Starting phenix.real_space_refine on Wed Feb 4 15:44:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3q_36856/02_2026/8k3q_36856.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3q_36856/02_2026/8k3q_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 { model { file = "/net/cci-nas-00/data/ceres_data/8k3q_36856/02_2026/8k3q_36856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3q_36856/02_2026/8k3q_36856.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k3q_36856/02_2026/8k3q_36856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3q_36856/02_2026/8k3q_36856.map" } resolution = 2.6 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= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11365 Number of models: 1 Model: "" Number of chains: 4 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: {'ARG:plan': 6, 'ASN:plan1': 5, 'GLU:plan': 10, 'ASP:plan': 8, 'TRP:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 5639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5639 Classifications: {'peptide': 724} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 21, 'TRANS': 702} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 274 Unresolved non-hydrogen angles: 342 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ARG:plan': 6, 'ASN:plan1': 5, 'GLU:plan': 10, 'ASP:plan': 8, 'TRP:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 157 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: 2.77, per 1000 atoms: 0.24 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: 0.89 Conformation dependent library (CDL) restraints added in 477.3 milliseconds 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: 0.25 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: 1.56 Time building geometry restraints manager: 1.20 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: 6403 1.56 - 1.68: 28 1.68 - 1.80: 104 Bond restraints: 11632 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 11627 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 15370 2.39 - 4.78: 356 4.78 - 7.17: 36 7.17 - 9.56: 6 9.56 - 11.95: 6 Bond angle restraints: 15774 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 15769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.63: 6484 25.63 - 51.25: 250 51.25 - 76.88: 58 76.88 - 102.51: 6 102.51 - 128.13: 2 Dihedral angle restraints: 6800 sinusoidal: 2534 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 6797 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: 2.26 - 2.79: 2727 2.79 - 3.32: 10636 3.32 - 3.84: 18482 3.84 - 4.37: 22017 4.37 - 4.90: 38437 Nonbonded interactions: 92299 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 2.259 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 92294 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 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: 2.040 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.860 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 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:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.670 ------------------------------------------------------------------------------- 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 11632 Z= 0.375 Angle : 0.869 11.949 15774 Z= 0.483 Chirality : 0.051 0.222 1792 Planarity : 0.005 0.057 1945 Dihedral : 14.742 128.132 4044 Min Nonbonded Distance : 2.259 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 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: 0.38 (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 ARG 0.007 0.001 ARG A1040 TYR 0.036 0.003 TYR B 249 PHE 0.047 0.003 PHE B1015 TRP 0.044 0.002 TRP B1103 HIS 0.005 0.002 HIS B 459 Details of bonding type rmsd covalent geometry : bond 0.00794 (11632) covalent geometry : angle 0.86917 (15774) hydrogen bonds : bond 0.15431 ( 679) hydrogen bonds : angle 6.51570 ( 1947) *********************** 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 : 0.336 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: 0.6460 time to fit residues: 122.2431 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 : 0.509 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.0670 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN A 560 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A1013 ASN B 426 ASN B 548 ASN B 560 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 HIS B1013 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.144488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.115022 restraints weight = 12822.431| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.78 r_work: 0.3231 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11632 Z= 0.126 Angle : 0.507 5.357 15774 Z= 0.277 Chirality : 0.041 0.173 1792 Planarity : 0.005 0.053 1945 Dihedral : 9.683 113.527 1643 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.63 % Allowed : 7.63 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.34 (0.22), residues: 1420 helix: 2.17 (0.18), residues: 772 sheet: 0.07 (0.39), residues: 156 loop : -0.94 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 749 TYR 0.015 0.001 TYR A 827 PHE 0.013 0.001 PHE B 864 TRP 0.011 0.001 TRP B1103 HIS 0.004 0.001 HIS A 965 Details of bonding type rmsd covalent geometry : bond 0.00269 (11632) covalent geometry : angle 0.50727 (15774) hydrogen bonds : bond 0.04729 ( 679) hydrogen bonds : angle 4.45195 ( 1947) *********************** 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 159 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.475 Fit side-chains REVERT: A 471 ASP cc_start: 0.7138 (m-30) cc_final: 0.6812 (m-30) REVERT: A 526 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.7192 (m-30) REVERT: A 577 LYS cc_start: 0.7563 (mtmt) cc_final: 0.7356 (mttp) REVERT: A 689 GLN cc_start: 0.8248 (tp40) cc_final: 0.7171 (mt0) REVERT: A 749 ARG cc_start: 0.8204 (mtp180) cc_final: 0.7669 (mmm-85) REVERT: A 859 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7665 (mppt) REVERT: A 1090 MET cc_start: 0.7835 (ttm) cc_final: 0.7548 (ttm) REVERT: A 1108 SER cc_start: 0.8524 (t) cc_final: 0.8219 (m) REVERT: B 471 ASP cc_start: 0.7190 (m-30) cc_final: 0.6794 (m-30) REVERT: B 594 ARG cc_start: 0.8409 (mmt180) cc_final: 0.8145 (mmp-170) REVERT: B 689 GLN cc_start: 0.8130 (tp40) cc_final: 0.7051 (mt0) REVERT: B 859 LYS cc_start: 0.8190 (mmtt) cc_final: 0.7597 (mppt) outliers start: 19 outliers final: 7 residues processed: 150 average time/residue: 0.5096 time to fit residues: 83.6342 Evaluate side-chains 138 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 ASP 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 21 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 560 GLN A 650 GLN A 937 HIS A1013 ASN B 545 ASN B 560 GLN B 650 GLN B 706 HIS B 856 ASN B 937 HIS B1013 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.143767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114359 restraints weight = 12844.207| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.77 r_work: 0.3224 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11632 Z= 0.118 Angle : 0.465 5.031 15774 Z= 0.254 Chirality : 0.040 0.171 1792 Planarity : 0.004 0.046 1945 Dihedral : 8.357 96.906 1637 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.63 % Allowed : 9.78 % Favored : 88.59 % 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: 1.78 (0.22), residues: 1420 helix: 2.61 (0.18), residues: 770 sheet: 0.26 (0.38), residues: 156 loop : -0.89 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 749 TYR 0.011 0.001 TYR B 827 PHE 0.018 0.001 PHE B 911 TRP 0.009 0.001 TRP B1103 HIS 0.003 0.001 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00260 (11632) covalent geometry : angle 0.46536 (15774) hydrogen bonds : bond 0.04548 ( 679) hydrogen bonds : angle 4.21099 ( 1947) *********************** 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 151 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.431 Fit side-chains REVERT: A 471 ASP cc_start: 0.7263 (m-30) cc_final: 0.6873 (m-30) REVERT: A 480 LYS cc_start: 0.6764 (OUTLIER) cc_final: 0.6482 (mptt) REVERT: A 525 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7409 (mtpp) REVERT: A 577 LYS cc_start: 0.7589 (mtmt) cc_final: 0.7349 (mttm) REVERT: A 749 ARG cc_start: 0.8141 (mtp180) cc_final: 0.7647 (mmm-85) REVERT: A 859 LYS cc_start: 0.8252 (mmtt) cc_final: 0.7719 (mppt) REVERT: A 921 THR cc_start: 0.7974 (t) cc_final: 0.7722 (m) REVERT: B 471 ASP cc_start: 0.7181 (m-30) cc_final: 0.6785 (m-30) REVERT: B 594 ARG cc_start: 0.8363 (mmt180) cc_final: 0.8128 (mmp-170) REVERT: B 859 LYS cc_start: 0.8240 (mmtt) cc_final: 0.7704 (mppt) outliers start: 19 outliers final: 7 residues processed: 140 average time/residue: 0.5302 time to fit residues: 81.0875 Evaluate side-chains 137 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 525 LYS 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 673 VAL Chi-restraints excluded: chain B residue 939 LEU 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 57 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 76 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN A 560 GLN A 650 GLN A1013 ASN B 419 GLN B 560 GLN B 650 GLN B 706 HIS B1013 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.142656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.113202 restraints weight = 12891.769| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.77 r_work: 0.3207 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11632 Z= 0.124 Angle : 0.465 5.098 15774 Z= 0.253 Chirality : 0.040 0.168 1792 Planarity : 0.004 0.045 1945 Dihedral : 7.387 84.649 1636 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.63 % Allowed : 11.41 % Favored : 86.96 % 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: 1.88 (0.22), residues: 1420 helix: 2.68 (0.18), residues: 770 sheet: 0.38 (0.38), residues: 156 loop : -0.85 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 749 TYR 0.012 0.001 TYR A 827 PHE 0.016 0.001 PHE B 911 TRP 0.009 0.001 TRP A 806 HIS 0.003 0.001 HIS A 965 Details of bonding type rmsd covalent geometry : bond 0.00280 (11632) covalent geometry : angle 0.46457 (15774) hydrogen bonds : bond 0.04534 ( 679) hydrogen bonds : angle 4.16026 ( 1947) *********************** 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 151 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.463 Fit side-chains REVERT: A 376 ARG cc_start: 0.6873 (mmm160) cc_final: 0.6663 (mmm160) REVERT: A 471 ASP cc_start: 0.7206 (m-30) cc_final: 0.6801 (m-30) REVERT: A 480 LYS cc_start: 0.6706 (OUTLIER) cc_final: 0.6432 (mptt) REVERT: A 525 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.6552 (mtpp) REVERT: A 577 LYS cc_start: 0.7571 (mtmt) cc_final: 0.7326 (mttm) REVERT: A 594 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.8090 (mmp-170) REVERT: A 749 ARG cc_start: 0.8128 (mtp180) cc_final: 0.7669 (mmm-85) REVERT: A 859 LYS cc_start: 0.8358 (mmtt) cc_final: 0.7878 (mppt) REVERT: B 376 ARG cc_start: 0.7246 (mmm160) cc_final: 0.6790 (mmm160) REVERT: B 471 ASP cc_start: 0.7188 (m-30) cc_final: 0.6781 (m-30) REVERT: B 594 ARG cc_start: 0.8319 (mmt180) cc_final: 0.8080 (mmp-170) REVERT: B 859 LYS cc_start: 0.8340 (mmtt) cc_final: 0.7847 (mppt) outliers start: 19 outliers final: 10 residues processed: 143 average time/residue: 0.6146 time to fit residues: 95.0490 Evaluate side-chains 140 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 594 ARG 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 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 132 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 23 optimal weight: 0.0670 chunk 119 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- 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 B 706 HIS B1013 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.136852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.106911 restraints weight = 12813.920| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.79 r_work: 0.3107 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11632 Z= 0.210 Angle : 0.560 6.242 15774 Z= 0.301 Chirality : 0.045 0.171 1792 Planarity : 0.004 0.042 1945 Dihedral : 7.967 96.983 1636 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.06 % Allowed : 11.49 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.48 (0.22), residues: 1420 helix: 2.28 (0.17), residues: 780 sheet: 0.11 (0.38), residues: 156 loop : -0.94 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 749 TYR 0.015 0.002 TYR A 254 PHE 0.021 0.002 PHE B 911 TRP 0.011 0.002 TRP B 806 HIS 0.006 0.002 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00502 (11632) covalent geometry : angle 0.55987 (15774) hydrogen bonds : bond 0.05690 ( 679) hydrogen bonds : angle 4.51479 ( 1947) *********************** 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 154 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.441 Fit side-chains REVERT: A 525 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.6581 (mtpp) REVERT: A 577 LYS cc_start: 0.7658 (mtmt) cc_final: 0.7390 (mttp) REVERT: A 594 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.8046 (mmp-170) REVERT: A 749 ARG cc_start: 0.8181 (mtp180) cc_final: 0.7663 (mmm-85) REVERT: A 859 LYS cc_start: 0.8187 (mmtt) cc_final: 0.7870 (mppt) REVERT: B 859 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7852 (mppt) REVERT: B 1108 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.7959 (m) outliers start: 24 outliers final: 10 residues processed: 145 average time/residue: 0.5601 time to fit residues: 88.1672 Evaluate side-chains 139 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 594 ARG 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 1090 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 939 LEU Chi-restraints excluded: chain B residue 1070 MET 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 60 optimal weight: 0.8980 chunk 139 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN A 937 HIS A1013 ASN B 560 GLN B 706 HIS B 937 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.139448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109837 restraints weight = 12841.913| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.78 r_work: 0.3147 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11632 Z= 0.128 Angle : 0.466 5.226 15774 Z= 0.255 Chirality : 0.041 0.165 1792 Planarity : 0.004 0.046 1945 Dihedral : 7.318 81.691 1636 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.14 % Allowed : 11.41 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.74 (0.22), residues: 1420 helix: 2.54 (0.18), residues: 780 sheet: 0.22 (0.39), residues: 156 loop : -0.89 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 749 TYR 0.010 0.001 TYR A 254 PHE 0.018 0.001 PHE B 911 TRP 0.010 0.001 TRP A 779 HIS 0.006 0.001 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00294 (11632) covalent geometry : angle 0.46626 (15774) hydrogen bonds : bond 0.04592 ( 679) hydrogen bonds : angle 4.21792 ( 1947) *********************** 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 154 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.439 Fit side-chains REVERT: A 471 ASP cc_start: 0.7130 (m-30) cc_final: 0.6793 (m-30) REVERT: A 525 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.6583 (mtpp) REVERT: A 577 LYS cc_start: 0.7582 (mtmt) cc_final: 0.7318 (mttm) REVERT: A 594 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.8018 (mmp-170) REVERT: A 749 ARG cc_start: 0.8158 (mtp180) cc_final: 0.7709 (mmm-85) REVERT: A 859 LYS cc_start: 0.8258 (mmtt) cc_final: 0.7902 (mppt) REVERT: B 376 ARG cc_start: 0.7098 (mmm160) cc_final: 0.6851 (mmm160) REVERT: B 471 ASP cc_start: 0.7117 (m-30) cc_final: 0.6782 (m-30) REVERT: B 594 ARG cc_start: 0.8312 (mmt180) cc_final: 0.8103 (mmp-170) REVERT: B 859 LYS cc_start: 0.8262 (mmtt) cc_final: 0.7888 (mppt) outliers start: 25 outliers final: 11 residues processed: 145 average time/residue: 0.5056 time to fit residues: 79.8106 Evaluate side-chains 140 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 594 ARG 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 1090 MET Chi-restraints excluded: chain A residue 1108 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 65 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 19 optimal weight: 0.0030 chunk 100 optimal weight: 0.1980 chunk 80 optimal weight: 0.6980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN A 937 HIS A1013 ASN B 706 HIS B 937 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.141992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.112472 restraints weight = 12868.519| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.78 r_work: 0.3183 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11632 Z= 0.101 Angle : 0.434 5.924 15774 Z= 0.236 Chirality : 0.039 0.161 1792 Planarity : 0.004 0.043 1945 Dihedral : 6.856 70.632 1636 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.97 % Allowed : 11.84 % Favored : 86.19 % 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: 1.98 (0.22), residues: 1420 helix: 2.75 (0.18), residues: 776 sheet: 0.39 (0.39), residues: 156 loop : -0.83 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 749 TYR 0.011 0.001 TYR A 827 PHE 0.014 0.001 PHE B 911 TRP 0.009 0.001 TRP A 779 HIS 0.005 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00217 (11632) covalent geometry : angle 0.43446 (15774) hydrogen bonds : bond 0.04031 ( 679) hydrogen bonds : angle 4.00357 ( 1947) *********************** 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 158 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.429 Fit side-chains REVERT: A 471 ASP cc_start: 0.7103 (m-30) cc_final: 0.6747 (m-30) REVERT: A 577 LYS cc_start: 0.7545 (mtmt) cc_final: 0.7304 (mttm) REVERT: A 749 ARG cc_start: 0.8115 (mtp180) cc_final: 0.7658 (mmm-85) REVERT: A 859 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7913 (mppt) REVERT: B 376 ARG cc_start: 0.7104 (mmm160) cc_final: 0.6849 (mmm160) REVERT: B 471 ASP cc_start: 0.7088 (m-30) cc_final: 0.6737 (m-30) REVERT: B 594 ARG cc_start: 0.8311 (mmt180) cc_final: 0.8106 (mmp-170) REVERT: B 859 LYS cc_start: 0.8253 (mmtt) cc_final: 0.7908 (mppt) outliers start: 23 outliers final: 12 residues processed: 149 average time/residue: 0.5218 time to fit residues: 84.6507 Evaluate side-chains 145 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 ASN 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 1070 MET Chi-restraints excluded: chain A residue 1090 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 886 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 35 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 706 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.137500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.107752 restraints weight = 12815.690| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.78 r_work: 0.3117 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11632 Z= 0.195 Angle : 0.534 5.874 15774 Z= 0.286 Chirality : 0.043 0.164 1792 Planarity : 0.004 0.044 1945 Dihedral : 7.575 91.603 1636 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.80 % Allowed : 11.23 % Favored : 86.96 % 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 (0.22), residues: 1420 helix: 2.43 (0.17), residues: 780 sheet: 0.26 (0.39), residues: 156 loop : -0.85 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 417 TYR 0.014 0.002 TYR B 475 PHE 0.020 0.002 PHE A 911 TRP 0.010 0.001 TRP A 806 HIS 0.007 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00468 (11632) covalent geometry : angle 0.53389 (15774) hydrogen bonds : bond 0.05326 ( 679) hydrogen bonds : angle 4.37827 ( 1947) *********************** 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 149 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 749 ARG cc_start: 0.8167 (mtp180) cc_final: 0.7706 (mmm-85) REVERT: A 859 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7898 (mppt) REVERT: B 376 ARG cc_start: 0.7040 (mmm160) cc_final: 0.6762 (mmm160) REVERT: B 532 LYS cc_start: 0.7591 (mmmt) cc_final: 0.7366 (mmmt) REVERT: B 594 ARG cc_start: 0.8330 (mmt180) cc_final: 0.8111 (mmp-170) REVERT: B 859 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7869 (mppt) outliers start: 21 outliers final: 14 residues processed: 140 average time/residue: 0.4848 time to fit residues: 74.0631 Evaluate side-chains 144 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 594 ARG 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 1090 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 673 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 63 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 64 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 HIS A 560 GLN B 706 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.138672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.109030 restraints weight = 12791.549| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.78 r_work: 0.3141 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11632 Z= 0.151 Angle : 0.491 5.387 15774 Z= 0.266 Chirality : 0.042 0.166 1792 Planarity : 0.004 0.043 1945 Dihedral : 7.388 85.555 1636 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.46 % Allowed : 12.44 % Favored : 86.11 % 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: 1.76 (0.22), residues: 1420 helix: 2.51 (0.18), residues: 780 sheet: 0.28 (0.40), residues: 156 loop : -0.84 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 749 TYR 0.012 0.001 TYR A 827 PHE 0.018 0.002 PHE A 911 TRP 0.009 0.001 TRP A 806 HIS 0.006 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00354 (11632) covalent geometry : angle 0.49094 (15774) hydrogen bonds : bond 0.04842 ( 679) hydrogen bonds : angle 4.25586 ( 1947) *********************** 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 146 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.340 Fit side-chains REVERT: A 577 LYS cc_start: 0.7566 (mttp) cc_final: 0.7358 (mttm) REVERT: A 749 ARG cc_start: 0.8181 (mtp180) cc_final: 0.7728 (mmm-85) REVERT: A 859 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7925 (mppt) REVERT: B 594 ARG cc_start: 0.8323 (mmt180) cc_final: 0.8107 (mmp-170) REVERT: B 859 LYS cc_start: 0.8174 (mmtt) cc_final: 0.7885 (mppt) outliers start: 17 outliers final: 13 residues processed: 139 average time/residue: 0.5357 time to fit residues: 80.8527 Evaluate side-chains 140 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 446 THR 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 1090 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 673 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 84 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN B 706 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.138192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.108414 restraints weight = 12882.323| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.78 r_work: 0.3127 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11632 Z= 0.156 Angle : 0.503 5.406 15774 Z= 0.272 Chirality : 0.042 0.167 1792 Planarity : 0.004 0.043 1945 Dihedral : 7.476 88.131 1636 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.37 % Allowed : 12.52 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.22), residues: 1420 helix: 2.48 (0.18), residues: 780 sheet: 0.27 (0.40), residues: 156 loop : -0.84 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 749 TYR 0.012 0.002 TYR B 827 PHE 0.019 0.002 PHE A 911 TRP 0.010 0.001 TRP A 806 HIS 0.007 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00368 (11632) covalent geometry : angle 0.50280 (15774) hydrogen bonds : bond 0.04966 ( 679) hydrogen bonds : angle 4.30402 ( 1947) ********************** 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 144 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.375 Fit side-chains REVERT: A 749 ARG cc_start: 0.8183 (mtp180) cc_final: 0.7725 (mmm-85) REVERT: A 859 LYS cc_start: 0.8231 (mmtt) cc_final: 0.7941 (mppt) REVERT: B 594 ARG cc_start: 0.8325 (mmt180) cc_final: 0.8099 (mmp-170) REVERT: B 859 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7928 (mppt) outliers start: 16 outliers final: 13 residues processed: 138 average time/residue: 0.5235 time to fit residues: 78.4380 Evaluate side-chains 139 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 446 THR 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 1090 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 673 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 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 560 GLN B 560 GLN B 706 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.139239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109577 restraints weight = 12893.571| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.78 r_work: 0.3148 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11632 Z= 0.132 Angle : 0.474 5.360 15774 Z= 0.258 Chirality : 0.041 0.164 1792 Planarity : 0.004 0.043 1945 Dihedral : 7.300 83.184 1636 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.37 % Allowed : 12.69 % Favored : 85.93 % 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: 1.82 (0.22), residues: 1420 helix: 2.56 (0.18), residues: 780 sheet: 0.33 (0.40), residues: 156 loop : -0.82 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 749 TYR 0.011 0.001 TYR A 827 PHE 0.017 0.001 PHE B 911 TRP 0.010 0.001 TRP A 779 HIS 0.006 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00303 (11632) covalent geometry : angle 0.47446 (15774) hydrogen bonds : bond 0.04618 ( 679) hydrogen bonds : angle 4.19084 ( 1947) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3954.12 seconds wall clock time: 68 minutes 4.78 seconds (4084.78 seconds total)