Starting phenix.real_space_refine on Sat Aug 23 03:13:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3u_36861/08_2025/8k3u_36861.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3u_36861/08_2025/8k3u_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k3u_36861/08_2025/8k3u_36861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3u_36861/08_2025/8k3u_36861.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3u_36861/08_2025/8k3u_36861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3u_36861/08_2025/8k3u_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-2.0-5787/lib/python3.9/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: 0.97 Conformation dependent library (CDL) restraints added in 247.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.20 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: 1.22 Time building geometry restraints manager: 1.17 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: 4984 21.41 - 42.81: 260 42.81 - 64.22: 84 64.22 - 85.62: 22 85.62 - 107.03: 6 Dihedral angle restraints: 5356 sinusoidal: 1842 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 5353 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.740 Find NCS groups from input model: 0.100 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 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 : 16.046 107.027 3076 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 aren 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 covalent geometry : bond 0.00850 ( 9104) covalent geometry : angle 1.06549 (12391) hydrogen bonds : bond 0.16137 ( 574) hydrogen bonds : angle 7.35710 ( 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 : 0.226 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: 0.7423 (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: 0.0722 time to fit residues: 18.2592 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 : 0.180 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B1051 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.229725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.189735 restraints weight = 9885.848| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 3.46 r_work: 0.4005 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.1922 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= 0.137 Angle : 0.549 6.085 12391 Z= 0.301 Chirality : 0.042 0.207 1455 Planarity : 0.004 0.054 1516 Dihedral : 13.679 94.471 1456 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.01 % Favored : 96.82 % Rotamer: Outliers : 2.07 % Allowed : 8.40 % Favored : 89.52 % 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 aren not related in a simple way. whole: -0.28 (0.24), residues: 1162 helix: 0.64 (0.19), residues: 710 sheet: -1.37 (0.39), residues: 152 loop : -1.29 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 718 TYR 0.013 0.001 TYR B 925 PHE 0.019 0.002 PHE A 812 TRP 0.009 0.001 TRP B 490 HIS 0.002 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9104) covalent geometry : angle 0.54944 (12391) hydrogen bonds : bond 0.04699 ( 574) hydrogen bonds : angle 4.65407 ( 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 161 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 500 ASP cc_start: 0.5720 (t0) cc_final: 0.5426 (t0) REVERT: A 535 MET cc_start: 0.6393 (ttt) cc_final: 0.6123 (mmm) REVERT: A 568 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7196 (mp) REVERT: A 580 ASN cc_start: 0.7466 (m110) cc_final: 0.7116 (m110) REVERT: A 772 PHE cc_start: 0.7489 (t80) cc_final: 0.7010 (t80) REVERT: A 1121 ILE cc_start: 0.7617 (mm) cc_final: 0.7376 (mm) REVERT: B 500 ASP cc_start: 0.5739 (t0) cc_final: 0.5384 (t0) REVERT: B 519 TYR cc_start: 0.4753 (t80) cc_final: 0.4477 (t80) REVERT: B 535 MET cc_start: 0.6357 (ttt) cc_final: 0.6087 (mmm) REVERT: B 567 LEU cc_start: 0.7264 (mt) cc_final: 0.7059 (mt) REVERT: B 580 ASN cc_start: 0.7384 (m110) cc_final: 0.7052 (m110) REVERT: B 772 PHE cc_start: 0.7412 (t80) cc_final: 0.6906 (t80) REVERT: B 1038 ASN cc_start: 0.8488 (m-40) cc_final: 0.8194 (m-40) REVERT: B 1121 ILE cc_start: 0.7650 (mm) cc_final: 0.7421 (mm) outliers start: 17 outliers final: 8 residues processed: 159 average time/residue: 0.0750 time to fit residues: 17.5813 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 : 0.379 ------------------------------------------------------------------------------- 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: 0.9980 chunk 19 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 11 optimal weight: 0.0040 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4574 r_free = 0.4574 target = 0.226201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.188930 restraints weight = 9819.586| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 2.28 r_work: 0.4041 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9104 Z= 0.145 Angle : 0.519 5.809 12391 Z= 0.284 Chirality : 0.041 0.170 1455 Planarity : 0.003 0.040 1516 Dihedral : 13.585 93.432 1452 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.10 % Favored : 96.73 % Rotamer: Outliers : 2.56 % Allowed : 13.64 % Favored : 83.80 % 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 aren not related in a simple way. whole: 0.28 (0.24), residues: 1162 helix: 1.15 (0.20), residues: 686 sheet: -1.27 (0.39), residues: 146 loop : -1.03 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 682 TYR 0.015 0.001 TYR A 842 PHE 0.017 0.002 PHE A 864 TRP 0.012 0.001 TRP B 490 HIS 0.003 0.001 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9104) covalent geometry : angle 0.51926 (12391) hydrogen bonds : bond 0.04256 ( 574) hydrogen bonds : angle 4.28004 ( 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 157 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 535 MET cc_start: 0.6434 (ttt) cc_final: 0.6064 (mmm) REVERT: A 580 ASN cc_start: 0.7138 (m110) cc_final: 0.6697 (m110) REVERT: A 772 PHE cc_start: 0.7482 (t80) cc_final: 0.7158 (t80) REVERT: B 500 ASP cc_start: 0.5400 (t0) cc_final: 0.5072 (t0) REVERT: B 568 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7356 (mp) REVERT: B 580 ASN cc_start: 0.7101 (m110) cc_final: 0.6687 (m110) REVERT: B 772 PHE cc_start: 0.7452 (t80) cc_final: 0.7136 (t80) REVERT: B 864 PHE cc_start: 0.7391 (t80) cc_final: 0.7145 (t80) outliers start: 21 outliers final: 11 residues processed: 154 average time/residue: 0.0761 time to fit residues: 17.7989 Evaluate side-chains 134 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 865 TYR Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain B residue 449 MET 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 865 TYR 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: 1.9990 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 27 optimal weight: 0.0370 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.223502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.184781 restraints weight = 9906.641| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 2.47 r_work: 0.4023 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.3264 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= 0.118 Angle : 0.488 6.676 12391 Z= 0.267 Chirality : 0.040 0.180 1455 Planarity : 0.003 0.040 1516 Dihedral : 12.870 89.566 1452 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.93 % Favored : 96.90 % Rotamer: Outliers : 2.07 % Allowed : 16.69 % Favored : 81.24 % 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 aren not related in a simple way. whole: 0.61 (0.24), residues: 1162 helix: 1.40 (0.20), residues: 688 sheet: -1.10 (0.40), residues: 146 loop : -0.88 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 777 TYR 0.018 0.001 TYR A 455 PHE 0.031 0.001 PHE A 942 TRP 0.009 0.001 TRP A 490 HIS 0.002 0.001 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9104) covalent geometry : angle 0.48790 (12391) hydrogen bonds : bond 0.03698 ( 574) hydrogen bonds : angle 3.99721 ( 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 152 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 535 MET cc_start: 0.6191 (ttt) cc_final: 0.5939 (mmm) REVERT: A 580 ASN cc_start: 0.7256 (m110) cc_final: 0.6773 (m110) REVERT: A 772 PHE cc_start: 0.7466 (t80) cc_final: 0.7170 (t80) REVERT: B 500 ASP cc_start: 0.5721 (t0) cc_final: 0.5309 (t0) REVERT: B 580 ASN cc_start: 0.7329 (m110) cc_final: 0.6861 (m110) REVERT: B 772 PHE cc_start: 0.7504 (t80) cc_final: 0.7092 (t80) REVERT: B 864 PHE cc_start: 0.7438 (t80) cc_final: 0.7190 (t80) REVERT: B 938 MET cc_start: 0.6515 (ttm) cc_final: 0.6226 (tpp) outliers start: 17 outliers final: 6 residues processed: 148 average time/residue: 0.0841 time to fit residues: 18.2763 Evaluate side-chains 126 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 835 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 78 optimal weight: 0.4980 chunk 23 optimal weight: 0.0060 chunk 73 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.224626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.181970 restraints weight = 9912.813| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 3.78 r_work: 0.3974 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.3603 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= 0.109 Angle : 0.470 6.396 12391 Z= 0.255 Chirality : 0.039 0.170 1455 Planarity : 0.003 0.039 1516 Dihedral : 11.730 85.887 1452 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.75 % Favored : 97.07 % Rotamer: Outliers : 2.68 % Allowed : 15.83 % 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 aren not related in a simple way. whole: 0.91 (0.25), residues: 1162 helix: 1.57 (0.20), residues: 694 sheet: -0.82 (0.41), residues: 146 loop : -0.72 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 777 TYR 0.012 0.001 TYR A 952 PHE 0.017 0.001 PHE A 942 TRP 0.010 0.001 TRP B 490 HIS 0.002 0.000 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 9104) covalent geometry : angle 0.46956 (12391) hydrogen bonds : bond 0.03485 ( 574) hydrogen bonds : angle 3.84105 ( 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 150 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 MET cc_start: 0.7196 (ttm) cc_final: 0.6822 (ttp) REVERT: A 535 MET cc_start: 0.6005 (ttt) cc_final: 0.5356 (mmm) REVERT: A 580 ASN cc_start: 0.7388 (m110) cc_final: 0.6860 (m110) REVERT: A 772 PHE cc_start: 0.7460 (t80) cc_final: 0.7215 (t80) REVERT: B 500 ASP cc_start: 0.5659 (t0) cc_final: 0.5179 (t0) REVERT: B 535 MET cc_start: 0.6062 (ttt) cc_final: 0.5416 (mmm) REVERT: B 565 ILE cc_start: 0.5559 (mm) cc_final: 0.5351 (mm) REVERT: B 580 ASN cc_start: 0.7430 (m110) cc_final: 0.6905 (m110) REVERT: B 772 PHE cc_start: 0.7443 (t80) cc_final: 0.7111 (t80) REVERT: B 1120 MET cc_start: 0.7134 (mmt) cc_final: 0.6831 (mmm) outliers start: 22 outliers final: 11 residues processed: 147 average time/residue: 0.0824 time to fit residues: 18.0545 Evaluate side-chains 129 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 802 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 426 ASN Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 518 CYS Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 835 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 109 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.221629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.179018 restraints weight = 9927.084| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 3.80 r_work: 0.3921 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.3756 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= 0.133 Angle : 0.505 6.190 12391 Z= 0.271 Chirality : 0.040 0.161 1455 Planarity : 0.003 0.030 1516 Dihedral : 10.627 87.104 1452 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.10 % Favored : 96.73 % Rotamer: Outliers : 3.65 % Allowed : 16.20 % Favored : 80.15 % 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 aren not related in a simple way. whole: 0.70 (0.24), residues: 1162 helix: 1.41 (0.20), residues: 688 sheet: -0.87 (0.41), residues: 146 loop : -0.81 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 777 TYR 0.019 0.001 TYR B 455 PHE 0.016 0.002 PHE B1052 TRP 0.011 0.001 TRP B 490 HIS 0.003 0.001 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9104) covalent geometry : angle 0.50500 (12391) hydrogen bonds : bond 0.03877 ( 574) hydrogen bonds : angle 3.93050 ( 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 154 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.353 Fit side-chains REVERT: A 449 MET cc_start: 0.7290 (ttm) cc_final: 0.7005 (ttp) REVERT: A 500 ASP cc_start: 0.5513 (t0) cc_final: 0.5017 (t0) REVERT: A 535 MET cc_start: 0.6269 (ttt) cc_final: 0.5491 (mmm) REVERT: A 580 ASN cc_start: 0.7192 (m110) cc_final: 0.6553 (m110) REVERT: A 772 PHE cc_start: 0.7535 (t80) cc_final: 0.7249 (t80) REVERT: A 1070 MET cc_start: 0.6171 (mtt) cc_final: 0.5810 (mtt) REVERT: B 500 ASP cc_start: 0.5631 (t0) cc_final: 0.5068 (t0) REVERT: B 752 GLU cc_start: 0.5693 (pm20) cc_final: 0.5435 (pm20) REVERT: B 772 PHE cc_start: 0.7514 (t80) cc_final: 0.7199 (t80) REVERT: B 864 PHE cc_start: 0.7446 (t80) cc_final: 0.7151 (t80) REVERT: B 1070 MET cc_start: 0.6430 (mtt) cc_final: 0.6120 (mtt) REVERT: B 1120 MET cc_start: 0.7022 (mmt) cc_final: 0.6395 (mmt) outliers start: 30 outliers final: 21 residues processed: 143 average time/residue: 0.0840 time to fit residues: 17.6933 Evaluate side-chains 131 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 518 CYS 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 518 CYS Chi-restraints excluded: chain B residue 567 LEU 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 951 SER 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: 0.9990 chunk 91 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 53 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.217996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.178626 restraints weight = 9985.218| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 2.47 r_work: 0.3952 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9104 Z= 0.171 Angle : 0.548 6.287 12391 Z= 0.295 Chirality : 0.042 0.145 1455 Planarity : 0.003 0.026 1516 Dihedral : 10.152 83.923 1452 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.58 % Favored : 97.25 % Rotamer: Outliers : 3.53 % Allowed : 16.93 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.24), residues: 1162 helix: 1.17 (0.20), residues: 686 sheet: -0.86 (0.41), residues: 146 loop : -0.85 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 682 TYR 0.018 0.001 TYR A 455 PHE 0.020 0.002 PHE A1052 TRP 0.012 0.001 TRP B 806 HIS 0.003 0.001 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 9104) covalent geometry : angle 0.54790 (12391) hydrogen bonds : bond 0.04311 ( 574) hydrogen bonds : angle 4.14243 ( 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 149 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.346 Fit side-chains REVERT: A 449 MET cc_start: 0.7424 (ttm) cc_final: 0.7095 (ttp) REVERT: A 500 ASP cc_start: 0.5803 (t0) cc_final: 0.5438 (t0) REVERT: A 565 ILE cc_start: 0.6114 (mm) cc_final: 0.5870 (mm) REVERT: A 772 PHE cc_start: 0.7570 (t80) cc_final: 0.7262 (t80) REVERT: A 794 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6933 (tm-30) REVERT: A 864 PHE cc_start: 0.7512 (t80) cc_final: 0.7243 (t80) REVERT: A 1070 MET cc_start: 0.6366 (mtt) cc_final: 0.6051 (mtt) REVERT: B 500 ASP cc_start: 0.5749 (t0) cc_final: 0.5262 (t0) REVERT: B 772 PHE cc_start: 0.7569 (t80) cc_final: 0.7260 (t80) REVERT: B 864 PHE cc_start: 0.7537 (t80) cc_final: 0.7272 (t80) REVERT: B 1070 MET cc_start: 0.6544 (mtt) cc_final: 0.6253 (mtt) REVERT: B 1092 SER cc_start: 0.7833 (t) cc_final: 0.7549 (p) REVERT: B 1120 MET cc_start: 0.6907 (mmt) cc_final: 0.6538 (mmm) outliers start: 29 outliers final: 21 residues processed: 141 average time/residue: 0.0712 time to fit residues: 15.5250 Evaluate side-chains 135 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 518 CYS 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 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 518 CYS Chi-restraints excluded: chain B residue 567 LEU 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 951 SER Chi-restraints excluded: chain B residue 1066 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 0.0870 chunk 67 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.219818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.175372 restraints weight = 9851.820| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.50 r_work: 0.3983 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9104 Z= 0.140 Angle : 0.527 7.569 12391 Z= 0.281 Chirality : 0.041 0.147 1455 Planarity : 0.003 0.023 1516 Dihedral : 9.942 74.846 1452 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.27 % Favored : 96.56 % Rotamer: Outliers : 2.80 % Allowed : 18.51 % Favored : 78.68 % 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 aren not related in a simple way. whole: 0.44 (0.24), residues: 1162 helix: 1.18 (0.20), residues: 688 sheet: -0.81 (0.41), residues: 146 loop : -0.92 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 718 TYR 0.017 0.001 TYR B 455 PHE 0.014 0.001 PHE B1052 TRP 0.010 0.001 TRP B 806 HIS 0.002 0.001 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9104) covalent geometry : angle 0.52722 (12391) hydrogen bonds : bond 0.03977 ( 574) hydrogen bonds : angle 4.01347 ( 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 141 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.353 Fit side-chains REVERT: A 449 MET cc_start: 0.7485 (ttm) cc_final: 0.7136 (ttp) REVERT: A 500 ASP cc_start: 0.5703 (t0) cc_final: 0.5349 (t0) REVERT: A 565 ILE cc_start: 0.5990 (mm) cc_final: 0.5755 (mm) REVERT: A 772 PHE cc_start: 0.7477 (t80) cc_final: 0.7153 (t80) REVERT: A 794 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6950 (tm-30) REVERT: A 1070 MET cc_start: 0.6255 (mtt) cc_final: 0.5950 (mtt) REVERT: B 449 MET cc_start: 0.7393 (ttm) cc_final: 0.6941 (ttp) REVERT: B 500 ASP cc_start: 0.5591 (t0) cc_final: 0.5220 (t0) REVERT: B 772 PHE cc_start: 0.7462 (t80) cc_final: 0.7140 (t80) REVERT: B 1070 MET cc_start: 0.6427 (mtt) cc_final: 0.6142 (mtt) REVERT: B 1120 MET cc_start: 0.6754 (mmt) cc_final: 0.6410 (mmm) outliers start: 23 outliers final: 21 residues processed: 134 average time/residue: 0.0727 time to fit residues: 14.7314 Evaluate side-chains 135 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 518 CYS 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 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 518 CYS Chi-restraints excluded: chain B residue 567 LEU 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 951 SER Chi-restraints excluded: chain B residue 1066 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.220805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.176501 restraints weight = 9798.158| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.51 r_work: 0.3995 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6304 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9104 Z= 0.131 Angle : 0.524 7.951 12391 Z= 0.277 Chirality : 0.040 0.146 1455 Planarity : 0.003 0.023 1516 Dihedral : 9.894 70.166 1452 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.93 % Favored : 96.90 % Rotamer: Outliers : 2.92 % Allowed : 18.76 % 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 aren not related in a simple way. whole: 0.49 (0.24), residues: 1162 helix: 1.22 (0.20), residues: 688 sheet: -0.82 (0.41), residues: 146 loop : -0.90 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 682 TYR 0.016 0.001 TYR A 455 PHE 0.016 0.001 PHE A 619 TRP 0.010 0.001 TRP B 806 HIS 0.002 0.001 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9104) covalent geometry : angle 0.52391 (12391) hydrogen bonds : bond 0.03853 ( 574) hydrogen bonds : angle 3.95718 ( 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 139 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.206 Fit side-chains REVERT: A 449 MET cc_start: 0.7437 (ttm) cc_final: 0.7031 (ttp) REVERT: A 500 ASP cc_start: 0.5822 (t0) cc_final: 0.5537 (t0) REVERT: A 565 ILE cc_start: 0.5983 (mm) cc_final: 0.5746 (mm) REVERT: A 772 PHE cc_start: 0.7495 (t80) cc_final: 0.7139 (t80) REVERT: A 794 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6881 (tm-30) REVERT: A 1070 MET cc_start: 0.6297 (mtt) cc_final: 0.5983 (mtt) REVERT: B 449 MET cc_start: 0.7319 (ttm) cc_final: 0.6872 (ttp) REVERT: B 500 ASP cc_start: 0.5531 (t0) cc_final: 0.5167 (t0) REVERT: B 772 PHE cc_start: 0.7436 (t80) cc_final: 0.7095 (t80) REVERT: B 938 MET cc_start: 0.6287 (tpp) cc_final: 0.5846 (tpp) REVERT: B 1070 MET cc_start: 0.6412 (mtt) cc_final: 0.6110 (mtt) outliers start: 24 outliers final: 20 residues processed: 132 average time/residue: 0.0663 time to fit residues: 13.3597 Evaluate side-chains 129 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 542 THR 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 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 518 CYS Chi-restraints excluded: chain B residue 640 VAL 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 951 SER 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: 0.9980 chunk 11 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 0.0170 chunk 82 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.222829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.178623 restraints weight = 9851.352| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 2.52 r_work: 0.4019 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9104 Z= 0.115 Angle : 0.520 15.837 12391 Z= 0.270 Chirality : 0.039 0.147 1455 Planarity : 0.003 0.021 1516 Dihedral : 9.744 69.490 1452 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.67 % Favored : 97.16 % Rotamer: Outliers : 2.31 % Allowed : 19.49 % Favored : 78.20 % 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 aren not related in a simple way. whole: 0.64 (0.24), residues: 1162 helix: 1.37 (0.20), residues: 688 sheet: -0.71 (0.42), residues: 134 loop : -0.95 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 777 TYR 0.018 0.001 TYR B1067 PHE 0.021 0.001 PHE B 812 TRP 0.011 0.001 TRP A1047 HIS 0.002 0.001 HIS A 783 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9104) covalent geometry : angle 0.52047 (12391) hydrogen bonds : bond 0.03616 ( 574) hydrogen bonds : angle 3.85095 ( 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: 19 poor density : 113 time to evaluate : 0.339 Fit side-chains REVERT: A 449 MET cc_start: 0.7400 (ttm) cc_final: 0.6825 (ttp) REVERT: A 500 ASP cc_start: 0.5614 (t0) cc_final: 0.5399 (t0) REVERT: A 772 PHE cc_start: 0.7451 (t80) cc_final: 0.7153 (t80) REVERT: A 794 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6893 (tm-30) REVERT: A 1070 MET cc_start: 0.6217 (mtt) cc_final: 0.5885 (mtt) REVERT: B 449 MET cc_start: 0.7277 (ttm) cc_final: 0.6885 (ttp) REVERT: B 500 ASP cc_start: 0.5387 (t0) cc_final: 0.5132 (t0) REVERT: B 772 PHE cc_start: 0.7436 (t80) cc_final: 0.7110 (t80) REVERT: B 938 MET cc_start: 0.6460 (tpp) cc_final: 0.6035 (tpp) REVERT: B 1070 MET cc_start: 0.6366 (mtt) cc_final: 0.6052 (mtt) REVERT: B 1120 MET cc_start: 0.6935 (mmt) cc_final: 0.6461 (mmt) outliers start: 19 outliers final: 16 residues processed: 124 average time/residue: 0.0718 time to fit residues: 13.9274 Evaluate side-chains 127 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 542 THR 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 1066 ASP Chi-restraints excluded: chain B residue 426 ASN Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 518 CYS 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: 0.9980 chunk 107 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 60 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN A 582 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.223278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.179519 restraints weight = 9773.132| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 2.50 r_work: 0.4029 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9104 Z= 0.113 Angle : 0.519 15.501 12391 Z= 0.268 Chirality : 0.039 0.149 1455 Planarity : 0.002 0.022 1516 Dihedral : 9.670 69.087 1452 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.84 % Favored : 96.99 % Rotamer: Outliers : 2.56 % Allowed : 19.73 % Favored : 77.71 % 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 aren not related in a simple way. whole: 0.71 (0.24), residues: 1162 helix: 1.45 (0.20), residues: 688 sheet: -0.62 (0.41), residues: 140 loop : -1.02 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 718 TYR 0.017 0.001 TYR A1067 PHE 0.029 0.001 PHE B 812 TRP 0.008 0.001 TRP A1047 HIS 0.002 0.001 HIS A 783 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9104) covalent geometry : angle 0.51923 (12391) hydrogen bonds : bond 0.03560 ( 574) hydrogen bonds : angle 3.80381 ( 1806) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2088.44 seconds wall clock time: 36 minutes 33.99 seconds (2193.99 seconds total)