------------------------------------- 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... A 472 ASN A 540 HIS A 548 ASN B 472 ASN B 540 HIS B 548 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.172326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.137481 restraints weight = 18213.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.141934 restraints weight = 8968.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.144953 restraints weight = 5811.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.146808 restraints weight = 4426.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.147916 restraints weight = 3742.452| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11323 Z= 0.144 Angle : 0.575 8.589 15354 Z= 0.304 Chirality : 0.042 0.167 1751 Planarity : 0.004 0.050 1886 Dihedral : 9.454 113.166 1574 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.10 % Allowed : 11.81 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.22), residues: 1380 helix: 2.08 (0.18), residues: 752 sheet: -0.09 (0.43), residues: 136 loop : -0.73 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 687 TYR 0.026 0.002 TYR A 827 PHE 0.022 0.002 PHE A 911 TRP 0.014 0.001 TRP B1047 HIS 0.011 0.002 HIS B 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (11323) covalent geometry : angle 0.57497 / 0.30 (15354) hydrogen bonds : bond 0.04654 / 3.13 ( 679) hydrogen bonds : angle 4.54296 / 3.16 ( 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 171 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 454 MET cc_start: 0.7302 (mtp) cc_final: 0.6905 (mtt) REVERT: A 601 LEU cc_start: 0.5625 (OUTLIER) cc_final: 0.5244 (mp) REVERT: A 653 GLU cc_start: 0.8650 (tt0) cc_final: 0.8408 (tt0) REVERT: A 876 MET cc_start: 0.8196 (tpp) cc_final: 0.7900 (tpp) REVERT: B 454 MET cc_start: 0.7309 (mtp) cc_final: 0.6941 (mtt) REVERT: B 601 LEU cc_start: 0.5622 (OUTLIER) cc_final: 0.5235 (mp) REVERT: B 653 GLU cc_start: 0.8651 (tt0) cc_final: 0.8409 (tt0) REVERT: B 875 MET cc_start: 0.8827 (mtp) cc_final: 0.8607 (mtm) REVERT: B 876 MET cc_start: 0.7759 (tpp) cc_final: 0.7406 (tpt) REVERT: B 1066 ASP cc_start: 0.6395 (t0) cc_final: 0.6053 (t0) REVERT: B 1070 MET cc_start: 0.5366 (mtm) cc_final: 0.4906 (mtm) outliers start: 24 outliers final: 8 residues processed: 165 average time/residue: 0.0818 time to fit residues: 20.7947 Evaluate side-chains 120 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 31 optimal weight: 0.0270 chunk 128 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN B 472 ASN B 548 ASN B 828 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.170175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.138644 restraints weight = 18396.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.141533 restraints weight = 8264.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.141399 restraints weight = 5806.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.142493 restraints weight = 6430.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.142447 restraints weight = 5264.418| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11323 Z= 0.126 Angle : 0.520 6.448 15354 Z= 0.277 Chirality : 0.041 0.173 1751 Planarity : 0.004 0.041 1886 Dihedral : 8.263 89.758 1574 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.49 % Allowed : 13.39 % 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 are not related in a simple way. whole: 1.55 (0.22), residues: 1380 helix: 2.25 (0.18), residues: 778 sheet: 0.15 (0.43), residues: 136 loop : -0.84 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 417 TYR 0.023 0.001 TYR A 827 PHE 0.020 0.002 PHE A 799 TRP 0.009 0.001 TRP B 806 HIS 0.009 0.001 HIS B 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (11323) covalent geometry : angle 0.52049 / 0.28 (15354) hydrogen bonds : bond 0.04314 / 2.89 ( 679) hydrogen bonds : angle 4.32194 / 2.99 ( 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 144 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 556 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7070 (mp) REVERT: A 610 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8276 (m-30) REVERT: A 653 GLU cc_start: 0.8664 (tt0) cc_final: 0.8433 (tt0) REVERT: A 760 TRP cc_start: 0.7761 (m-10) cc_final: 0.7371 (m-10) REVERT: A 876 MET cc_start: 0.8111 (tpp) cc_final: 0.7800 (tpp) REVERT: B 571 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8349 (tt) REVERT: B 653 GLU cc_start: 0.8659 (tt0) cc_final: 0.8437 (tt0) REVERT: B 760 TRP cc_start: 0.7755 (m-10) cc_final: 0.7362 (m-10) REVERT: B 876 MET cc_start: 0.8002 (tpp) cc_final: 0.7725 (tpp) outliers start: 17 outliers final: 5 residues processed: 141 average time/residue: 0.0807 time to fit residues: 17.6396 Evaluate side-chains 118 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain B residue 571 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 GLN B 650 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.156673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.122730 restraints weight = 18945.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.126368 restraints weight = 9999.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.128786 restraints weight = 6787.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.130224 restraints weight = 5358.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.130829 restraints weight = 4658.938| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11323 Z= 0.263 Angle : 0.673 6.245 15354 Z= 0.357 Chirality : 0.046 0.162 1751 Planarity : 0.005 0.047 1886 Dihedral : 8.854 103.919 1574 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.71 % Allowed : 14.44 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.22), residues: 1380 helix: 1.87 (0.18), residues: 782 sheet: -0.22 (0.42), residues: 136 loop : -1.14 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 594 TYR 0.019 0.002 TYR B1028 PHE 0.022 0.003 PHE B 387 TRP 0.015 0.002 TRP B 806 HIS 0.007 0.002 HIS B 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.26 (11323) covalent geometry : angle 0.67262 / 0.36 (15354) hydrogen bonds : bond 0.05475 / 3.66 ( 679) hydrogen bonds : angle 4.70420 / 3.25 ( 1947) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.437 Fit side-chains REVERT: A 601 LEU cc_start: 0.5962 (OUTLIER) cc_final: 0.5724 (mp) REVERT: A 610 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8395 (m-30) REVERT: A 760 TRP cc_start: 0.7987 (m-10) cc_final: 0.7718 (m-10) REVERT: A 876 MET cc_start: 0.8210 (tpp) cc_final: 0.7939 (tpp) REVERT: A 1005 TYR cc_start: 0.7114 (t80) cc_final: 0.6795 (t80) REVERT: B 601 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5835 (mp) REVERT: B 610 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8395 (m-30) REVERT: B 760 TRP cc_start: 0.7986 (m-10) cc_final: 0.7710 (m-10) REVERT: B 876 MET cc_start: 0.8166 (tpp) cc_final: 0.7905 (tpp) REVERT: B 1005 TYR cc_start: 0.7069 (t80) cc_final: 0.6755 (t80) REVERT: B 1066 ASP cc_start: 0.6453 (t0) cc_final: 0.6055 (t0) outliers start: 31 outliers final: 10 residues processed: 159 average time/residue: 0.0798 time to fit residues: 19.0601 Evaluate side-chains 122 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 825 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 821 VAL Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1040 ARG Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 97 optimal weight: 0.2980 chunk 122 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 GLN A 472 ASN A 545 ASN B 419 GLN B 545 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.167533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.132295 restraints weight = 18635.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.136544 restraints weight = 9427.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.139392 restraints weight = 6181.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.141117 restraints weight = 4735.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.142254 restraints weight = 4034.872| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11323 Z= 0.114 Angle : 0.558 10.279 15354 Z= 0.285 Chirality : 0.043 0.397 1751 Planarity : 0.004 0.041 1886 Dihedral : 7.782 79.863 1574 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.75 % Allowed : 16.36 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.23), residues: 1380 helix: 2.39 (0.18), residues: 780 sheet: 0.15 (0.39), residues: 152 loop : -1.00 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 594 TYR 0.019 0.001 TYR B 827 PHE 0.016 0.001 PHE B 800 TRP 0.011 0.001 TRP B 485 HIS 0.004 0.001 HIS A 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (11323) covalent geometry : angle 0.55751 / 0.29 (15354) hydrogen bonds : bond 0.04188 / 2.80 ( 679) hydrogen bonds : angle 4.27999 / 2.95 ( 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 144 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.408 Fit side-chains REVERT: A 583 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7672 (ttm-80) REVERT: A 601 LEU cc_start: 0.5913 (OUTLIER) cc_final: 0.5600 (mp) REVERT: A 610 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8417 (m-30) REVERT: A 653 GLU cc_start: 0.8724 (tt0) cc_final: 0.8446 (tt0) REVERT: A 760 TRP cc_start: 0.7855 (m-10) cc_final: 0.7622 (m-10) REVERT: B 571 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8252 (tt) REVERT: B 601 LEU cc_start: 0.6097 (OUTLIER) cc_final: 0.5561 (mp) REVERT: B 653 GLU cc_start: 0.8726 (tt0) cc_final: 0.8447 (tt0) REVERT: B 656 MET cc_start: 0.7715 (mmm) cc_final: 0.7417 (ttp) REVERT: B 760 TRP cc_start: 0.7854 (m-10) cc_final: 0.7604 (m-10) REVERT: B 876 MET cc_start: 0.8168 (tpp) cc_final: 0.7895 (tpp) REVERT: B 886 MET cc_start: 0.7591 (mmm) cc_final: 0.6942 (mmm) outliers start: 20 outliers final: 7 residues processed: 140 average time/residue: 0.0724 time to fit residues: 16.0089 Evaluate side-chains 126 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 825 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 12 optimal weight: 30.0000 chunk 65 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 HIS B 536 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.163820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.128117 restraints weight = 18942.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.132375 restraints weight = 9369.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.135240 restraints weight = 6088.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.136722 restraints weight = 4657.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.137982 restraints weight = 4010.183| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11323 Z= 0.168 Angle : 0.577 8.223 15354 Z= 0.301 Chirality : 0.043 0.302 1751 Planarity : 0.004 0.043 1886 Dihedral : 7.901 78.694 1574 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.19 % Allowed : 16.19 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.23), residues: 1380 helix: 2.42 (0.18), residues: 778 sheet: 0.16 (0.40), residues: 152 loop : -1.01 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 594 TYR 0.018 0.001 TYR B 827 PHE 0.028 0.002 PHE B 387 TRP 0.012 0.001 TRP A 806 HIS 0.004 0.001 HIS B 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (11323) covalent geometry : angle 0.57684 / 0.30 (15354) hydrogen bonds : bond 0.04419 / 2.96 ( 679) hydrogen bonds : angle 4.35824 / 3.01 ( 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 145 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.397 Fit side-chains REVERT: A 583 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7675 (ttm-80) REVERT: A 601 LEU cc_start: 0.6012 (OUTLIER) cc_final: 0.5785 (mp) REVERT: A 760 TRP cc_start: 0.7951 (m-10) cc_final: 0.7705 (m-10) REVERT: A 945 TYR cc_start: 0.8868 (t80) cc_final: 0.8642 (t80) REVERT: B 583 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7723 (ttm-80) REVERT: B 601 LEU cc_start: 0.6195 (OUTLIER) cc_final: 0.5912 (mp) REVERT: B 610 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8404 (m-30) REVERT: B 656 MET cc_start: 0.7680 (mmm) cc_final: 0.7427 (ttp) REVERT: B 760 TRP cc_start: 0.7975 (m-10) cc_final: 0.7720 (m-10) REVERT: B 876 MET cc_start: 0.8102 (tpp) cc_final: 0.7861 (tpp) REVERT: B 886 MET cc_start: 0.7578 (mmm) cc_final: 0.7237 (mmm) REVERT: B 1005 TYR cc_start: 0.6741 (t80) cc_final: 0.6521 (t80) outliers start: 25 outliers final: 9 residues processed: 139 average time/residue: 0.0702 time to fit residues: 15.3192 Evaluate side-chains 129 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 810 SER Chi-restraints excluded: chain A residue 821 VAL 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 793 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 982 ILE 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: 6.9990 chunk 86 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.157153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.120656 restraints weight = 19576.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.124549 restraints weight = 9879.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.127132 restraints weight = 6553.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.128618 restraints weight = 5113.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.129486 restraints weight = 4426.312| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 11323 Z= 0.336 Angle : 0.738 9.887 15354 Z= 0.390 Chirality : 0.048 0.170 1751 Planarity : 0.005 0.043 1886 Dihedral : 9.395 111.351 1574 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.27 % Allowed : 17.32 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.22), residues: 1380 helix: 1.78 (0.18), residues: 778 sheet: -0.40 (0.44), residues: 136 loop : -1.23 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1040 TYR 0.018 0.002 TYR B1028 PHE 0.023 0.003 PHE A1052 TRP 0.019 0.002 TRP B 806 HIS 0.006 0.002 HIS B 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00800 / 0.34 (11323) covalent geometry : angle 0.73838 / 0.39 (15354) hydrogen bonds : bond 0.05671 / 3.80 ( 679) hydrogen bonds : angle 4.90456 / 3.38 ( 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 147 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 448 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8696 (mp) REVERT: A 475 TYR cc_start: 0.8432 (t80) cc_final: 0.8206 (t80) REVERT: A 523 PHE cc_start: 0.5007 (OUTLIER) cc_final: 0.3907 (p90) REVERT: A 601 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5946 (mp) REVERT: A 760 TRP cc_start: 0.8107 (m-10) cc_final: 0.7900 (m-10) REVERT: B 475 TYR cc_start: 0.8526 (t80) cc_final: 0.8296 (t80) REVERT: B 523 PHE cc_start: 0.4901 (OUTLIER) cc_final: 0.3770 (p90) REVERT: B 601 LEU cc_start: 0.6251 (OUTLIER) cc_final: 0.6034 (mp) REVERT: B 610 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8273 (t0) REVERT: B 760 TRP cc_start: 0.8110 (m-10) cc_final: 0.7902 (m-10) REVERT: B 876 MET cc_start: 0.8037 (tpp) cc_final: 0.7816 (tpp) outliers start: 26 outliers final: 13 residues processed: 140 average time/residue: 0.0738 time to fit residues: 16.3776 Evaluate side-chains 134 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 494 VAL 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 764 SER Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 494 VAL 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 793 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 75 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 ASN A 756 GLN B 756 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.164025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.128274 restraints weight = 19090.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.132515 restraints weight = 9466.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.135303 restraints weight = 6197.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.136976 restraints weight = 4793.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.137912 restraints weight = 4089.442| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11323 Z= 0.121 Angle : 0.571 9.872 15354 Z= 0.294 Chirality : 0.042 0.274 1751 Planarity : 0.004 0.046 1886 Dihedral : 8.175 88.048 1574 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.49 % Allowed : 18.46 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.23), residues: 1380 helix: 2.38 (0.18), residues: 776 sheet: -0.22 (0.43), residues: 140 loop : -1.03 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 594 TYR 0.020 0.001 TYR A 945 PHE 0.028 0.001 PHE A 387 TRP 0.009 0.001 TRP A 806 HIS 0.003 0.001 HIS A 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (11323) covalent geometry : angle 0.57063 / 0.29 (15354) hydrogen bonds : bond 0.04187 / 2.80 ( 679) hydrogen bonds : angle 4.32909 / 2.98 ( 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 143 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 583 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7897 (ttm-80) REVERT: A 601 LEU cc_start: 0.6052 (OUTLIER) cc_final: 0.5820 (mp) REVERT: A 1103 TRP cc_start: 0.7816 (m100) cc_final: 0.7596 (m100) REVERT: B 475 TYR cc_start: 0.8452 (t80) cc_final: 0.8185 (t80) REVERT: B 583 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7897 (ttm-80) REVERT: B 601 LEU cc_start: 0.6302 (OUTLIER) cc_final: 0.6094 (mp) REVERT: B 653 GLU cc_start: 0.8699 (tt0) cc_final: 0.8376 (tt0) REVERT: B 876 MET cc_start: 0.8136 (tpp) cc_final: 0.7881 (tpp) REVERT: B 886 MET cc_start: 0.7540 (mmt) cc_final: 0.7310 (mmm) REVERT: B 945 TYR cc_start: 0.8821 (t80) cc_final: 0.8548 (t80) REVERT: B 1103 TRP cc_start: 0.7828 (m100) cc_final: 0.7597 (m100) outliers start: 17 outliers final: 7 residues processed: 139 average time/residue: 0.0863 time to fit residues: 18.3417 Evaluate side-chains 130 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 793 VAL 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 825 LEU Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 27 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 87 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 937 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.154833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.121411 restraints weight = 19079.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.125072 restraints weight = 9868.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.127466 restraints weight = 6624.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.128897 restraints weight = 5241.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.129801 restraints weight = 4552.933| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11323 Z= 0.221 Angle : 0.641 9.255 15354 Z= 0.333 Chirality : 0.044 0.231 1751 Planarity : 0.004 0.052 1886 Dihedral : 8.616 89.523 1574 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.57 % Allowed : 18.29 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.23), residues: 1380 helix: 2.15 (0.18), residues: 785 sheet: -0.34 (0.44), residues: 139 loop : -1.08 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 594 TYR 0.023 0.002 TYR A 475 PHE 0.017 0.002 PHE B 813 TRP 0.015 0.001 TRP B 806 HIS 0.004 0.001 HIS B 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 (11323) covalent geometry : angle 0.64074 / 0.33 (15354) hydrogen bonds : bond 0.04727 / 3.18 ( 679) hydrogen bonds : angle 4.52521 / 3.11 ( 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 141 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 416 MET cc_start: 0.7495 (tmm) cc_final: 0.7119 (tmm) REVERT: A 583 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7864 (ttm-80) REVERT: A 601 LEU cc_start: 0.6181 (OUTLIER) cc_final: 0.5923 (mp) REVERT: A 612 ILE cc_start: 0.8016 (mm) cc_final: 0.7508 (mt) REVERT: A 1103 TRP cc_start: 0.7860 (m100) cc_final: 0.7614 (m100) REVERT: B 416 MET cc_start: 0.7525 (tmm) cc_final: 0.7134 (tmm) REVERT: B 475 TYR cc_start: 0.8479 (t80) cc_final: 0.8221 (t80) REVERT: B 523 PHE cc_start: 0.4918 (OUTLIER) cc_final: 0.3969 (p90) REVERT: B 583 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7906 (ttm-80) REVERT: B 601 LEU cc_start: 0.6249 (OUTLIER) cc_final: 0.6007 (mp) REVERT: B 876 MET cc_start: 0.8185 (tpp) cc_final: 0.7930 (tpp) REVERT: B 945 TYR cc_start: 0.8950 (t80) cc_final: 0.8727 (t80) REVERT: B 1103 TRP cc_start: 0.7883 (m100) cc_final: 0.7634 (m100) outliers start: 18 outliers final: 7 residues processed: 137 average time/residue: 0.0804 time to fit residues: 17.3091 Evaluate side-chains 132 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 793 VAL 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 601 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 102 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 106 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.163873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.128841 restraints weight = 19320.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.133009 restraints weight = 9579.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.135807 restraints weight = 6263.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.137483 restraints weight = 4818.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.138264 restraints weight = 4108.251| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11323 Z= 0.110 Angle : 0.562 9.844 15354 Z= 0.288 Chirality : 0.041 0.224 1751 Planarity : 0.004 0.046 1886 Dihedral : 7.831 88.282 1574 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.96 % Allowed : 19.16 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.23), residues: 1380 helix: 2.50 (0.18), residues: 776 sheet: -0.16 (0.44), residues: 140 loop : -0.95 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 594 TYR 0.022 0.001 TYR A 945 PHE 0.027 0.001 PHE B 387 TRP 0.009 0.001 TRP B 806 HIS 0.003 0.000 HIS B 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (11323) covalent geometry : angle 0.56161 / 0.29 (15354) hydrogen bonds : bond 0.03977 / 2.67 ( 679) hydrogen bonds : angle 4.21886 / 2.90 ( 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 137 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 416 MET cc_start: 0.7352 (tmm) cc_final: 0.7074 (tmm) REVERT: A 583 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7938 (ttm-80) REVERT: A 601 LEU cc_start: 0.6117 (OUTLIER) cc_final: 0.5891 (mp) REVERT: A 612 ILE cc_start: 0.7899 (mm) cc_final: 0.7430 (mt) REVERT: B 416 MET cc_start: 0.7399 (tmm) cc_final: 0.7107 (tmm) REVERT: B 583 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7922 (ttm-80) REVERT: B 601 LEU cc_start: 0.6312 (OUTLIER) cc_final: 0.6109 (mp) REVERT: B 945 TYR cc_start: 0.8851 (t80) cc_final: 0.8616 (t80) REVERT: B 1070 MET cc_start: 0.5395 (mtt) cc_final: 0.5167 (mtt) REVERT: B 1090 MET cc_start: 0.2583 (ttp) cc_final: 0.1969 (ttp) REVERT: B 1103 TRP cc_start: 0.7805 (m100) cc_final: 0.7581 (m100) outliers start: 11 outliers final: 5 residues processed: 134 average time/residue: 0.0765 time to fit residues: 16.1515 Evaluate side-chains 126 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 793 VAL 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 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: 6.9990 chunk 10 optimal weight: 0.4980 chunk 82 optimal weight: 30.0000 chunk 92 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 68 optimal weight: 0.0170 chunk 12 optimal weight: 30.0000 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.173133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.137087 restraints weight = 19871.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.141595 restraints weight = 9827.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.144487 restraints weight = 6368.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.146270 restraints weight = 4899.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.147254 restraints weight = 4169.294| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11323 Z= 0.103 Angle : 0.558 11.109 15354 Z= 0.282 Chirality : 0.041 0.290 1751 Planarity : 0.004 0.045 1886 Dihedral : 7.361 82.122 1574 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.96 % Allowed : 19.86 % 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 are not related in a simple way. whole: 1.83 (0.23), residues: 1380 helix: 2.64 (0.18), residues: 776 sheet: 0.00 (0.44), residues: 140 loop : -0.94 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 594 TYR 0.019 0.001 TYR B 827 PHE 0.031 0.001 PHE B 800 TRP 0.023 0.001 TRP B 760 HIS 0.003 0.001 HIS B 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (11323) covalent geometry : angle 0.55796 / 0.28 (15354) hydrogen bonds : bond 0.03665 / 2.47 ( 679) hydrogen bonds : angle 4.10390 / 2.82 ( 1947) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1763.37 seconds wall clock time: 31 minutes 21.34 seconds (1881.34 seconds total)