Starting phenix.real_space_refine on Thu Jul 2 16:52:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8k3u_36861/07_2026/8k3u_36861.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3u_36861/07_2026/8k3u_36861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8k3u_36861/07_2026/8k3u_36861.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8k3u_36861/07_2026/8k3u_36861.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k3u_36861/07_2026/8k3u_36861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3u_36861/07_2026/8k3u_36861.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3u_36861/07_2026/8k3u_36861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3u_36861/07_2026/8k3u_36861.cif" } resolution = 3.06 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= 0.004 sd= 0.091 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 4 5.21 5 S 58 5.16 5 C 5792 2.51 5 N 1440 2.21 5 O 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 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: 8914 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4374 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PTRANS': 16, 'TRANS': 580} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 518 Unresolved non-hydrogen angles: 656 Unresolved non-hydrogen dihedrals: 437 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'PHE:plan': 7, 'ARG:plan': 12, 'GLN:plan1': 6, 'GLU:plan': 13, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 5, 'HIS:plan': 2, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 283 Chain: "B" Number of atoms: 4360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4360 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PTRANS': 16, 'TRANS': 580} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 534 Unresolved non-hydrogen angles: 677 Unresolved non-hydrogen dihedrals: 452 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'PHE:plan': 8, 'ARG:plan': 12, 'GLN:plan1': 6, 'GLU:plan': 13, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 5, 'HIS:plan': 3, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 294 Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 90 Unusual residues: {' MG': 2, 'NAG': 1, 'POV': 1, 'UDP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 90 Unusual residues: {' MG': 2, 'NAG': 1, 'POV': 1, 'UDP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 1.76, per 1000 atoms: 0.20 Number of scatterers: 8914 At special positions: 0 Unit cell: (132.5, 75.26, 96.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 6 15.00 Mg 4 11.99 O 1614 8.00 N 1440 7.00 C 5792 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: 0.73 Conformation dependent library (CDL) restraints added in 397.7 milliseconds 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2280 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 6 sheets defined 62.6% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 458 through 478 removed outlier: 3.612A pdb=" N THR A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A 471 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 removed outlier: 3.549A pdb=" N LYS A 491 " --> pdb=" O ASP A 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 491' Processing helix chain 'A' and resid 506 through 516 removed outlier: 3.519A pdb=" N LEU A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 588 removed outlier: 3.742A pdb=" N SER A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 594 removed outlier: 3.543A pdb=" N LEU A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 617 removed outlier: 3.638A pdb=" N GLN A 614 " --> pdb=" O ASP A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 640 Processing helix chain 'A' and resid 650 through 669 removed outlier: 3.502A pdb=" N MET A 656 " --> pdb=" O PHE A 652 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS A 662 " --> pdb=" O ASN A 658 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.651A 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 718 through 726 removed outlier: 4.044A pdb=" N PHE A 722 " --> pdb=" O ARG A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 774 removed outlier: 4.157A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.514A pdb=" N SER A 781 " --> pdb=" O VAL A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 807 removed outlier: 3.544A pdb=" N PHE A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 825 Processing helix chain 'A' and resid 830 through 855 Processing helix chain 'A' and resid 861 through 890 removed outlier: 3.703A pdb=" N TYR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 932 Processing helix chain 'A' and resid 935 through 940 Processing helix chain 'A' and resid 941 through 947 removed outlier: 4.157A pdb=" N LEU A 947 " --> pdb=" O GLN A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 954 Processing helix chain 'A' and resid 954 through 962 Processing helix chain 'A' and resid 1029 through 1057 removed outlier: 3.625A pdb=" N ILE A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1075 removed outlier: 3.732A pdb=" N THR A1075 " --> pdb=" O LYS A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1127 removed outlier: 3.998A pdb=" N SER A1095 " --> pdb=" O THR A1091 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A1101 " --> pdb=" O TYR A1097 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 428 Processing helix chain 'B' and resid 458 through 478 removed outlier: 3.611A pdb=" N THR B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 491 removed outlier: 3.547A pdb=" N LYS B 491 " --> pdb=" O ASP B 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 506 through 516 removed outlier: 3.519A pdb=" N LEU B 510 " --> pdb=" O ASN B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 588 removed outlier: 3.742A pdb=" N SER B 581 " --> pdb=" O LYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 594 removed outlier: 3.544A pdb=" N LEU B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 617 removed outlier: 3.639A pdb=" N GLN B 614 " --> pdb=" O ASP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 650 through 669 removed outlier: 3.502A pdb=" N MET B 656 " --> pdb=" O PHE B 652 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER B 657 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS B 662 " --> pdb=" O ASN B 658 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) removed outlier: 3.650A 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 718 through 726 removed outlier: 4.045A pdb=" N PHE B 722 " --> pdb=" O ARG B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 774 removed outlier: 4.158A pdb=" N ARG B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.514A pdb=" N SER B 781 " --> pdb=" O VAL B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 807 removed outlier: 3.545A pdb=" N PHE B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 825 Processing helix chain 'B' and resid 830 through 855 Processing helix chain 'B' and resid 861 through 890 removed outlier: 3.704A pdb=" N TYR B 865 " --> pdb=" O THR B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 932 Processing helix chain 'B' and resid 935 through 940 Processing helix chain 'B' and resid 941 through 947 removed outlier: 4.157A pdb=" N LEU B 947 " --> pdb=" O GLN B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 954 Processing helix chain 'B' and resid 954 through 962 Processing helix chain 'B' and resid 1029 through 1057 removed outlier: 3.626A pdb=" N ILE B1045 " --> pdb=" O SER B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1075 removed outlier: 3.732A pdb=" N THR B1075 " --> pdb=" O LYS B1071 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1127 removed outlier: 3.997A pdb=" N SER B1095 " --> pdb=" O THR B1091 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B1101 " --> pdb=" O TYR B1097 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 417 through 421 removed outlier: 3.752A pdb=" N ARG A 417 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 539 " --> pdb=" O ARG A 417 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLN A 566 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 494 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N MET A 449 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 601 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N VAL A 451 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N PHE A 678 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLY A 625 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 15.279A pdb=" N ARG A 738 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 15.914A pdb=" N GLY A 626 " --> pdb=" O ARG A 738 " (cutoff:3.500A) removed outlier: 12.705A pdb=" N SER A 740 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N CYS A 628 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N ALA A 742 " --> pdb=" O CYS A 628 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU A 630 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR A 744 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ARG A 632 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 417 through 421 removed outlier: 3.752A pdb=" N ARG A 417 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 539 " --> pdb=" O ARG A 417 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLN A 566 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 494 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N MET A 449 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 601 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N VAL A 451 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N PHE A 678 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLY A 625 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 545 through 549 removed outlier: 5.488A pdb=" N ILE A 546 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLU A 557 " --> pdb=" O ILE A 546 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN A 548 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 417 through 421 removed outlier: 3.753A pdb=" N ARG B 417 " --> pdb=" O GLU B 539 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU B 539 " --> pdb=" O ARG B 417 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLN B 566 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 494 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N MET B 449 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU B 601 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N VAL B 451 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N PHE B 678 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLY B 625 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 15.280A pdb=" N ARG B 738 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 15.914A pdb=" N GLY B 626 " --> pdb=" O ARG B 738 " (cutoff:3.500A) removed outlier: 12.705A pdb=" N SER B 740 " --> pdb=" O GLY B 626 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N CYS B 628 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N ALA B 742 " --> pdb=" O CYS B 628 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU B 630 " --> pdb=" O ALA B 742 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR B 744 " --> pdb=" O GLU B 630 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG B 632 " --> pdb=" O THR B 744 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 417 through 421 removed outlier: 3.753A pdb=" N ARG B 417 " --> pdb=" O GLU B 539 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU B 539 " --> pdb=" O ARG B 417 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLN B 566 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 494 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N MET B 449 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU B 601 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N VAL B 451 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N PHE B 678 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLY B 625 " --> pdb=" O ARG B 682 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 545 through 549 removed outlier: 5.486A pdb=" N ILE B 546 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLU B 557 " --> pdb=" O ILE B 546 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN B 548 " --> pdb=" O SER B 555 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1806 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: 1.41 Time building geometry restraints manager: 0.92 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: 1364 1.31 - 1.43: 2622 1.43 - 1.56: 5004 1.56 - 1.69: 28 1.69 - 1.81: 86 Bond restraints: 9104 Sorted by residual: bond pdb=" C31 POV B1201 " pdb=" O31 POV B1201 " ideal model delta sigma weight residual 1.327 1.433 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" C31 POV A1505 " pdb=" O31 POV A1505 " ideal model delta sigma weight residual 1.327 1.432 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb="C312 POV B1201 " pdb="C313 POV B1201 " ideal model delta sigma weight residual 1.523 1.604 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb="C312 POV A1505 " pdb="C313 POV A1505 " ideal model delta sigma weight residual 1.523 1.603 -0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C21 POV B1201 " pdb=" O21 POV B1201 " ideal model delta sigma weight residual 1.330 1.405 -0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 9099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 11870 2.41 - 4.82: 449 4.82 - 7.23: 54 7.23 - 9.64: 8 9.64 - 12.05: 10 Bond angle restraints: 12391 Sorted by residual: angle pdb=" N LEU B 939 " pdb=" CA LEU B 939 " pdb=" C LEU B 939 " ideal model delta sigma weight residual 114.39 106.13 8.26 1.45e+00 4.76e-01 3.25e+01 angle pdb=" N ARG A 718 " pdb=" CA ARG A 718 " pdb=" C ARG A 718 " ideal model delta sigma weight residual 114.12 106.26 7.86 1.39e+00 5.18e-01 3.20e+01 angle pdb=" N ARG B 718 " pdb=" CA ARG B 718 " pdb=" C ARG B 718 " ideal model delta sigma weight residual 114.12 106.27 7.85 1.39e+00 5.18e-01 3.19e+01 angle pdb=" N LEU A 939 " pdb=" CA LEU A 939 " pdb=" C LEU A 939 " ideal model delta sigma weight residual 114.39 106.21 8.18 1.45e+00 4.76e-01 3.18e+01 angle pdb=" N LEU B 642 " pdb=" CA LEU B 642 " pdb=" C LEU B 642 " ideal model delta sigma weight residual 112.87 107.18 5.69 1.20e+00 6.94e-01 2.25e+01 ... (remaining 12386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.41: 4932 21.41 - 42.81: 234 42.81 - 64.22: 58 64.22 - 85.62: 4 85.62 - 107.03: 4 Dihedral angle restraints: 5232 sinusoidal: 1718 harmonic: 3514 Sorted by residual: dihedral pdb=" CA VAL B 673 " pdb=" C VAL B 673 " pdb=" N LEU B 674 " pdb=" CA LEU B 674 " ideal model delta harmonic sigma weight residual 180.00 155.77 24.23 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA VAL A 673 " pdb=" C VAL A 673 " pdb=" N LEU A 674 " pdb=" CA LEU A 674 " ideal model delta harmonic sigma weight residual 180.00 155.83 24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" C27 POV A1505 " pdb=" C28 POV A1505 " pdb=" C29 POV A1505 " pdb="C210 POV A1505 " ideal model delta sinusoidal sigma weight residual 127.48 -125.49 -107.03 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 5229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 883 0.045 - 0.089: 331 0.089 - 0.134: 158 0.134 - 0.178: 71 0.178 - 0.223: 12 Chirality restraints: 1455 Sorted by residual: chirality pdb=" CA ILE A1096 " pdb=" N ILE A1096 " pdb=" C ILE A1096 " pdb=" CB ILE A1096 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ILE B1096 " pdb=" N ILE B1096 " pdb=" C ILE B1096 " pdb=" CB ILE B1096 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA LEU B 939 " pdb=" N LEU B 939 " pdb=" C LEU B 939 " pdb=" CB LEU B 939 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1452 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 674 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.42e+00 pdb=" N PRO B 675 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 675 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 675 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 674 " 0.048 5.00e-02 4.00e+02 7.24e-02 8.39e+00 pdb=" N PRO A 675 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 675 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 675 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 750 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.08e+00 pdb=" N PRO B 751 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 751 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 751 " -0.025 5.00e-02 4.00e+02 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 142 2.64 - 3.20: 8701 3.20 - 3.77: 13850 3.77 - 4.33: 18786 4.33 - 4.90: 30992 Nonbonded interactions: 72471 Sorted by model distance: nonbonded pdb="MG MG A1501 " pdb=" O1A UDP A1504 " model vdw 2.072 2.170 nonbonded pdb="MG MG B1202 " pdb=" O1A UDP B1205 " model vdw 2.073 2.170 nonbonded pdb="MG MG B1203 " pdb=" O3' UDP B1205 " model vdw 2.163 2.170 nonbonded pdb="MG MG A1502 " pdb=" O3' UDP A1504 " model vdw 2.163 2.170 nonbonded pdb=" O CYS A 845 " pdb=" OG1 THR A 849 " model vdw 2.230 3.040 ... (remaining 72466 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' and (resid 415 through 936 or (resid 937 and (name N or name CA or na \ me C or name O or name CB )) or resid 938 through 941 or (resid 942 through 945 \ and (name N or name CA or name C or name O or name CB )) or resid 946 or (resid \ 947 and (name N or name CA or name C or name O or name CB )) or resid 948 throug \ h 1127 or resid 1502)) selection = (chain 'B' and (resid 415 through 1127 or resid 1202)) } 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: 0.940 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.680 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 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 : 0.009 0.106 9104 Z= 0.529 Angle : 1.065 12.052 12391 Z= 0.696 Chirality : 0.064 0.223 1455 Planarity : 0.005 0.073 1516 Dihedral : 13.997 107.027 2952 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.85 % Favored : 93.98 % Rotamer: Outliers : 0.73 % Allowed : 2.56 % Favored : 96.71 % 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: -1.45 (0.23), residues: 1162 helix: -0.39 (0.18), residues: 686 sheet: -1.15 (0.43), residues: 142 loop : -1.77 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 682 TYR 0.027 0.002 TYR A 865 PHE 0.021 0.002 PHE A 812 TRP 0.012 0.001 TRP B 616 HIS 0.002 0.001 HIS B 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00850 / 0.53 ( 9104) covalent geometry : angle 1.06549 / 0.70 (12391) hydrogen bonds : bond 0.16137 / 11.31 ( 574) hydrogen bonds : angle 7.35710 / 5.23 ( 1806) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 176 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 ASN cc_start: 0.7250 (m110) cc_final: 0.7050 (m110) REVERT: B 580 ASN cc_start: 0.7412 (m110) cc_final: 0.7148 (m110) REVERT: B 661 ASP cc_start: 0.7689 (m-30) cc_final: 0.7424 (m-30) REVERT: B 665 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7016 (mt-10) REVERT: B 772 PHE cc_start: 0.6997 (t80) cc_final: 0.6545 (t80) outliers start: 6 outliers final: 2 residues processed: 180 average time/residue: 0.0820 time to fit residues: 20.7702 Evaluate side-chains 135 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain B residue 946 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1051 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.230668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.193769 restraints weight = 9895.799| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 2.33 r_work: 0.4090 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9104 Z= 0.136 Angle : 0.547 6.409 12391 Z= 0.297 Chirality : 0.041 0.205 1455 Planarity : 0.004 0.054 1516 Dihedral : 9.551 94.306 1332 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.10 % Favored : 96.73 % Rotamer: Outliers : 1.95 % Allowed : 8.77 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.27 (0.24), residues: 1162 helix: 0.66 (0.19), residues: 710 sheet: -1.42 (0.39), residues: 152 loop : -1.30 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 718 TYR 0.014 0.001 TYR B 925 PHE 0.019 0.002 PHE A 812 TRP 0.008 0.001 TRP A 779 HIS 0.002 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 9104) covalent geometry : angle 0.54674 / 0.30 (12391) hydrogen bonds : bond 0.04585 / 3.25 ( 574) hydrogen bonds : angle 4.63587 / 3.26 ( 1806) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 500 ASP cc_start: 0.5760 (t0) cc_final: 0.5483 (t0) REVERT: A 535 MET cc_start: 0.6411 (ttt) cc_final: 0.6141 (mmm) REVERT: A 568 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7232 (mp) REVERT: A 580 ASN cc_start: 0.7445 (m110) cc_final: 0.7095 (m110) REVERT: A 772 PHE cc_start: 0.7435 (t80) cc_final: 0.6969 (t80) REVERT: A 1121 ILE cc_start: 0.7591 (mm) cc_final: 0.7351 (mm) REVERT: B 500 ASP cc_start: 0.5761 (t0) cc_final: 0.5432 (t0) REVERT: B 519 TYR cc_start: 0.4755 (t80) cc_final: 0.4485 (t80) REVERT: B 535 MET cc_start: 0.6376 (ttt) cc_final: 0.6106 (mmm) REVERT: B 580 ASN cc_start: 0.7366 (m110) cc_final: 0.7035 (m110) REVERT: B 772 PHE cc_start: 0.7405 (t80) cc_final: 0.6896 (t80) REVERT: B 1038 ASN cc_start: 0.8461 (m-40) cc_final: 0.8164 (m-40) REVERT: B 1121 ILE cc_start: 0.7643 (mm) cc_final: 0.7414 (mm) outliers start: 16 outliers final: 8 residues processed: 158 average time/residue: 0.0751 time to fit residues: 17.7180 Evaluate side-chains 131 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 1117 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 0.0060 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.227289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.190157 restraints weight = 9804.268| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 2.31 r_work: 0.4069 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9104 Z= 0.134 Angle : 0.502 5.808 12391 Z= 0.272 Chirality : 0.040 0.174 1455 Planarity : 0.003 0.039 1516 Dihedral : 8.821 92.595 1328 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.36 % Favored : 96.47 % Rotamer: Outliers : 2.44 % Allowed : 13.52 % Favored : 84.04 % 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: 0.40 (0.24), residues: 1162 helix: 1.26 (0.20), residues: 686 sheet: -1.31 (0.39), residues: 146 loop : -0.95 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 682 TYR 0.016 0.001 TYR A 842 PHE 0.015 0.002 PHE A 864 TRP 0.010 0.001 TRP B 490 HIS 0.003 0.001 HIS A 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 9104) covalent geometry : angle 0.50158 / 0.27 (12391) hydrogen bonds : bond 0.04101 / 2.92 ( 574) hydrogen bonds : angle 4.20891 / 2.96 ( 1806) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 443 PRO cc_start: 0.7933 (Cg_exo) cc_final: 0.7725 (Cg_endo) REVERT: A 476 MET cc_start: 0.6744 (mmt) cc_final: 0.6335 (mmt) REVERT: A 500 ASP cc_start: 0.5202 (t0) cc_final: 0.4908 (t0) REVERT: A 535 MET cc_start: 0.6386 (ttt) cc_final: 0.6061 (mmm) REVERT: A 580 ASN cc_start: 0.7322 (m110) cc_final: 0.6864 (m110) REVERT: A 772 PHE cc_start: 0.7447 (t80) cc_final: 0.7130 (t80) REVERT: A 1121 ILE cc_start: 0.7646 (mm) cc_final: 0.7432 (mm) REVERT: B 535 MET cc_start: 0.6345 (ttt) cc_final: 0.6001 (mmm) REVERT: B 568 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7298 (mp) REVERT: B 580 ASN cc_start: 0.7292 (m110) cc_final: 0.6710 (m110) REVERT: B 772 PHE cc_start: 0.7492 (t80) cc_final: 0.7128 (t80) REVERT: B 938 MET cc_start: 0.6612 (ttm) cc_final: 0.6187 (tpp) REVERT: B 1120 MET cc_start: 0.6965 (mmt) cc_final: 0.6535 (mmt) outliers start: 20 outliers final: 8 residues processed: 152 average time/residue: 0.0746 time to fit residues: 17.0732 Evaluate side-chains 132 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 1117 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 95 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.220610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.176433 restraints weight = 10012.377| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 2.40 r_work: 0.3998 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9104 Z= 0.201 Angle : 0.580 6.280 12391 Z= 0.314 Chirality : 0.043 0.170 1455 Planarity : 0.004 0.042 1516 Dihedral : 8.530 95.944 1328 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.44 % Favored : 96.39 % Rotamer: Outliers : 3.90 % Allowed : 14.62 % Favored : 81.49 % 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: 0.01 (0.24), residues: 1162 helix: 0.92 (0.19), residues: 686 sheet: -1.21 (0.38), residues: 152 loop : -1.20 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 777 TYR 0.017 0.002 TYR B 455 PHE 0.027 0.002 PHE A 942 TRP 0.013 0.001 TRP A 490 HIS 0.002 0.001 HIS B 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 ( 9104) covalent geometry : angle 0.58023 / 0.31 (12391) hydrogen bonds : bond 0.04718 / 3.36 ( 574) hydrogen bonds : angle 4.43625 / 3.14 ( 1806) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 476 MET cc_start: 0.7220 (mmt) cc_final: 0.6742 (mmt) REVERT: A 500 ASP cc_start: 0.5836 (t0) cc_final: 0.5606 (t0) REVERT: A 580 ASN cc_start: 0.7228 (m110) cc_final: 0.6653 (m110) REVERT: A 752 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.5939 (pt0) REVERT: A 772 PHE cc_start: 0.7571 (t80) cc_final: 0.7348 (t80) REVERT: A 794 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6732 (tm-30) REVERT: A 1070 MET cc_start: 0.6332 (mtt) cc_final: 0.6047 (mtt) REVERT: B 500 ASP cc_start: 0.5552 (t0) cc_final: 0.5259 (t0) REVERT: B 580 ASN cc_start: 0.7159 (m110) cc_final: 0.6704 (m110) REVERT: B 752 GLU cc_start: 0.6284 (OUTLIER) cc_final: 0.5872 (pm20) REVERT: B 864 PHE cc_start: 0.7587 (t80) cc_final: 0.7376 (t80) REVERT: B 938 MET cc_start: 0.6611 (ttm) cc_final: 0.6292 (tpp) REVERT: B 1120 MET cc_start: 0.7171 (mmt) cc_final: 0.6694 (mmt) outliers start: 32 outliers final: 17 residues processed: 153 average time/residue: 0.0782 time to fit residues: 17.7855 Evaluate side-chains 145 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain B residue 426 ASN Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 865 TYR Chi-restraints excluded: chain B residue 1066 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 23 optimal weight: 0.0270 chunk 73 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 957 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.222465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.178302 restraints weight = 9845.826| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 2.49 r_work: 0.4013 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9104 Z= 0.114 Angle : 0.476 7.340 12391 Z= 0.258 Chirality : 0.039 0.186 1455 Planarity : 0.003 0.028 1516 Dihedral : 7.383 74.829 1328 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.84 % Favored : 96.99 % Rotamer: Outliers : 2.68 % Allowed : 16.20 % Favored : 81.12 % 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: 0.60 (0.24), residues: 1162 helix: 1.40 (0.20), residues: 684 sheet: -0.87 (0.41), residues: 146 loop : -1.02 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1040 TYR 0.013 0.001 TYR B 842 PHE 0.043 0.001 PHE A 942 TRP 0.012 0.001 TRP B 490 HIS 0.002 0.001 HIS A 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 9104) covalent geometry : angle 0.47566 / 0.26 (12391) hydrogen bonds : bond 0.03593 / 2.56 ( 574) hydrogen bonds : angle 3.91255 / 2.77 ( 1806) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.315 Fit side-chains REVERT: A 449 MET cc_start: 0.7176 (ttm) cc_final: 0.6611 (ttp) REVERT: A 500 ASP cc_start: 0.5754 (t0) cc_final: 0.5453 (t0) REVERT: A 580 ASN cc_start: 0.7143 (m110) cc_final: 0.6633 (m110) REVERT: A 772 PHE cc_start: 0.7427 (t80) cc_final: 0.7073 (t80) REVERT: A 1070 MET cc_start: 0.6356 (mtt) cc_final: 0.5963 (mtt) REVERT: B 580 ASN cc_start: 0.7109 (m110) cc_final: 0.6637 (m110) REVERT: B 772 PHE cc_start: 0.7427 (t80) cc_final: 0.7071 (t80) REVERT: B 1038 ASN cc_start: 0.8509 (m-40) cc_final: 0.8178 (m-40) REVERT: B 1120 MET cc_start: 0.7180 (mmt) cc_final: 0.6576 (mmt) outliers start: 22 outliers final: 9 residues processed: 150 average time/residue: 0.0732 time to fit residues: 16.4930 Evaluate side-chains 125 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 865 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 109 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.218185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.173419 restraints weight = 9963.036| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 2.54 r_work: 0.3961 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9104 Z= 0.162 Angle : 0.533 6.792 12391 Z= 0.286 Chirality : 0.041 0.182 1455 Planarity : 0.003 0.024 1516 Dihedral : 7.679 78.259 1328 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.27 % Favored : 96.56 % Rotamer: Outliers : 3.05 % Allowed : 17.54 % Favored : 79.42 % 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: 0.37 (0.24), residues: 1162 helix: 1.17 (0.20), residues: 688 sheet: -0.88 (0.41), residues: 146 loop : -1.06 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 682 TYR 0.018 0.001 TYR A 455 PHE 0.028 0.002 PHE A 942 TRP 0.012 0.001 TRP B 490 HIS 0.002 0.001 HIS A 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 9104) covalent geometry : angle 0.53252 / 0.29 (12391) hydrogen bonds : bond 0.04189 / 2.98 ( 574) hydrogen bonds : angle 4.12322 / 2.92 ( 1806) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.316 Fit side-chains REVERT: A 449 MET cc_start: 0.7415 (ttm) cc_final: 0.6868 (ttp) REVERT: A 500 ASP cc_start: 0.5983 (t0) cc_final: 0.5507 (t0) REVERT: A 571 LEU cc_start: 0.5986 (tt) cc_final: 0.5475 (tt) REVERT: A 772 PHE cc_start: 0.7545 (t80) cc_final: 0.7252 (t80) REVERT: A 1070 MET cc_start: 0.6382 (mtt) cc_final: 0.6077 (mtt) REVERT: B 500 ASP cc_start: 0.6188 (t0) cc_final: 0.5772 (t0) REVERT: B 580 ASN cc_start: 0.7129 (m110) cc_final: 0.6644 (m110) REVERT: B 772 PHE cc_start: 0.7531 (t80) cc_final: 0.7245 (t80) REVERT: B 864 PHE cc_start: 0.7488 (t80) cc_final: 0.7212 (t80) REVERT: B 938 MET cc_start: 0.6426 (tpp) cc_final: 0.6000 (tpp) REVERT: B 1120 MET cc_start: 0.6895 (mmt) cc_final: 0.6542 (mmm) outliers start: 25 outliers final: 15 residues processed: 138 average time/residue: 0.0718 time to fit residues: 15.1932 Evaluate side-chains 127 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain B residue 426 ASN Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 865 TYR Chi-restraints excluded: chain B residue 1066 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 35 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 711 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.212503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.169534 restraints weight = 10041.179| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.55 r_work: 0.3830 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9104 Z= 0.240 Angle : 0.649 7.261 12391 Z= 0.347 Chirality : 0.046 0.174 1455 Planarity : 0.004 0.025 1516 Dihedral : 8.343 85.573 1328 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.61 % Favored : 96.21 % Rotamer: Outliers : 3.53 % Allowed : 18.15 % Favored : 78.32 % 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: -0.30 (0.24), residues: 1162 helix: 0.67 (0.19), residues: 680 sheet: -1.05 (0.40), residues: 146 loop : -1.44 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 682 TYR 0.016 0.002 TYR B 925 PHE 0.023 0.002 PHE A1052 TRP 0.017 0.002 TRP A 806 HIS 0.003 0.001 HIS B 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.24 ( 9104) covalent geometry : angle 0.64889 / 0.35 (12391) hydrogen bonds : bond 0.05139 / 3.64 ( 574) hydrogen bonds : angle 4.61537 / 3.28 ( 1806) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.341 Fit side-chains REVERT: A 449 MET cc_start: 0.7530 (ttm) cc_final: 0.7208 (ttp) REVERT: A 535 MET cc_start: 0.5347 (mmm) cc_final: 0.4852 (mmm) REVERT: A 711 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7275 (m110) REVERT: A 794 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: B 449 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7148 (ttp) REVERT: B 500 ASP cc_start: 0.6027 (t0) cc_final: 0.5504 (t0) REVERT: B 864 PHE cc_start: 0.7651 (t80) cc_final: 0.7381 (t80) outliers start: 29 outliers final: 16 residues processed: 147 average time/residue: 0.0709 time to fit residues: 16.0024 Evaluate side-chains 139 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain B residue 426 ASN Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 865 TYR Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1117 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 667 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.217055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.172277 restraints weight = 9827.390| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.52 r_work: 0.3949 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9104 Z= 0.151 Angle : 0.549 7.361 12391 Z= 0.294 Chirality : 0.041 0.166 1455 Planarity : 0.003 0.032 1516 Dihedral : 7.593 74.710 1328 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.58 % Favored : 97.25 % Rotamer: Outliers : 2.44 % Allowed : 19.61 % Favored : 77.95 % 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: 0.04 (0.24), residues: 1162 helix: 0.95 (0.19), residues: 676 sheet: -1.06 (0.40), residues: 146 loop : -1.20 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1040 TYR 0.015 0.001 TYR B 455 PHE 0.039 0.002 PHE A 942 TRP 0.010 0.001 TRP A 490 HIS 0.003 0.001 HIS A 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 9104) covalent geometry : angle 0.54933 / 0.29 (12391) hydrogen bonds : bond 0.04286 / 3.05 ( 574) hydrogen bonds : angle 4.25585 / 3.02 ( 1806) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.343 Fit side-chains REVERT: A 449 MET cc_start: 0.7532 (ttm) cc_final: 0.6996 (ttp) REVERT: A 565 ILE cc_start: 0.6231 (mm) cc_final: 0.5977 (mm) REVERT: A 794 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6865 (tm-30) REVERT: B 449 MET cc_start: 0.7353 (ttm) cc_final: 0.6994 (ttp) REVERT: B 500 ASP cc_start: 0.6431 (t0) cc_final: 0.6023 (t0) REVERT: B 864 PHE cc_start: 0.7540 (t80) cc_final: 0.7258 (t80) REVERT: B 1120 MET cc_start: 0.6564 (mmt) cc_final: 0.6220 (mmm) outliers start: 20 outliers final: 18 residues processed: 137 average time/residue: 0.0746 time to fit residues: 15.4974 Evaluate side-chains 132 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain B residue 426 ASN Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 865 TYR Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1117 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 2 optimal weight: 0.2980 chunk 30 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 582 HIS A 957 ASN B 582 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.221103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.177138 restraints weight = 9790.398| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 2.50 r_work: 0.4005 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9104 Z= 0.118 Angle : 0.509 7.881 12391 Z= 0.269 Chirality : 0.040 0.188 1455 Planarity : 0.003 0.022 1516 Dihedral : 6.991 65.461 1328 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.67 % Favored : 97.16 % Rotamer: Outliers : 2.31 % Allowed : 20.46 % Favored : 77.22 % 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: 0.39 (0.24), residues: 1162 helix: 1.19 (0.20), residues: 690 sheet: -0.88 (0.40), residues: 146 loop : -1.09 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 718 TYR 0.016 0.001 TYR B1067 PHE 0.035 0.001 PHE A 942 TRP 0.007 0.001 TRP B 806 HIS 0.003 0.001 HIS A 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 9104) covalent geometry : angle 0.50936 / 0.27 (12391) hydrogen bonds : bond 0.03684 / 2.62 ( 574) hydrogen bonds : angle 3.96191 / 2.81 ( 1806) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.317 Fit side-chains REVERT: A 449 MET cc_start: 0.7480 (ttm) cc_final: 0.7054 (ttp) REVERT: A 535 MET cc_start: 0.5258 (OUTLIER) cc_final: 0.4804 (tmm) REVERT: A 565 ILE cc_start: 0.6122 (mm) cc_final: 0.5894 (mm) REVERT: A 772 PHE cc_start: 0.7443 (t80) cc_final: 0.7101 (t80) REVERT: B 449 MET cc_start: 0.7307 (ttm) cc_final: 0.7041 (ttp) REVERT: B 500 ASP cc_start: 0.6160 (t0) cc_final: 0.5879 (t0) REVERT: B 1120 MET cc_start: 0.6574 (mmt) cc_final: 0.6186 (mmt) outliers start: 19 outliers final: 16 residues processed: 130 average time/residue: 0.0629 time to fit residues: 12.6086 Evaluate side-chains 131 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain B residue 426 ASN Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 865 TYR Chi-restraints excluded: chain B residue 1066 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 64 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 582 HIS B 576 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.215220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.176224 restraints weight = 9955.565| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.43 r_work: 0.3923 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9104 Z= 0.187 Angle : 0.578 8.220 12391 Z= 0.305 Chirality : 0.043 0.132 1455 Planarity : 0.003 0.024 1516 Dihedral : 7.626 69.103 1328 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.53 % Favored : 96.39 % Rotamer: Outliers : 2.07 % Allowed : 20.71 % Favored : 77.22 % 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: 0.14 (0.24), residues: 1162 helix: 0.95 (0.20), residues: 686 sheet: -0.99 (0.40), residues: 146 loop : -1.06 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 718 TYR 0.018 0.002 TYR A 455 PHE 0.018 0.002 PHE B1052 TRP 0.015 0.001 TRP B 806 HIS 0.003 0.001 HIS A 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 ( 9104) covalent geometry : angle 0.57760 / 0.31 (12391) hydrogen bonds : bond 0.04480 / 3.18 ( 574) hydrogen bonds : angle 4.24125 / 3.01 ( 1806) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.315 Fit side-chains REVERT: A 449 MET cc_start: 0.7625 (ttm) cc_final: 0.7213 (ttp) REVERT: A 535 MET cc_start: 0.5449 (mmm) cc_final: 0.4930 (mmm) REVERT: A 565 ILE cc_start: 0.6203 (mm) cc_final: 0.5955 (mm) REVERT: B 449 MET cc_start: 0.7453 (ttm) cc_final: 0.7056 (ttp) REVERT: B 500 ASP cc_start: 0.6249 (t0) cc_final: 0.5746 (t0) REVERT: B 864 PHE cc_start: 0.7577 (t80) cc_final: 0.7309 (t80) REVERT: B 1120 MET cc_start: 0.6663 (mmt) cc_final: 0.6327 (mmm) outliers start: 17 outliers final: 14 residues processed: 126 average time/residue: 0.0697 time to fit residues: 13.4806 Evaluate side-chains 129 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain B residue 426 ASN Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 865 TYR Chi-restraints excluded: chain B residue 1066 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 76 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 60 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 95 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 582 HIS B 576 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.222209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.178477 restraints weight = 9794.572| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 2.50 r_work: 0.4015 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9104 Z= 0.108 Angle : 0.488 8.336 12391 Z= 0.258 Chirality : 0.039 0.137 1455 Planarity : 0.002 0.021 1516 Dihedral : 6.872 64.195 1328 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.58 % Favored : 97.33 % Rotamer: Outliers : 1.71 % Allowed : 21.07 % Favored : 77.22 % 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: 0.54 (0.25), residues: 1162 helix: 1.22 (0.20), residues: 690 sheet: -0.78 (0.41), residues: 146 loop : -0.81 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 777 TYR 0.017 0.001 TYR B 455 PHE 0.019 0.001 PHE B 812 TRP 0.011 0.001 TRP B1047 HIS 0.003 0.001 HIS B 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 9104) covalent geometry : angle 0.48835 / 0.26 (12391) hydrogen bonds : bond 0.03570 / 2.54 ( 574) hydrogen bonds : angle 3.87726 / 2.75 ( 1806) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1922.46 seconds wall clock time: 33 minutes 50.08 seconds (2030.08 seconds total)