Starting phenix.real_space_refine on Fri Jul 3 02:35:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8k3q_36856/07_2026/8k3q_36856.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3q_36856/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k3q_36856/07_2026/8k3q_36856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3q_36856/07_2026/8k3q_36856.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8k3q_36856/07_2026/8k3q_36856.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8k3q_36856/07_2026/8k3q_36856.cif" model { file = "/net/cci-nas-00/data/ceres_data/8k3q_36856/07_2026/8k3q_36856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3q_36856/07_2026/8k3q_36856.cif" } 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-dev-6108/lib/python3.11/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: 2.91, per 1000 atoms: 0.26 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: 1.05 Conformation dependent library (CDL) restraints added in 558.3 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: 0.38 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: 2.17 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 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: 6474 25.63 - 51.25: 248 51.25 - 76.88: 58 76.88 - 102.51: 6 102.51 - 128.13: 2 Dihedral angle restraints: 6788 sinusoidal: 2522 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 6785 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: 2.450 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.530 Find NCS groups from input model: 0.220 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:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 : 14.711 128.132 4032 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/Z covalent geometry : bond 0.00794 / 0.37 (11632) covalent geometry : angle 0.86917 / 0.48 (15774) hydrogen bonds : bond 0.15431 / 9.66 ( 679) hydrogen bonds : angle 6.51570 / 4.49 ( 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 : 0.413 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: 0.6490 time to fit residues: 123.4916 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 : 0.467 ------------------------------------------------------------------------------- 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... 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 = 0.3708 r_free = 0.3708 target = 0.143949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114355 restraints weight = 12817.148| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.78 r_work: 0.3220 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11632 Z= 0.129 Angle : 0.511 5.270 15774 Z= 0.280 Chirality : 0.041 0.173 1792 Planarity : 0.004 0.053 1945 Dihedral : 9.676 115.076 1631 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.46 % Allowed : 7.89 % Favored : 90.65 % 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: 1.33 (0.22), residues: 1420 helix: 2.17 (0.18), residues: 772 sheet: 0.07 (0.39), residues: 156 loop : -0.96 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 749 TYR 0.015 0.001 TYR A 827 PHE 0.014 0.001 PHE A 911 TRP 0.011 0.001 TRP B1103 HIS 0.004 0.001 HIS A 965 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (11632) covalent geometry : angle 0.51121 / 0.28 (15774) hydrogen bonds : bond 0.04951 / 3.30 ( 679) hydrogen bonds : angle 4.53564 / 3.09 ( 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 153 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.388 Fit side-chains REVERT: A 471 ASP cc_start: 0.7161 (m-30) cc_final: 0.6833 (m-30) REVERT: A 577 LYS cc_start: 0.7598 (mtmt) cc_final: 0.7364 (mttp) REVERT: A 689 GLN cc_start: 0.8195 (tp40) cc_final: 0.7072 (mt0) REVERT: A 749 ARG cc_start: 0.8224 (mtp180) cc_final: 0.7679 (mmm-85) REVERT: A 859 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7688 (mppt) REVERT: A 921 THR cc_start: 0.7986 (t) cc_final: 0.7734 (m) REVERT: A 1108 SER cc_start: 0.8520 (t) cc_final: 0.8216 (m) REVERT: B 471 ASP cc_start: 0.7196 (m-30) cc_final: 0.6796 (m-30) REVERT: B 594 ARG cc_start: 0.8408 (mmt180) cc_final: 0.8168 (mmp-170) REVERT: B 689 GLN cc_start: 0.8143 (tp40) cc_final: 0.7051 (mt0) REVERT: B 859 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7571 (mppt) outliers start: 17 outliers final: 8 residues processed: 144 average time/residue: 0.4473 time to fit residues: 70.3972 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 : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 SER 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: 7.9990 chunk 75 optimal weight: 0.0070 chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 GLN A 545 ASN A 560 GLN A 650 GLN A 937 HIS A1013 ASN B 419 GLN B 545 ASN B 560 GLN B 650 GLN B 706 HIS B 937 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.141099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.111592 restraints weight = 12858.409| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.77 r_work: 0.3183 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11632 Z= 0.156 Angle : 0.517 5.365 15774 Z= 0.280 Chirality : 0.042 0.172 1792 Planarity : 0.004 0.046 1945 Dihedral : 8.473 99.815 1625 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.80 % Allowed : 9.95 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.54 (0.22), residues: 1420 helix: 2.38 (0.18), residues: 776 sheet: 0.16 (0.38), residues: 156 loop : -0.98 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 687 TYR 0.016 0.002 TYR B1008 PHE 0.018 0.002 PHE A 911 TRP 0.010 0.001 TRP A 779 HIS 0.005 0.002 HIS B 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (11632) covalent geometry : angle 0.51700 / 0.28 (15774) hydrogen bonds : bond 0.05212 / 3.45 ( 679) hydrogen bonds : angle 4.40614 / 2.99 ( 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 153 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.395 Fit side-chains REVERT: A 471 ASP cc_start: 0.7246 (m-30) cc_final: 0.6914 (m-30) REVERT: A 577 LYS cc_start: 0.7686 (mtmt) cc_final: 0.7421 (mttm) REVERT: A 749 ARG cc_start: 0.8156 (mtp180) cc_final: 0.7650 (mmm-85) REVERT: A 859 LYS cc_start: 0.8348 (mmtt) cc_final: 0.7876 (mppt) REVERT: A 921 THR cc_start: 0.8006 (t) cc_final: 0.7735 (m) REVERT: B 471 ASP cc_start: 0.7246 (m-30) cc_final: 0.6915 (m-30) REVERT: B 594 ARG cc_start: 0.8410 (mmt180) cc_final: 0.8135 (mmp-170) REVERT: B 689 GLN cc_start: 0.8407 (tp40) cc_final: 0.8201 (tp-100) REVERT: B 859 LYS cc_start: 0.8331 (mmtt) cc_final: 0.7838 (mppt) outliers start: 21 outliers final: 7 residues processed: 141 average time/residue: 0.4592 time to fit residues: 71.0605 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 : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 57 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 138 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 560 GLN A 650 GLN A1013 ASN B 560 GLN B 650 GLN B 706 HIS B1013 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.139290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109396 restraints weight = 12857.233| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.80 r_work: 0.3133 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11632 Z= 0.151 Angle : 0.497 5.274 15774 Z= 0.271 Chirality : 0.042 0.175 1792 Planarity : 0.004 0.044 1945 Dihedral : 7.827 94.599 1624 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.97 % Allowed : 10.81 % Favored : 87.22 % 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: 1.62 (0.22), residues: 1420 helix: 2.42 (0.18), residues: 780 sheet: 0.16 (0.38), residues: 156 loop : -0.91 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 687 TYR 0.013 0.002 TYR A 254 PHE 0.017 0.002 PHE B 911 TRP 0.009 0.001 TRP A 779 HIS 0.004 0.001 HIS A 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (11632) covalent geometry : angle 0.49738 / 0.27 (15774) hydrogen bonds : bond 0.04931 / 3.28 ( 679) hydrogen bonds : angle 4.31946 / 2.93 ( 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 152 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.451 Fit side-chains REVERT: A 471 ASP cc_start: 0.7215 (m-30) cc_final: 0.6838 (m-30) REVERT: A 577 LYS cc_start: 0.7564 (mtmt) cc_final: 0.7305 (mttm) REVERT: A 594 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.8082 (mmp-170) REVERT: A 749 ARG cc_start: 0.8138 (mtp180) cc_final: 0.7630 (mmm-85) REVERT: A 859 LYS cc_start: 0.8262 (mmtt) cc_final: 0.7882 (mppt) REVERT: B 594 ARG cc_start: 0.8331 (mmt180) cc_final: 0.8055 (mmp-170) REVERT: B 689 GLN cc_start: 0.8445 (tp40) cc_final: 0.8237 (tp-100) REVERT: B 859 LYS cc_start: 0.8275 (mmtt) cc_final: 0.7859 (mppt) outliers start: 23 outliers final: 11 residues processed: 144 average time/residue: 0.4984 time to fit residues: 78.4919 Evaluate side-chains 140 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 103 optimal weight: 0.2980 chunk 113 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 23 optimal weight: 0.0020 chunk 119 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 560 GLN A 650 GLN A1013 ASN B 560 GLN B 650 GLN B 706 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.140068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110189 restraints weight = 12788.865| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.79 r_work: 0.3153 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11632 Z= 0.129 Angle : 0.469 5.235 15774 Z= 0.256 Chirality : 0.041 0.166 1792 Planarity : 0.004 0.043 1945 Dihedral : 7.174 81.470 1624 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.63 % Allowed : 11.92 % 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: 1.78 (0.22), residues: 1420 helix: 2.61 (0.18), residues: 772 sheet: 0.21 (0.39), residues: 156 loop : -0.87 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 687 TYR 0.011 0.001 TYR B 827 PHE 0.018 0.001 PHE A 911 TRP 0.009 0.001 TRP A 779 HIS 0.004 0.001 HIS A 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (11632) covalent geometry : angle 0.46876 / 0.26 (15774) hydrogen bonds : bond 0.04607 / 3.06 ( 679) hydrogen bonds : angle 4.20208 / 2.86 ( 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 156 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.289 Fit side-chains REVERT: A 471 ASP cc_start: 0.7193 (m-30) cc_final: 0.6808 (m-30) REVERT: A 577 LYS cc_start: 0.7583 (mtmt) cc_final: 0.7342 (mttp) REVERT: A 594 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.8042 (mmp-170) REVERT: A 749 ARG cc_start: 0.8128 (mtp180) cc_final: 0.7692 (mmm-85) REVERT: A 859 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7894 (mppt) REVERT: A 992 MET cc_start: 0.7829 (mmm) cc_final: 0.7489 (mmm) REVERT: B 471 ASP cc_start: 0.7148 (m-30) cc_final: 0.6794 (m-30) REVERT: B 594 ARG cc_start: 0.8337 (mmt180) cc_final: 0.8056 (mmp-170) REVERT: B 689 GLN cc_start: 0.8459 (tp40) cc_final: 0.8206 (tp-100) REVERT: B 859 LYS cc_start: 0.8254 (mmtt) cc_final: 0.7876 (mppt) outliers start: 19 outliers final: 11 residues processed: 149 average time/residue: 0.5455 time to fit residues: 88.2048 Evaluate side-chains 147 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 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 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: 8.9990 chunk 139 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 111 optimal weight: 0.0970 chunk 57 optimal weight: 2.9990 chunk 118 optimal weight: 0.4980 chunk 54 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 560 GLN A1013 ASN B 560 GLN B 650 GLN B 706 HIS B1013 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.136776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107023 restraints weight = 12855.203| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.78 r_work: 0.3115 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11632 Z= 0.200 Angle : 0.544 6.158 15774 Z= 0.293 Chirality : 0.044 0.173 1792 Planarity : 0.004 0.042 1945 Dihedral : 7.747 94.472 1624 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.23 % Allowed : 11.15 % 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 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: 1.49 (0.22), residues: 1420 helix: 2.30 (0.17), residues: 780 sheet: 0.08 (0.39), residues: 156 loop : -0.93 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 687 TYR 0.013 0.002 TYR A 254 PHE 0.020 0.002 PHE B 911 TRP 0.010 0.001 TRP B 806 HIS 0.005 0.001 HIS A 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (11632) covalent geometry : angle 0.54363 / 0.29 (15774) hydrogen bonds : bond 0.05520 / 3.67 ( 679) hydrogen bonds : angle 4.47579 / 3.03 ( 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 161 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.290 Fit side-chains REVERT: A 577 LYS cc_start: 0.7568 (mtmt) cc_final: 0.7318 (mttp) REVERT: A 594 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.8052 (mmp-170) REVERT: A 749 ARG cc_start: 0.8171 (mtp180) cc_final: 0.7652 (mmm-85) REVERT: A 859 LYS cc_start: 0.8138 (mmtt) cc_final: 0.7858 (mppt) REVERT: B 376 ARG cc_start: 0.7179 (mmm160) cc_final: 0.6943 (mmm160) REVERT: B 859 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7857 (mppt) outliers start: 26 outliers final: 11 residues processed: 152 average time/residue: 0.4654 time to fit residues: 77.1871 Evaluate side-chains 142 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 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 939 LEU Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1090 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: 0.8980 chunk 140 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 116 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 100 optimal weight: 0.0970 chunk 80 optimal weight: 0.3980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 560 GLN A1013 ASN B 560 GLN B 706 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.140866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.111248 restraints weight = 12844.746| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.78 r_work: 0.3161 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11632 Z= 0.104 Angle : 0.445 5.668 15774 Z= 0.243 Chirality : 0.040 0.163 1792 Planarity : 0.004 0.043 1945 Dihedral : 6.885 75.756 1624 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.72 % Allowed : 12.18 % 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: 1.90 (0.22), residues: 1420 helix: 2.71 (0.18), residues: 772 sheet: 0.40 (0.39), residues: 152 loop : -0.88 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 687 TYR 0.010 0.001 TYR A 827 PHE 0.017 0.001 PHE B 911 TRP 0.011 0.001 TRP A 779 HIS 0.007 0.001 HIS A 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (11632) covalent geometry : angle 0.44479 / 0.24 (15774) hydrogen bonds : bond 0.04235 / 2.82 ( 679) hydrogen bonds : angle 4.09435 / 2.79 ( 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 150 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.415 Fit side-chains REVERT: A 471 ASP cc_start: 0.7093 (m-30) cc_final: 0.6761 (m-30) REVERT: A 577 LYS cc_start: 0.7562 (mtmt) cc_final: 0.7314 (mttm) REVERT: A 594 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.8030 (mmp-170) REVERT: A 749 ARG cc_start: 0.8130 (mtp180) cc_final: 0.7683 (mmm-85) REVERT: A 859 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7900 (mppt) REVERT: B 376 ARG cc_start: 0.7128 (mmm160) cc_final: 0.6893 (mmm160) REVERT: B 471 ASP cc_start: 0.7099 (m-30) cc_final: 0.6781 (m-30) REVERT: B 594 ARG cc_start: 0.8296 (mmt180) cc_final: 0.8082 (mmp-170) REVERT: B 859 LYS cc_start: 0.8245 (mmtt) cc_final: 0.7918 (mppt) outliers start: 20 outliers final: 6 residues processed: 142 average time/residue: 0.4835 time to fit residues: 74.7231 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 : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1108 SER 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: 4.9990 chunk 42 optimal weight: 0.0470 chunk 121 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 560 GLN A1013 ASN B 560 GLN B 706 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.136818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107164 restraints weight = 12809.365| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.77 r_work: 0.3117 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11632 Z= 0.202 Angle : 0.541 6.205 15774 Z= 0.291 Chirality : 0.044 0.164 1792 Planarity : 0.004 0.043 1945 Dihedral : 7.558 92.496 1624 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.80 % Allowed : 12.61 % Favored : 85.59 % 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: 1.58 (0.22), residues: 1420 helix: 2.37 (0.17), residues: 780 sheet: 0.11 (0.39), residues: 156 loop : -0.88 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 687 TYR 0.013 0.002 TYR B 475 PHE 0.020 0.002 PHE B 911 TRP 0.010 0.002 TRP B 806 HIS 0.007 0.001 HIS A 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 (11632) covalent geometry : angle 0.54075 / 0.29 (15774) hydrogen bonds : bond 0.05459 / 3.63 ( 679) hydrogen bonds : angle 4.45243 / 3.01 ( 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 148 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.458 Fit side-chains REVERT: A 577 LYS cc_start: 0.7675 (mtmt) cc_final: 0.7413 (mttp) REVERT: A 594 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.8063 (mmp-170) REVERT: A 749 ARG cc_start: 0.8187 (mtp180) cc_final: 0.7750 (mmm-85) REVERT: A 859 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7918 (mppt) REVERT: B 594 ARG cc_start: 0.8321 (mmt180) cc_final: 0.8101 (mmp-170) REVERT: B 859 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7891 (mppt) outliers start: 21 outliers final: 14 residues processed: 140 average time/residue: 0.5210 time to fit residues: 79.8467 Evaluate side-chains 141 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 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 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: 7.9990 chunk 102 optimal weight: 2.9990 chunk 80 optimal weight: 0.0470 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 103 optimal weight: 0.0870 chunk 72 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 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 = 0.3652 r_free = 0.3652 target = 0.141347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111950 restraints weight = 12769.635| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.76 r_work: 0.3179 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11632 Z= 0.095 Angle : 0.433 5.029 15774 Z= 0.238 Chirality : 0.039 0.164 1792 Planarity : 0.004 0.044 1945 Dihedral : 6.732 73.138 1624 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.03 % Allowed : 13.64 % Favored : 85.33 % 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: 2.76 (0.18), residues: 772 sheet: 0.47 (0.40), residues: 152 loop : -0.84 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 687 TYR 0.010 0.001 TYR A 827 PHE 0.015 0.001 PHE B 911 TRP 0.011 0.001 TRP A 779 HIS 0.005 0.001 HIS A 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.10 (11632) covalent geometry : angle 0.43310 / 0.24 (15774) hydrogen bonds : bond 0.04050 / 2.69 ( 679) hydrogen bonds : angle 4.03920 / 2.75 ( 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 143 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.392 Fit side-chains REVERT: A 471 ASP cc_start: 0.7073 (m-30) cc_final: 0.6731 (m-30) REVERT: A 577 LYS cc_start: 0.7565 (mtmt) cc_final: 0.7323 (mttm) REVERT: A 594 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.8027 (mmp-170) REVERT: A 749 ARG cc_start: 0.8118 (mtp180) cc_final: 0.7685 (mmm-85) REVERT: A 859 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7923 (mppt) REVERT: B 471 ASP cc_start: 0.7068 (m-30) cc_final: 0.6772 (m-30) REVERT: B 594 ARG cc_start: 0.8293 (mmt180) cc_final: 0.8081 (mmp-170) REVERT: B 859 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7901 (mppt) outliers start: 12 outliers final: 7 residues processed: 138 average time/residue: 0.4836 time to fit residues: 72.7837 Evaluate side-chains 137 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 656 MET Chi-restraints excluded: chain A residue 673 VAL 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 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: 0.9980 chunk 97 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3631 r_free = 0.3631 target = 0.139394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109821 restraints weight = 12885.212| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.78 r_work: 0.3153 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11632 Z= 0.129 Angle : 0.469 6.019 15774 Z= 0.255 Chirality : 0.041 0.162 1792 Planarity : 0.004 0.043 1945 Dihedral : 6.894 80.802 1624 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.29 % Allowed : 13.29 % Favored : 85.42 % 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: 1.90 (0.22), residues: 1420 helix: 2.66 (0.18), residues: 776 sheet: 0.30 (0.40), residues: 156 loop : -0.79 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 687 TYR 0.013 0.001 TYR A 475 PHE 0.017 0.001 PHE B 911 TRP 0.010 0.001 TRP A 806 HIS 0.006 0.001 HIS A 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (11632) covalent geometry : angle 0.46931 / 0.26 (15774) hydrogen bonds : bond 0.04568 / 3.04 ( 679) hydrogen bonds : angle 4.15736 / 2.83 ( 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: 15 poor density : 129 time to evaluate : 0.271 Fit side-chains REVERT: A 577 LYS cc_start: 0.7606 (mtmt) cc_final: 0.7353 (mttm) REVERT: A 594 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.8024 (mmp-170) REVERT: A 749 ARG cc_start: 0.8144 (mtp180) cc_final: 0.7704 (mmm-85) REVERT: A 859 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7934 (mppt) REVERT: B 594 ARG cc_start: 0.8311 (mmt180) cc_final: 0.8104 (mmp-170) REVERT: B 859 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7903 (mppt) outliers start: 15 outliers final: 12 residues processed: 137 average time/residue: 0.5049 time to fit residues: 75.2572 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 : 0.352 ------------------------------------------------------------------------------- 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 602 ASP 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 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 1108 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 105 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3637 r_free = 0.3637 target = 0.139936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110314 restraints weight = 12913.429| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.78 r_work: 0.3157 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2662 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= 0.121 Angle : 0.462 7.878 15774 Z= 0.251 Chirality : 0.040 0.162 1792 Planarity : 0.004 0.043 1945 Dihedral : 6.850 79.456 1624 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.46 % Allowed : 12.86 % Favored : 85.68 % 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: 1.95 (0.22), residues: 1420 helix: 2.69 (0.18), residues: 776 sheet: 0.32 (0.39), residues: 156 loop : -0.74 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 687 TYR 0.012 0.001 TYR A 475 PHE 0.016 0.001 PHE B 911 TRP 0.010 0.001 TRP B 779 HIS 0.005 0.001 HIS B 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (11632) covalent geometry : angle 0.46208 / 0.25 (15774) hydrogen bonds : bond 0.04443 / 2.96 ( 679) hydrogen bonds : angle 4.11565 / 2.80 ( 1947) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3767.81 seconds wall clock time: 64 minutes 57.06 seconds (3897.06 seconds total)