Starting phenix.real_space_refine on Wed Apr 30 08:53:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3u_36861/04_2025/8k3u_36861.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3u_36861/04_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_36861/04_2025/8k3u_36861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3u_36861/04_2025/8k3u_36861.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3u_36861/04_2025/8k3u_36861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3u_36861/04_2025/8k3u_36861.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 7, 'GLU:plan': 13, 'ARG:plan': 12} 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: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 8, 'GLU:plan': 13, 'ARG:plan': 12} 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: 5.89, per 1000 atoms: 0.66 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: 2.44 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.11 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: 2.96 Time building geometry restraints manager: 2.83 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: 0.460 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.450 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.720 ------------------------------------------------------------------------------- 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 : 18.03 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (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 TRP 0.012 0.001 TRP B 616 HIS 0.002 0.001 HIS B 783 PHE 0.021 0.002 PHE A 812 TYR 0.027 0.002 TYR A 865 ARG 0.008 0.001 ARG B 682 Details of bonding type rmsd hydrogen bonds : bond 0.16137 ( 574) hydrogen bonds : angle 7.35710 ( 1806) covalent geometry : bond 0.00850 ( 9104) covalent geometry : angle 1.06549 (12391) *********************** 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 : 1.002 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: 0.2955 time to fit residues: 73.5755 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 : 1.287 ------------------------------------------------------------------------------- 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 99 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.4543 r_free = 0.4543 target = 0.222948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.185488 restraints weight = 9829.443| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 2.28 r_work: 0.3965 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9104 Z= 0.189 Angle : 0.607 6.551 12391 Z= 0.332 Chirality : 0.043 0.206 1455 Planarity : 0.004 0.058 1516 Dihedral : 14.070 98.662 1456 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.53 % Favored : 96.30 % Rotamer: Outliers : 2.07 % Allowed : 9.50 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.23), residues: 1162 helix: 0.25 (0.19), residues: 712 sheet: -1.45 (0.39), residues: 152 loop : -1.39 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 490 HIS 0.002 0.001 HIS A 582 PHE 0.020 0.002 PHE A 812 TYR 0.017 0.002 TYR B 455 ARG 0.005 0.001 ARG A 682 Details of bonding type rmsd hydrogen bonds : bond 0.05370 ( 574) hydrogen bonds : angle 4.96115 ( 1806) covalent geometry : bond 0.00428 ( 9104) covalent geometry : angle 0.60716 (12391) *********************** 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: 17 poor density : 143 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 476 MET cc_start: 0.7485 (mmm) cc_final: 0.7129 (mmt) REVERT: A 567 LEU cc_start: 0.7264 (mt) cc_final: 0.7051 (mt) REVERT: A 568 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7227 (mp) REVERT: A 580 ASN cc_start: 0.7316 (m110) cc_final: 0.6999 (m110) REVERT: A 772 PHE cc_start: 0.7514 (t80) cc_final: 0.7258 (t80) REVERT: A 1070 MET cc_start: 0.6053 (mtt) cc_final: 0.5677 (mtt) REVERT: A 1121 ILE cc_start: 0.7635 (mm) cc_final: 0.7406 (mm) REVERT: B 476 MET cc_start: 0.7606 (mmm) cc_final: 0.7218 (mmt) REVERT: B 500 ASP cc_start: 0.5886 (t0) cc_final: 0.5543 (t0) REVERT: B 519 TYR cc_start: 0.4976 (t80) cc_final: 0.4704 (t80) REVERT: B 580 ASN cc_start: 0.7460 (m110) cc_final: 0.7150 (m110) REVERT: B 665 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6930 (mt-10) REVERT: B 752 GLU cc_start: 0.6166 (pm20) cc_final: 0.5918 (pm20) REVERT: B 772 PHE cc_start: 0.7513 (t80) cc_final: 0.7229 (t80) REVERT: B 1070 MET cc_start: 0.6353 (mtt) cc_final: 0.6007 (mtt) REVERT: B 1121 ILE cc_start: 0.7690 (mm) cc_final: 0.7463 (mm) outliers start: 17 outliers final: 10 residues processed: 158 average time/residue: 0.1933 time to fit residues: 45.0987 Evaluate side-chains 136 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 946 ILE 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 62 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 68 optimal weight: 0.0770 chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.224902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.187407 restraints weight = 9861.112| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 2.30 r_work: 0.4049 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.2831 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= 0.143 Angle : 0.513 5.958 12391 Z= 0.281 Chirality : 0.041 0.177 1455 Planarity : 0.003 0.039 1516 Dihedral : 13.404 90.757 1456 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.18 % Favored : 96.64 % Rotamer: Outliers : 3.05 % Allowed : 13.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.24), residues: 1162 helix: 1.03 (0.20), residues: 686 sheet: -1.26 (0.39), residues: 152 loop : -1.14 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 490 HIS 0.003 0.001 HIS A 536 PHE 0.015 0.002 PHE A 812 TYR 0.016 0.001 TYR A 842 ARG 0.004 0.000 ARG A 682 Details of bonding type rmsd hydrogen bonds : bond 0.04248 ( 574) hydrogen bonds : angle 4.30026 ( 1806) covalent geometry : bond 0.00319 ( 9104) covalent geometry : angle 0.51277 (12391) *********************** 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 162 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 476 MET cc_start: 0.7591 (mmm) cc_final: 0.7297 (mmt) REVERT: A 500 ASP cc_start: 0.5958 (t0) cc_final: 0.5743 (t0) REVERT: A 580 ASN cc_start: 0.7178 (m110) cc_final: 0.6701 (m110) REVERT: A 748 GLU cc_start: 0.4070 (pm20) cc_final: 0.3840 (mt-10) REVERT: A 772 PHE cc_start: 0.7495 (t80) cc_final: 0.7197 (t80) REVERT: A 938 MET cc_start: 0.6129 (ttm) cc_final: 0.5748 (tpp) REVERT: B 476 MET cc_start: 0.7613 (mmm) cc_final: 0.7316 (mmt) REVERT: B 500 ASP cc_start: 0.5634 (t0) cc_final: 0.5311 (t0) REVERT: B 580 ASN cc_start: 0.7115 (m110) cc_final: 0.6695 (m110) REVERT: B 752 GLU cc_start: 0.5931 (OUTLIER) cc_final: 0.5602 (pm20) REVERT: B 772 PHE cc_start: 0.7447 (t80) cc_final: 0.7157 (t80) REVERT: B 864 PHE cc_start: 0.7319 (t80) cc_final: 0.7100 (t80) REVERT: B 938 MET cc_start: 0.6717 (ttm) cc_final: 0.6356 (tpp) outliers start: 25 outliers final: 11 residues processed: 156 average time/residue: 0.1589 time to fit residues: 37.3422 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 : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1117 SER Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 499 SER 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 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 96 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.0070 chunk 15 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 70 optimal weight: 30.0000 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.4539 r_free = 0.4539 target = 0.222924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.184632 restraints weight = 9848.900| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.42 r_work: 0.4026 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9104 Z= 0.115 Angle : 0.480 6.634 12391 Z= 0.263 Chirality : 0.039 0.181 1455 Planarity : 0.003 0.031 1516 Dihedral : 12.577 85.631 1452 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.18 % Favored : 96.64 % Rotamer: Outliers : 2.19 % Allowed : 14.98 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.24), residues: 1162 helix: 1.40 (0.20), residues: 688 sheet: -1.04 (0.40), residues: 152 loop : -1.06 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1047 HIS 0.003 0.001 HIS A 536 PHE 0.032 0.001 PHE A 942 TYR 0.018 0.001 TYR A 455 ARG 0.003 0.000 ARG B 718 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 574) hydrogen bonds : angle 3.98270 ( 1806) covalent geometry : bond 0.00249 ( 9104) covalent geometry : angle 0.47963 (12391) *********************** 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 153 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 449 MET cc_start: 0.7402 (ttm) cc_final: 0.6880 (ttp) REVERT: A 476 MET cc_start: 0.7603 (mmm) cc_final: 0.7270 (mmt) REVERT: A 500 ASP cc_start: 0.6014 (t0) cc_final: 0.5641 (t0) REVERT: A 580 ASN cc_start: 0.7199 (m110) cc_final: 0.6593 (m110) REVERT: A 748 GLU cc_start: 0.4283 (pm20) cc_final: 0.3390 (tp30) REVERT: A 772 PHE cc_start: 0.7435 (t80) cc_final: 0.7110 (t80) REVERT: A 879 MET cc_start: 0.7517 (mtp) cc_final: 0.7293 (mtp) REVERT: A 938 MET cc_start: 0.6515 (ttm) cc_final: 0.5868 (tpp) REVERT: B 476 MET cc_start: 0.7610 (mmm) cc_final: 0.7285 (mmt) REVERT: B 500 ASP cc_start: 0.5781 (t0) cc_final: 0.5426 (t0) REVERT: B 580 ASN cc_start: 0.7341 (m110) cc_final: 0.6871 (m110) REVERT: B 772 PHE cc_start: 0.7394 (t80) cc_final: 0.7045 (t80) REVERT: B 938 MET cc_start: 0.6527 (ttm) cc_final: 0.6265 (tpp) outliers start: 18 outliers final: 10 residues processed: 150 average time/residue: 0.1678 time to fit residues: 37.3977 Evaluate side-chains 129 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 535 MET 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 640 VAL Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 865 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 80 optimal weight: 2.9990 chunk 100 optimal weight: 0.1980 chunk 117 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4506 r_free = 0.4506 target = 0.218789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.174570 restraints weight = 9796.136| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 2.48 r_work: 0.3975 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.3534 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= 0.151 Angle : 0.521 6.369 12391 Z= 0.282 Chirality : 0.041 0.161 1455 Planarity : 0.003 0.045 1516 Dihedral : 12.543 89.830 1452 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.18 % Favored : 96.64 % Rotamer: Outliers : 3.90 % Allowed : 13.64 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1162 helix: 1.33 (0.20), residues: 686 sheet: -0.88 (0.41), residues: 152 loop : -1.12 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 490 HIS 0.002 0.001 HIS B 965 PHE 0.020 0.002 PHE B 813 TYR 0.013 0.001 TYR B 681 ARG 0.003 0.000 ARG B 777 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 574) hydrogen bonds : angle 4.10924 ( 1806) covalent geometry : bond 0.00345 ( 9104) covalent geometry : angle 0.52120 (12391) *********************** 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 162 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.967 Fit side-chains REVERT: A 449 MET cc_start: 0.7608 (ttm) cc_final: 0.7249 (ttp) REVERT: A 500 ASP cc_start: 0.5867 (t0) cc_final: 0.5604 (t0) REVERT: A 580 ASN cc_start: 0.7110 (m110) cc_final: 0.6506 (m110) REVERT: A 748 GLU cc_start: 0.4137 (pm20) cc_final: 0.3273 (tp30) REVERT: A 772 PHE cc_start: 0.7546 (t80) cc_final: 0.7259 (t80) REVERT: A 794 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6257 (tm-30) REVERT: A 938 MET cc_start: 0.6362 (ttm) cc_final: 0.6038 (tpp) REVERT: A 1070 MET cc_start: 0.6269 (mtt) cc_final: 0.5961 (mtt) REVERT: B 449 MET cc_start: 0.7350 (ttm) cc_final: 0.7040 (ttp) REVERT: B 500 ASP cc_start: 0.5830 (t0) cc_final: 0.5386 (t0) REVERT: B 580 ASN cc_start: 0.7132 (m110) cc_final: 0.6524 (m110) REVERT: B 752 GLU cc_start: 0.5961 (OUTLIER) cc_final: 0.5754 (pm20) REVERT: B 772 PHE cc_start: 0.7545 (t80) cc_final: 0.7261 (t80) REVERT: B 1120 MET cc_start: 0.7026 (mmt) cc_final: 0.6385 (mmt) outliers start: 32 outliers final: 16 residues processed: 153 average time/residue: 0.1759 time to fit residues: 39.6236 Evaluate side-chains 137 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 499 SER 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 640 VAL Chi-restraints excluded: chain B residue 656 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 96 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.4513 r_free = 0.4513 target = 0.219714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.175931 restraints weight = 9776.740| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 2.50 r_work: 0.3987 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9104 Z= 0.136 Angle : 0.504 6.333 12391 Z= 0.275 Chirality : 0.040 0.166 1455 Planarity : 0.003 0.025 1516 Dihedral : 11.802 84.486 1452 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.01 % Favored : 96.82 % Rotamer: Outliers : 2.92 % Allowed : 16.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1162 helix: 1.32 (0.20), residues: 688 sheet: -0.79 (0.41), residues: 152 loop : -1.10 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1047 HIS 0.003 0.001 HIS A 536 PHE 0.018 0.001 PHE B 813 TYR 0.018 0.001 TYR A 455 ARG 0.002 0.000 ARG B 682 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 574) hydrogen bonds : angle 4.00434 ( 1806) covalent geometry : bond 0.00307 ( 9104) covalent geometry : angle 0.50353 (12391) *********************** 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 152 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.947 Fit side-chains REVERT: A 449 MET cc_start: 0.7612 (ttm) cc_final: 0.7115 (ttp) REVERT: A 500 ASP cc_start: 0.5835 (t0) cc_final: 0.5507 (t0) REVERT: A 580 ASN cc_start: 0.7186 (m110) cc_final: 0.6540 (m110) REVERT: A 748 GLU cc_start: 0.4205 (pm20) cc_final: 0.3457 (tp30) REVERT: A 772 PHE cc_start: 0.7503 (t80) cc_final: 0.7181 (t80) REVERT: A 794 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6266 (tm-30) REVERT: A 875 MET cc_start: 0.6317 (mtp) cc_final: 0.6027 (mtm) REVERT: A 1070 MET cc_start: 0.6268 (mtt) cc_final: 0.5965 (mtt) REVERT: B 449 MET cc_start: 0.7474 (ttm) cc_final: 0.7017 (ttp) REVERT: B 500 ASP cc_start: 0.5776 (t0) cc_final: 0.5430 (t0) REVERT: B 535 MET cc_start: 0.4670 (mmm) cc_final: 0.4238 (mmm) REVERT: B 772 PHE cc_start: 0.7496 (t80) cc_final: 0.7181 (t80) REVERT: B 1070 MET cc_start: 0.6459 (mtt) cc_final: 0.6126 (mtt) REVERT: B 1120 MET cc_start: 0.6896 (mmt) cc_final: 0.6543 (mmm) outliers start: 24 outliers final: 16 residues processed: 142 average time/residue: 0.1714 time to fit residues: 36.0057 Evaluate side-chains 134 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 567 LEU 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.221808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.178067 restraints weight = 9872.090| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 2.51 r_work: 0.4012 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9104 Z= 0.118 Angle : 0.487 6.594 12391 Z= 0.263 Chirality : 0.039 0.159 1455 Planarity : 0.003 0.025 1516 Dihedral : 10.536 77.130 1452 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.75 % Favored : 97.07 % Rotamer: Outliers : 2.31 % Allowed : 17.78 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.24), residues: 1162 helix: 1.40 (0.20), residues: 692 sheet: -0.70 (0.41), residues: 152 loop : -0.97 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1047 HIS 0.003 0.001 HIS A 536 PHE 0.014 0.001 PHE B 813 TYR 0.012 0.001 TYR A 681 ARG 0.002 0.000 ARG B1040 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 574) hydrogen bonds : angle 3.86290 ( 1806) covalent geometry : bond 0.00257 ( 9104) covalent geometry : angle 0.48708 (12391) *********************** 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 144 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.880 Fit side-chains REVERT: A 476 MET cc_start: 0.7146 (mmt) cc_final: 0.6684 (mmt) REVERT: A 748 GLU cc_start: 0.4212 (pm20) cc_final: 0.3480 (tp30) REVERT: A 772 PHE cc_start: 0.7435 (t80) cc_final: 0.7103 (t80) REVERT: A 875 MET cc_start: 0.6295 (mtp) cc_final: 0.6054 (mtm) REVERT: A 1070 MET cc_start: 0.6218 (mtt) cc_final: 0.5885 (mtt) REVERT: B 476 MET cc_start: 0.7206 (mmt) cc_final: 0.6778 (mmt) REVERT: B 535 MET cc_start: 0.4867 (mmm) cc_final: 0.4427 (mmm) REVERT: B 772 PHE cc_start: 0.7394 (t80) cc_final: 0.7024 (t80) REVERT: B 938 MET cc_start: 0.6271 (tpp) cc_final: 0.5858 (tpp) REVERT: B 1120 MET cc_start: 0.6949 (mmt) cc_final: 0.6621 (mmm) outliers start: 19 outliers final: 14 residues processed: 138 average time/residue: 0.1564 time to fit residues: 32.6468 Evaluate side-chains 130 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 567 LEU 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 1066 ASP Chi-restraints excluded: chain B residue 426 ASN 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 865 TYR 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 75 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 8 optimal weight: 0.0870 chunk 17 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.223266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.179489 restraints weight = 9943.766| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 2.51 r_work: 0.4027 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.4186 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= 0.110 Angle : 0.491 7.351 12391 Z= 0.260 Chirality : 0.039 0.154 1455 Planarity : 0.003 0.025 1516 Dihedral : 9.775 83.373 1452 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.67 % Favored : 97.16 % Rotamer: Outliers : 2.07 % Allowed : 18.76 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.25), residues: 1162 helix: 1.49 (0.20), residues: 692 sheet: -0.65 (0.41), residues: 152 loop : -0.93 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1047 HIS 0.003 0.001 HIS A 536 PHE 0.017 0.001 PHE B 812 TYR 0.021 0.001 TYR A 455 ARG 0.002 0.000 ARG A 718 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 574) hydrogen bonds : angle 3.79495 ( 1806) covalent geometry : bond 0.00240 ( 9104) covalent geometry : angle 0.49140 (12391) *********************** 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 144 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.894 Fit side-chains REVERT: A 449 MET cc_start: 0.7469 (ttm) cc_final: 0.6909 (ttp) REVERT: A 476 MET cc_start: 0.7114 (mmt) cc_final: 0.6895 (mmt) REVERT: A 500 ASP cc_start: 0.5895 (t0) cc_final: 0.5548 (t0) REVERT: A 748 GLU cc_start: 0.4184 (pm20) cc_final: 0.3384 (tp30) REVERT: A 772 PHE cc_start: 0.7400 (t80) cc_final: 0.7110 (t80) REVERT: A 794 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6258 (tm-30) REVERT: A 1070 MET cc_start: 0.6209 (mtt) cc_final: 0.5878 (mtt) REVERT: B 449 MET cc_start: 0.7357 (ttm) cc_final: 0.6890 (ttp) REVERT: B 476 MET cc_start: 0.7131 (mmt) cc_final: 0.6930 (mmt) REVERT: B 500 ASP cc_start: 0.6029 (t0) cc_final: 0.5679 (t0) REVERT: B 535 MET cc_start: 0.4932 (mmm) cc_final: 0.4473 (mmm) REVERT: B 772 PHE cc_start: 0.7393 (t80) cc_final: 0.7039 (t80) REVERT: B 938 MET cc_start: 0.6228 (tpp) cc_final: 0.5815 (tpp) outliers start: 17 outliers final: 14 residues processed: 139 average time/residue: 0.1632 time to fit residues: 34.2646 Evaluate side-chains 132 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 567 LEU 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 640 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 865 TYR Chi-restraints excluded: chain B residue 948 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 43 optimal weight: 0.7980 chunk 59 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.221387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.182367 restraints weight = 9936.833| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 2.54 r_work: 0.3996 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.4247 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= 0.133 Angle : 0.538 14.562 12391 Z= 0.279 Chirality : 0.040 0.149 1455 Planarity : 0.003 0.024 1516 Dihedral : 9.780 74.822 1452 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.84 % Favored : 96.99 % Rotamer: Outliers : 2.31 % Allowed : 18.88 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.24), residues: 1162 helix: 1.39 (0.20), residues: 690 sheet: -0.67 (0.40), residues: 152 loop : -0.95 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 806 HIS 0.003 0.001 HIS A 536 PHE 0.022 0.002 PHE B 812 TYR 0.020 0.001 TYR B 842 ARG 0.002 0.000 ARG B 718 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 574) hydrogen bonds : angle 3.87926 ( 1806) covalent geometry : bond 0.00300 ( 9104) covalent geometry : angle 0.53785 (12391) *********************** 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 141 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 1.010 Fit side-chains REVERT: A 449 MET cc_start: 0.7532 (ttm) cc_final: 0.6981 (ttp) REVERT: A 476 MET cc_start: 0.7217 (mmt) cc_final: 0.6979 (mmt) REVERT: A 500 ASP cc_start: 0.5920 (t0) cc_final: 0.5515 (t0) REVERT: A 748 GLU cc_start: 0.4131 (pm20) cc_final: 0.3389 (tp30) REVERT: A 772 PHE cc_start: 0.7483 (t80) cc_final: 0.7183 (t80) REVERT: A 794 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6263 (tm-30) REVERT: A 1070 MET cc_start: 0.6310 (mtt) cc_final: 0.6005 (mtt) REVERT: B 449 MET cc_start: 0.7439 (ttm) cc_final: 0.6904 (ttp) REVERT: B 476 MET cc_start: 0.7227 (mmt) cc_final: 0.6863 (mmt) REVERT: B 500 ASP cc_start: 0.5862 (t0) cc_final: 0.5465 (t0) REVERT: B 535 MET cc_start: 0.5048 (mmm) cc_final: 0.4597 (mmm) REVERT: B 772 PHE cc_start: 0.7435 (t80) cc_final: 0.7116 (t80) REVERT: B 842 TYR cc_start: 0.6218 (t80) cc_final: 0.6017 (t80) REVERT: B 938 MET cc_start: 0.6281 (tpp) cc_final: 0.5852 (tpp) REVERT: B 1070 MET cc_start: 0.6477 (mtt) cc_final: 0.6146 (mtt) REVERT: B 1120 MET cc_start: 0.6790 (mmt) cc_final: 0.6459 (mmm) outliers start: 19 outliers final: 16 residues processed: 134 average time/residue: 0.1745 time to fit residues: 35.3114 Evaluate side-chains 133 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 567 LEU 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 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 948 LEU 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 39 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 114 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4543 r_free = 0.4543 target = 0.223208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.179332 restraints weight = 9911.686| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 2.53 r_work: 0.4027 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.4358 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= 0.117 Angle : 0.532 15.630 12391 Z= 0.272 Chirality : 0.040 0.150 1455 Planarity : 0.003 0.024 1516 Dihedral : 9.638 71.552 1452 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.67 % Favored : 97.16 % Rotamer: Outliers : 1.95 % Allowed : 19.24 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.25), residues: 1162 helix: 1.45 (0.20), residues: 692 sheet: -0.60 (0.41), residues: 152 loop : -0.88 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A1047 HIS 0.002 0.001 HIS A 536 PHE 0.026 0.001 PHE B 812 TYR 0.017 0.001 TYR A 455 ARG 0.002 0.000 ARG A 718 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 574) hydrogen bonds : angle 3.80760 ( 1806) covalent geometry : bond 0.00258 ( 9104) covalent geometry : angle 0.53231 (12391) ********************** 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 134 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.870 Fit side-chains REVERT: A 449 MET cc_start: 0.7541 (ttm) cc_final: 0.7019 (ttp) REVERT: A 476 MET cc_start: 0.7153 (mmt) cc_final: 0.6934 (mmt) REVERT: A 500 ASP cc_start: 0.5837 (t0) cc_final: 0.5520 (t0) REVERT: A 748 GLU cc_start: 0.4130 (pm20) cc_final: 0.3345 (tp30) REVERT: A 772 PHE cc_start: 0.7444 (t80) cc_final: 0.7186 (t80) REVERT: A 794 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6284 (tm-30) REVERT: A 1070 MET cc_start: 0.6263 (mtt) cc_final: 0.5947 (mtt) REVERT: B 449 MET cc_start: 0.7433 (ttm) cc_final: 0.6973 (ttp) REVERT: B 476 MET cc_start: 0.7158 (mmt) cc_final: 0.6822 (mmt) REVERT: B 500 ASP cc_start: 0.5973 (t0) cc_final: 0.5614 (t0) REVERT: B 535 MET cc_start: 0.5007 (mmm) cc_final: 0.4566 (mmm) REVERT: B 772 PHE cc_start: 0.7443 (t80) cc_final: 0.7125 (t80) REVERT: B 876 MET cc_start: 0.5482 (mtp) cc_final: 0.5237 (mtp) REVERT: B 938 MET cc_start: 0.6456 (tpp) cc_final: 0.6032 (tpp) REVERT: B 1070 MET cc_start: 0.6378 (mtt) cc_final: 0.6050 (mtt) outliers start: 16 outliers final: 15 residues processed: 129 average time/residue: 0.1528 time to fit residues: 30.2236 Evaluate side-chains 131 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 567 LEU 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 640 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 865 TYR Chi-restraints excluded: chain B residue 948 LEU 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 83 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 47 optimal weight: 0.2980 chunk 32 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.4508 r_free = 0.4508 target = 0.219012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.177601 restraints weight = 9979.481| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 3.18 r_work: 0.3944 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9104 Z= 0.157 Angle : 0.586 15.899 12391 Z= 0.301 Chirality : 0.042 0.145 1455 Planarity : 0.003 0.022 1516 Dihedral : 9.873 69.120 1452 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.44 % Favored : 96.39 % Rotamer: Outliers : 2.31 % Allowed : 19.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1162 helix: 1.24 (0.20), residues: 690 sheet: -0.67 (0.40), residues: 152 loop : -1.00 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A1047 HIS 0.002 0.001 HIS A 937 PHE 0.031 0.002 PHE B 812 TYR 0.013 0.001 TYR B 925 ARG 0.002 0.000 ARG A 682 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 574) hydrogen bonds : angle 4.01687 ( 1806) covalent geometry : bond 0.00361 ( 9104) covalent geometry : angle 0.58595 (12391) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4330.44 seconds wall clock time: 75 minutes 17.25 seconds (4517.25 seconds total)