Starting phenix.real_space_refine on Wed May 14 09:50:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3q_36856/05_2025/8k3q_36856.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3q_36856/05_2025/8k3q_36856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k3q_36856/05_2025/8k3q_36856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3q_36856/05_2025/8k3q_36856.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3q_36856/05_2025/8k3q_36856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3q_36856/05_2025/8k3q_36856.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.095 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 68 5.16 5 C 7444 2.51 5 N 1833 2.21 5 O 2018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11365 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5630 Classifications: {'peptide': 724} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 21, 'TRANS': 702} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Restraints were copied for chains: B Time building chain proxies: 12.12, per 1000 atoms: 1.07 Number of scatterers: 11365 At special positions: 0 Unit cell: (134.62, 83.74, 118.72, 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 68 16.00 P 2 15.00 O 2018 8.00 N 1833 7.00 C 7444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.5 seconds 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2756 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 8 sheets defined 62.6% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 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: 4.099A 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: 3.968A 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: 5.913A 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: 3.557A 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: 3.715A 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: 4.100A 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: 4.099A 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: 3.968A 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: 3.550A pdb=" N PHE B 639 " --> pdb=" O GLY B 636 " (cutoff:3.500A) removed outlier: 5.913A 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: 3.711A 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: 3.927A 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: 4.103A 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: 3.554A 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: 3.906A 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: 3.533A 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: 3.798A 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: 7.373A 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: 3.552A 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: 7.574A 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: 6.386A 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: 4.261A 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: 4.431A 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: 6.748A 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: 6.688A 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: 3.637A 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: 6.715A pdb=" N LEU B 448 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.574A 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: 7.125A 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: 6.812A 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: 7.261A 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: 4.431A 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: 3.759A pdb=" N ASN B 548 " --> pdb=" O SER B 555 " (cutoff:3.500A) 679 hydrogen bonds defined for protein. 1947 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.68 Time building geometry restraints manager: 3.07 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: 1742 1.31 - 1.43: 3355 1.43 - 1.56: 6401 1.56 - 1.68: 28 1.68 - 1.80: 104 Bond restraints: 11630 Sorted by residual: bond pdb=" C31 POV A1301 " pdb=" O31 POV A1301 " ideal model delta sigma weight residual 1.327 1.437 -0.110 2.00e-02 2.50e+03 3.03e+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 3.00e+01 bond pdb=" C21 POV B1301 " pdb=" O21 POV B1301 " ideal model delta sigma weight residual 1.330 1.412 -0.082 2.00e-02 2.50e+03 1.70e+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 B1301 " pdb="C313 POV B1301 " ideal model delta sigma weight residual 1.523 1.599 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 11625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 15366 2.39 - 4.78: 355 4.78 - 7.17: 36 7.17 - 9.56: 6 9.56 - 11.95: 6 Bond angle restraints: 15769 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 112.89 107.63 5.26 1.24e+00 6.50e-01 1.80e+01 angle pdb=" CA VAL B 435 " pdb=" C VAL B 435 " pdb=" O VAL B 435 " ideal model delta sigma weight residual 121.67 117.28 4.39 1.05e+00 9.07e-01 1.75e+01 angle pdb=" CA VAL A 435 " pdb=" C VAL A 435 " pdb=" O VAL A 435 " ideal model delta sigma weight residual 121.67 117.29 4.38 1.05e+00 9.07e-01 1.74e+01 angle pdb=" O13 POV B1301 " pdb=" P POV B1301 " pdb=" O14 POV B1301 " ideal model delta sigma weight residual 121.11 109.16 11.95 3.00e+00 1.11e-01 1.59e+01 ... (remaining 15764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.63: 6481 25.63 - 51.25: 248 51.25 - 76.88: 58 76.88 - 102.51: 6 102.51 - 128.13: 2 Dihedral angle restraints: 6795 sinusoidal: 2529 harmonic: 4266 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 -152.36 -27.64 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 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+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 180.00 154.83 25.17 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 6792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1155 0.044 - 0.089: 493 0.089 - 0.133: 114 0.133 - 0.177: 24 0.177 - 0.222: 6 Chirality restraints: 1792 Sorted by residual: 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 1.23e+00 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=" 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 2.61 -0.18 2.00e-01 2.50e+01 8.43e-01 ... (remaining 1789 not shown) Planarity restraints: 1945 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 504 " -0.017 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C LYS B 504 " 0.057 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=" 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=" CB PHE B1015 " -0.025 2.00e-02 2.50e+03 2.08e-02 7.58e+00 pdb=" CG PHE B1015 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B1015 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B1015 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B1015 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B1015 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B1015 " -0.009 2.00e-02 2.50e+03 ... (remaining 1942 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 2 2.18 - 2.86: 4003 2.86 - 3.54: 15476 3.54 - 4.22: 26036 4.22 - 4.90: 46789 Nonbonded interactions: 92306 Sorted by model distance: nonbonded pdb=" CB HIS B 706 " pdb=" CG HIS B 706 " model vdw 1.495 3.660 nonbonded pdb=" CB LYS B1007 " pdb=" CG LYS B1007 " model vdw 1.521 3.840 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 2.259 3.120 nonbonded pdb=" OG1 THR A 394 " pdb=" NE2 GLN B1002 " model vdw 2.273 3.120 ... (remaining 92301 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 245 through 705 or (resid 706 and (name N or name CA or na \ me C or name O or name CB )) or resid 707 through 1006 or (resid 1007 and (name \ N or name CA or name C or name O or name CB )) or resid 1008 through 1125 or res \ id 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 individual isotropic 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 32.730 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 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 0.110 11630 Z= 0.375 Angle : 0.869 11.949 15769 Z= 0.483 Chirality : 0.051 0.222 1792 Planarity : 0.005 0.057 1945 Dihedral : 14.726 128.132 4039 Min Nonbonded Distance : 1.495 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.89 % Allowed : 0.51 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.22), residues: 1420 helix: 1.35 (0.19), residues: 752 sheet: -0.21 (0.39), residues: 166 loop : -1.27 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B1103 HIS 0.005 0.002 HIS B 459 PHE 0.047 0.003 PHE B1015 TYR 0.036 0.003 TYR B 249 ARG 0.007 0.001 ARG A1040 Details of bonding type rmsd hydrogen bonds : bond 0.15431 ( 679) hydrogen bonds : angle 6.51570 ( 1947) covalent geometry : bond 0.00794 (11630) covalent geometry : angle 0.86899 (15769) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 1.169 Fit side-chains REVERT: A 656 MET cc_start: 0.8932 (mmt) cc_final: 0.8521 (mmt) REVERT: A 689 GLN cc_start: 0.8016 (tp40) cc_final: 0.7347 (mt0) REVERT: A 859 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7682 (mppt) REVERT: A 1108 SER cc_start: 0.8412 (t) cc_final: 0.8189 (m) REVERT: B 388 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7649 (t0) REVERT: B 594 ARG cc_start: 0.7909 (mmt180) cc_final: 0.7653 (mmp-170) REVERT: B 656 MET cc_start: 0.8861 (mmt) cc_final: 0.8394 (mmt) REVERT: B 689 GLN cc_start: 0.7923 (tp40) cc_final: 0.7338 (mt0) REVERT: B 859 LYS cc_start: 0.7803 (mmtt) cc_final: 0.7522 (mppt) REVERT: B 875 MET cc_start: 0.8570 (ttm) cc_final: 0.8322 (mtp) outliers start: 22 outliers final: 2 residues processed: 177 average time/residue: 1.3733 time to fit residues: 261.3500 Evaluate side-chains 131 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 817 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 130 optimal weight: 0.5980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 426 ASN A 545 ASN A 560 GLN A 650 GLN A 856 ASN A1013 ASN B 419 GLN B 426 ASN B 545 ASN B 548 ASN B 560 GLN B 650 GLN B1013 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.139988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109976 restraints weight = 12654.328| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.80 r_work: 0.3146 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11630 Z= 0.179 Angle : 0.558 5.735 15769 Z= 0.304 Chirality : 0.043 0.174 1792 Planarity : 0.005 0.054 1945 Dihedral : 10.014 115.555 1643 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.46 % Allowed : 8.40 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.22), residues: 1420 helix: 2.04 (0.18), residues: 766 sheet: -0.14 (0.38), residues: 156 loop : -1.02 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1103 HIS 0.005 0.002 HIS A 828 PHE 0.015 0.002 PHE A 708 TYR 0.017 0.002 TYR A1008 ARG 0.005 0.001 ARG B 749 Details of bonding type rmsd hydrogen bonds : bond 0.05486 ( 679) hydrogen bonds : angle 4.67766 ( 1947) covalent geometry : bond 0.00417 (11630) covalent geometry : angle 0.55782 (15769) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 1.201 Fit side-chains REVERT: A 471 ASP cc_start: 0.7200 (m-30) cc_final: 0.6902 (m-30) REVERT: A 577 LYS cc_start: 0.7561 (mtmt) cc_final: 0.7351 (mttp) REVERT: A 689 GLN cc_start: 0.8294 (tp40) cc_final: 0.7172 (mt0) REVERT: A 749 ARG cc_start: 0.8206 (mtp180) cc_final: 0.7708 (mmm-85) REVERT: A 859 LYS cc_start: 0.8261 (mmtt) cc_final: 0.7717 (mppt) REVERT: A 1108 SER cc_start: 0.8481 (t) cc_final: 0.8154 (m) REVERT: B 471 ASP cc_start: 0.7163 (m-30) cc_final: 0.6798 (m-30) REVERT: B 594 ARG cc_start: 0.8419 (mmt180) cc_final: 0.8165 (mmp-170) REVERT: B 689 GLN cc_start: 0.8235 (tp40) cc_final: 0.7127 (mt0) REVERT: B 859 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7687 (mppt) outliers start: 17 outliers final: 7 residues processed: 142 average time/residue: 1.0889 time to fit residues: 169.4769 Evaluate side-chains 135 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 118 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 126 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN A 560 GLN A 937 HIS A1013 ASN B 548 ASN B 560 GLN B 650 GLN B 937 HIS B1013 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.141992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.112451 restraints weight = 12915.099| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.78 r_work: 0.3194 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11630 Z= 0.134 Angle : 0.486 5.270 15769 Z= 0.266 Chirality : 0.041 0.176 1792 Planarity : 0.004 0.046 1945 Dihedral : 8.690 97.086 1637 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.06 % Allowed : 10.21 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.22), residues: 1420 helix: 2.44 (0.18), residues: 772 sheet: 0.14 (0.38), residues: 156 loop : -0.97 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 779 HIS 0.004 0.001 HIS B 828 PHE 0.017 0.001 PHE A 911 TYR 0.012 0.001 TYR B 827 ARG 0.004 0.001 ARG B 749 Details of bonding type rmsd hydrogen bonds : bond 0.04840 ( 679) hydrogen bonds : angle 4.34080 ( 1947) covalent geometry : bond 0.00305 (11630) covalent geometry : angle 0.48634 (15769) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.188 Fit side-chains REVERT: A 376 ARG cc_start: 0.6982 (mmm160) cc_final: 0.6768 (mmm160) REVERT: A 471 ASP cc_start: 0.7218 (m-30) cc_final: 0.6834 (m-30) REVERT: A 577 LYS cc_start: 0.7678 (mtmt) cc_final: 0.7413 (mttm) REVERT: A 594 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.8105 (mmp-170) REVERT: A 749 ARG cc_start: 0.8170 (mtp180) cc_final: 0.7672 (mmm-85) REVERT: A 859 LYS cc_start: 0.8345 (mmtt) cc_final: 0.7878 (mppt) REVERT: A 875 MET cc_start: 0.8687 (mtp) cc_final: 0.8427 (ttm) REVERT: A 921 THR cc_start: 0.7970 (t) cc_final: 0.7702 (m) REVERT: B 471 ASP cc_start: 0.7186 (m-30) cc_final: 0.6797 (m-30) REVERT: B 594 ARG cc_start: 0.8399 (mmt180) cc_final: 0.8147 (mmp-170) REVERT: B 706 HIS cc_start: 0.6983 (m-70) cc_final: 0.5722 (t-170) REVERT: B 859 LYS cc_start: 0.8310 (mmtt) cc_final: 0.7829 (mppt) REVERT: B 875 MET cc_start: 0.8688 (mtp) cc_final: 0.8409 (ttm) REVERT: B 1090 MET cc_start: 0.7973 (ttm) cc_final: 0.7769 (ttm) outliers start: 24 outliers final: 10 residues processed: 148 average time/residue: 1.0693 time to fit residues: 173.4339 Evaluate side-chains 140 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN A 650 GLN A1013 ASN B 560 GLN B 650 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.137915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.108132 restraints weight = 12749.584| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.78 r_work: 0.3120 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11630 Z= 0.178 Angle : 0.529 5.531 15769 Z= 0.286 Chirality : 0.043 0.178 1792 Planarity : 0.004 0.046 1945 Dihedral : 8.333 97.238 1636 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.57 % Allowed : 10.03 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.22), residues: 1420 helix: 2.30 (0.18), residues: 780 sheet: 0.05 (0.38), residues: 156 loop : -0.93 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 806 HIS 0.004 0.001 HIS B 965 PHE 0.020 0.002 PHE B 911 TYR 0.013 0.002 TYR A 254 ARG 0.003 0.001 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.05351 ( 679) hydrogen bonds : angle 4.45628 ( 1947) covalent geometry : bond 0.00420 (11630) covalent geometry : angle 0.52889 (15769) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 1.158 Fit side-chains REVERT: A 577 LYS cc_start: 0.7597 (mtmt) cc_final: 0.7342 (mttm) REVERT: A 594 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.8054 (mmp-170) REVERT: A 749 ARG cc_start: 0.8154 (mtp180) cc_final: 0.7647 (mmm-85) REVERT: A 859 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7889 (mppt) REVERT: B 594 ARG cc_start: 0.8375 (mmt180) cc_final: 0.8106 (mmp-170) REVERT: B 706 HIS cc_start: 0.6874 (m-70) cc_final: 0.6490 (m-70) REVERT: B 859 LYS cc_start: 0.8282 (mmtt) cc_final: 0.7899 (mppt) outliers start: 30 outliers final: 13 residues processed: 146 average time/residue: 1.1793 time to fit residues: 188.4079 Evaluate side-chains 140 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 886 MET Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 103 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 68 optimal weight: 0.0970 chunk 1 optimal weight: 0.0040 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN A 650 GLN A1013 ASN B 560 GLN B 650 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.141868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.112120 restraints weight = 12728.033| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.78 r_work: 0.3146 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11630 Z= 0.100 Angle : 0.440 5.023 15769 Z= 0.241 Chirality : 0.040 0.167 1792 Planarity : 0.004 0.044 1945 Dihedral : 7.334 73.751 1636 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.72 % Allowed : 11.75 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.22), residues: 1420 helix: 2.70 (0.18), residues: 772 sheet: 0.30 (0.38), residues: 156 loop : -0.86 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 779 HIS 0.003 0.001 HIS A 828 PHE 0.016 0.001 PHE A 911 TYR 0.011 0.001 TYR B 827 ARG 0.004 0.000 ARG B 687 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 679) hydrogen bonds : angle 4.08567 ( 1947) covalent geometry : bond 0.00213 (11630) covalent geometry : angle 0.44004 (15769) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 1.314 Fit side-chains REVERT: A 471 ASP cc_start: 0.7167 (m-30) cc_final: 0.6835 (m-30) REVERT: A 577 LYS cc_start: 0.7584 (mtmt) cc_final: 0.7336 (mttm) REVERT: A 594 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.8055 (mmp-170) REVERT: A 749 ARG cc_start: 0.8143 (mtp180) cc_final: 0.7708 (mmm-85) REVERT: A 859 LYS cc_start: 0.8304 (mmtt) cc_final: 0.7950 (mppt) REVERT: A 875 MET cc_start: 0.8616 (mtp) cc_final: 0.8374 (ttm) REVERT: A 992 MET cc_start: 0.7635 (mmm) cc_final: 0.7391 (mmm) REVERT: B 471 ASP cc_start: 0.7131 (m-30) cc_final: 0.6800 (m-30) REVERT: B 594 ARG cc_start: 0.8342 (mmt180) cc_final: 0.8073 (mmp-170) REVERT: B 706 HIS cc_start: 0.7024 (m-70) cc_final: 0.5673 (t-170) REVERT: B 859 LYS cc_start: 0.8280 (mmtt) cc_final: 0.7906 (mppt) outliers start: 20 outliers final: 10 residues processed: 148 average time/residue: 1.2249 time to fit residues: 197.2056 Evaluate side-chains 148 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 886 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 1007 LYS Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 113 optimal weight: 0.6980 chunk 111 optimal weight: 0.4980 chunk 110 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN A1013 ASN B 560 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.140122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110441 restraints weight = 12944.603| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.78 r_work: 0.3155 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11630 Z= 0.125 Angle : 0.460 5.243 15769 Z= 0.251 Chirality : 0.041 0.165 1792 Planarity : 0.004 0.046 1945 Dihedral : 7.312 79.062 1636 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.72 % Allowed : 11.66 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.22), residues: 1420 helix: 2.66 (0.18), residues: 776 sheet: 0.29 (0.38), residues: 156 loop : -0.83 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 806 HIS 0.006 0.001 HIS A 828 PHE 0.016 0.001 PHE A 911 TYR 0.011 0.001 TYR A 827 ARG 0.004 0.000 ARG B 687 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 679) hydrogen bonds : angle 4.15213 ( 1947) covalent geometry : bond 0.00283 (11630) covalent geometry : angle 0.46026 (15769) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 1.405 Fit side-chains REVERT: A 471 ASP cc_start: 0.7139 (m-30) cc_final: 0.6783 (m-30) REVERT: A 577 LYS cc_start: 0.7589 (mtmt) cc_final: 0.7335 (mttm) REVERT: A 594 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.8041 (mmp-170) REVERT: A 749 ARG cc_start: 0.8143 (mtp180) cc_final: 0.7698 (mmm-85) REVERT: A 859 LYS cc_start: 0.8187 (mmtt) cc_final: 0.7889 (mppt) REVERT: A 992 MET cc_start: 0.7716 (mmm) cc_final: 0.7378 (mmm) REVERT: B 471 ASP cc_start: 0.7119 (m-30) cc_final: 0.6761 (m-30) REVERT: B 594 ARG cc_start: 0.8343 (mmt180) cc_final: 0.8067 (mmp-170) REVERT: B 706 HIS cc_start: 0.7055 (m-70) cc_final: 0.5687 (t-170) REVERT: B 859 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7899 (mppt) outliers start: 20 outliers final: 11 residues processed: 154 average time/residue: 1.1664 time to fit residues: 195.2097 Evaluate side-chains 146 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1007 LYS Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 33 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN A1013 ASN B 560 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.137420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.107677 restraints weight = 12996.896| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.78 r_work: 0.3091 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11630 Z= 0.179 Angle : 0.520 5.707 15769 Z= 0.281 Chirality : 0.043 0.165 1792 Planarity : 0.004 0.044 1945 Dihedral : 7.838 91.865 1636 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.97 % Allowed : 12.01 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.22), residues: 1420 helix: 2.45 (0.17), residues: 780 sheet: 0.16 (0.39), residues: 156 loop : -0.89 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 806 HIS 0.007 0.001 HIS A 828 PHE 0.019 0.002 PHE A 911 TYR 0.013 0.002 TYR A 254 ARG 0.003 0.001 ARG B 749 Details of bonding type rmsd hydrogen bonds : bond 0.05259 ( 679) hydrogen bonds : angle 4.40373 ( 1947) covalent geometry : bond 0.00426 (11630) covalent geometry : angle 0.52025 (15769) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.187 Fit side-chains REVERT: A 594 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8066 (mmp-170) REVERT: A 749 ARG cc_start: 0.8195 (mtp180) cc_final: 0.7758 (mmm-85) REVERT: A 859 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7911 (mppt) REVERT: B 594 ARG cc_start: 0.8356 (mmt180) cc_final: 0.8078 (mmp-170) REVERT: B 859 LYS cc_start: 0.8168 (mmtt) cc_final: 0.7900 (mppt) REVERT: B 992 MET cc_start: 0.7368 (mmm) cc_final: 0.6998 (tpt) outliers start: 23 outliers final: 14 residues processed: 148 average time/residue: 1.0803 time to fit residues: 175.3325 Evaluate side-chains 144 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1007 LYS Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 73 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 95 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN B 560 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.137774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.108090 restraints weight = 12971.976| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.78 r_work: 0.3128 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11630 Z= 0.167 Angle : 0.506 6.122 15769 Z= 0.274 Chirality : 0.043 0.167 1792 Planarity : 0.004 0.045 1945 Dihedral : 7.758 88.917 1636 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.14 % Allowed : 12.61 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.22), residues: 1420 helix: 2.47 (0.17), residues: 780 sheet: 0.14 (0.39), residues: 156 loop : -0.90 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 806 HIS 0.008 0.001 HIS B 828 PHE 0.020 0.002 PHE B 911 TYR 0.012 0.001 TYR A 827 ARG 0.003 0.000 ARG B 749 Details of bonding type rmsd hydrogen bonds : bond 0.05085 ( 679) hydrogen bonds : angle 4.34890 ( 1947) covalent geometry : bond 0.00396 (11630) covalent geometry : angle 0.50645 (15769) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 1.252 Fit side-chains REVERT: A 577 LYS cc_start: 0.7585 (mttp) cc_final: 0.7357 (mttm) REVERT: A 594 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.8037 (mmp-170) REVERT: A 749 ARG cc_start: 0.8185 (mtp180) cc_final: 0.7749 (mmm-85) REVERT: A 859 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7913 (mppt) REVERT: A 886 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8060 (mmm) REVERT: A 992 MET cc_start: 0.7651 (mmm) cc_final: 0.7199 (mmm) REVERT: B 594 ARG cc_start: 0.8335 (mmt180) cc_final: 0.8057 (mmp-170) REVERT: B 859 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7899 (mppt) outliers start: 25 outliers final: 14 residues processed: 143 average time/residue: 1.2000 time to fit residues: 186.3412 Evaluate side-chains 143 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 886 MET Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1007 LYS Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.138128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.108408 restraints weight = 12913.985| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.77 r_work: 0.3135 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11630 Z= 0.152 Angle : 0.491 5.366 15769 Z= 0.267 Chirality : 0.042 0.167 1792 Planarity : 0.004 0.043 1945 Dihedral : 7.620 86.717 1636 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.80 % Allowed : 13.04 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.22), residues: 1420 helix: 2.52 (0.17), residues: 780 sheet: 0.24 (0.39), residues: 156 loop : -0.87 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 806 HIS 0.007 0.001 HIS B 828 PHE 0.018 0.002 PHE A 911 TYR 0.012 0.001 TYR A 827 ARG 0.003 0.000 ARG B 749 Details of bonding type rmsd hydrogen bonds : bond 0.04902 ( 679) hydrogen bonds : angle 4.30418 ( 1947) covalent geometry : bond 0.00356 (11630) covalent geometry : angle 0.49148 (15769) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 1.161 Fit side-chains REVERT: A 577 LYS cc_start: 0.7566 (mttp) cc_final: 0.7349 (mttm) REVERT: A 594 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.8031 (mmp-170) REVERT: A 749 ARG cc_start: 0.8176 (mtp180) cc_final: 0.7740 (mmm-85) REVERT: A 859 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7942 (mppt) REVERT: A 886 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8054 (mmm) REVERT: B 594 ARG cc_start: 0.8329 (mmt180) cc_final: 0.8051 (mmp-170) REVERT: B 859 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7936 (mppt) outliers start: 21 outliers final: 14 residues processed: 139 average time/residue: 1.2524 time to fit residues: 189.0188 Evaluate side-chains 145 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 886 MET Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1007 LYS Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 86 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 88 optimal weight: 0.4980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN B 560 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.137414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.107785 restraints weight = 12852.384| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.77 r_work: 0.3092 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11630 Z= 0.169 Angle : 0.512 5.390 15769 Z= 0.277 Chirality : 0.043 0.168 1792 Planarity : 0.004 0.045 1945 Dihedral : 7.785 89.695 1636 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.54 % Allowed : 13.29 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.22), residues: 1420 helix: 2.44 (0.18), residues: 780 sheet: 0.20 (0.40), residues: 156 loop : -0.86 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 779 HIS 0.008 0.001 HIS B 828 PHE 0.019 0.002 PHE B 911 TYR 0.012 0.002 TYR A 827 ARG 0.003 0.000 ARG B 749 Details of bonding type rmsd hydrogen bonds : bond 0.05154 ( 679) hydrogen bonds : angle 4.37284 ( 1947) covalent geometry : bond 0.00402 (11630) covalent geometry : angle 0.51166 (15769) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 1.232 Fit side-chains REVERT: A 577 LYS cc_start: 0.7586 (mttp) cc_final: 0.7371 (mttm) REVERT: A 594 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.8034 (mmp-170) REVERT: A 749 ARG cc_start: 0.8171 (mtp180) cc_final: 0.7656 (mmm-85) REVERT: A 859 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7937 (mppt) REVERT: A 886 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8040 (mmm) REVERT: B 594 ARG cc_start: 0.8337 (mmt180) cc_final: 0.8058 (mmp-170) REVERT: B 859 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7932 (mppt) outliers start: 18 outliers final: 15 residues processed: 138 average time/residue: 1.1945 time to fit residues: 179.8853 Evaluate side-chains 146 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 886 MET Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1007 LYS Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 113 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 132 optimal weight: 0.2980 chunk 139 optimal weight: 0.9980 chunk 117 optimal weight: 0.4980 chunk 127 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 128 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN B 560 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.141270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.111672 restraints weight = 12816.635| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.77 r_work: 0.3171 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11630 Z= 0.102 Angle : 0.439 5.052 15769 Z= 0.240 Chirality : 0.040 0.164 1792 Planarity : 0.004 0.043 1945 Dihedral : 7.126 75.134 1636 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.46 % Allowed : 13.46 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.22), residues: 1420 helix: 2.74 (0.18), residues: 776 sheet: 0.35 (0.40), residues: 156 loop : -0.79 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 779 HIS 0.005 0.001 HIS B 828 PHE 0.014 0.001 PHE B 911 TYR 0.012 0.001 TYR A 827 ARG 0.003 0.000 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 679) hydrogen bonds : angle 4.04296 ( 1947) covalent geometry : bond 0.00218 (11630) covalent geometry : angle 0.43896 (15769) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7973.97 seconds wall clock time: 137 minutes 53.77 seconds (8273.77 seconds total)