Starting phenix.real_space_refine on Thu Feb 13 20:46:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3u_36861/02_2025/8k3u_36861.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3u_36861/02_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_36861/02_2025/8k3u_36861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3u_36861/02_2025/8k3u_36861.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3u_36861/02_2025/8k3u_36861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3u_36861/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.95, per 1000 atoms: 0.67 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: 2.38 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: 1.15 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: 3.33 Time building geometry restraints manager: 2.65 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.190 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.770 ------------------------------------------------------------------------------- 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= 0.564 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 *********************** 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 : 0.951 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: 0.2113 time to fit residues: 52.7778 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 : 0.983 ------------------------------------------------------------------------------- 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 = 0.222921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.185422 restraints weight = 9833.398| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 2.29 r_work: 0.3966 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 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= 0.285 Angle : 0.607 6.551 12391 Z= 0.332 Chirality : 0.043 0.206 1455 Planarity : 0.004 0.058 1516 Dihedral : 14.070 98.663 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 *********************** 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 : 0.975 Fit side-chains revert: symmetry clash REVERT: A 476 MET cc_start: 0.7488 (mmm) cc_final: 0.7130 (mmt) REVERT: A 567 LEU cc_start: 0.7275 (mt) cc_final: 0.7062 (mt) REVERT: A 568 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7234 (mp) REVERT: A 580 ASN cc_start: 0.7317 (m110) cc_final: 0.6999 (m110) REVERT: A 772 PHE cc_start: 0.7515 (t80) cc_final: 0.7258 (t80) REVERT: A 1070 MET cc_start: 0.6053 (mtt) cc_final: 0.5678 (mtt) REVERT: A 1121 ILE cc_start: 0.7635 (mm) cc_final: 0.7405 (mm) REVERT: B 476 MET cc_start: 0.7607 (mmm) cc_final: 0.7220 (mmt) REVERT: B 500 ASP cc_start: 0.5897 (t0) cc_final: 0.5558 (t0) REVERT: B 519 TYR cc_start: 0.4989 (t80) cc_final: 0.4718 (t80) REVERT: B 580 ASN cc_start: 0.7462 (m110) cc_final: 0.7152 (m110) REVERT: B 665 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6935 (mt-10) REVERT: B 752 GLU cc_start: 0.6173 (pm20) cc_final: 0.5925 (pm20) REVERT: B 772 PHE cc_start: 0.7514 (t80) cc_final: 0.7229 (t80) REVERT: B 1070 MET cc_start: 0.6363 (mtt) cc_final: 0.6015 (mtt) REVERT: B 1121 ILE cc_start: 0.7693 (mm) cc_final: 0.7466 (mm) outliers start: 17 outliers final: 10 residues processed: 158 average time/residue: 0.1810 time to fit residues: 41.9100 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 : 0.956 ------------------------------------------------------------------------------- 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: 0.0980 chunk 2 optimal weight: 0.0060 chunk 56 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- 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 = 0.4556 r_free = 0.4556 target = 0.224432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.186847 restraints weight = 9860.526| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 2.30 r_work: 0.4040 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9104 Z= 0.213 Angle : 0.519 5.959 12391 Z= 0.284 Chirality : 0.041 0.177 1455 Planarity : 0.003 0.039 1516 Dihedral : 13.454 91.658 1456 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.53 % Favored : 96.30 % Rotamer: Outliers : 2.68 % Allowed : 13.52 % 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: 0.08 (0.24), residues: 1162 helix: 0.99 (0.20), residues: 686 sheet: -1.31 (0.38), residues: 152 loop : -1.14 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 490 HIS 0.003 0.001 HIS A 536 PHE 0.015 0.002 PHE B 812 TYR 0.015 0.001 TYR A 842 ARG 0.004 0.000 ARG B 682 *********************** 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: 22 poor density : 135 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 476 MET cc_start: 0.7595 (mmm) cc_final: 0.7294 (mmt) REVERT: A 500 ASP cc_start: 0.5987 (t0) cc_final: 0.5764 (t0) REVERT: A 580 ASN cc_start: 0.7175 (m110) cc_final: 0.6799 (m110) REVERT: A 748 GLU cc_start: 0.4096 (pm20) cc_final: 0.3166 (tp30) REVERT: A 752 GLU cc_start: 0.5891 (OUTLIER) cc_final: 0.5580 (pm20) REVERT: A 772 PHE cc_start: 0.7504 (t80) cc_final: 0.7206 (t80) REVERT: A 938 MET cc_start: 0.6156 (ttm) cc_final: 0.5785 (tpp) REVERT: A 1121 ILE cc_start: 0.7642 (mm) cc_final: 0.7441 (mm) REVERT: B 476 MET cc_start: 0.7614 (mmm) cc_final: 0.7309 (mmt) REVERT: B 500 ASP cc_start: 0.5613 (t0) cc_final: 0.5244 (t0) REVERT: B 568 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7314 (mp) REVERT: B 580 ASN cc_start: 0.7081 (m110) cc_final: 0.6717 (m110) REVERT: B 752 GLU cc_start: 0.5942 (OUTLIER) cc_final: 0.5616 (pm20) REVERT: B 772 PHE cc_start: 0.7487 (t80) cc_final: 0.7185 (t80) REVERT: B 938 MET cc_start: 0.6613 (ttm) cc_final: 0.6260 (tpp) outliers start: 22 outliers final: 8 residues processed: 151 average time/residue: 0.1731 time to fit residues: 39.1263 Evaluate side-chains 134 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 568 LEU 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: 0.9990 chunk 14 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 70 optimal weight: 30.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4569 r_free = 0.4569 target = 0.225852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.182403 restraints weight = 9833.691| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.39 r_work: 0.4056 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.3203 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= 0.183 Angle : 0.494 6.627 12391 Z= 0.271 Chirality : 0.040 0.175 1455 Planarity : 0.003 0.031 1516 Dihedral : 12.743 86.548 1452 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.27 % Favored : 96.56 % Rotamer: Outliers : 2.80 % Allowed : 14.37 % 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: 0.49 (0.24), residues: 1162 helix: 1.35 (0.20), residues: 686 sheet: -1.07 (0.40), residues: 152 loop : -1.07 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 490 HIS 0.003 0.001 HIS A 536 PHE 0.029 0.002 PHE A 942 TYR 0.015 0.001 TYR B 455 ARG 0.003 0.000 ARG B 718 *********************** 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 157 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 476 MET cc_start: 0.7611 (mmm) cc_final: 0.7250 (mmt) REVERT: A 500 ASP cc_start: 0.6052 (t0) cc_final: 0.5668 (t0) REVERT: A 580 ASN cc_start: 0.7138 (m110) cc_final: 0.6554 (m110) REVERT: A 748 GLU cc_start: 0.4205 (pm20) cc_final: 0.3332 (tp30) REVERT: A 772 PHE cc_start: 0.7460 (t80) cc_final: 0.7134 (t80) REVERT: A 879 MET cc_start: 0.7491 (mtp) cc_final: 0.7260 (mtp) REVERT: A 938 MET cc_start: 0.6511 (ttm) cc_final: 0.5846 (tpp) REVERT: A 1070 MET cc_start: 0.6023 (mtt) cc_final: 0.5647 (mtt) REVERT: B 476 MET cc_start: 0.7644 (mmm) cc_final: 0.7291 (mmt) REVERT: B 500 ASP cc_start: 0.5783 (t0) cc_final: 0.5496 (t0) REVERT: B 580 ASN cc_start: 0.7136 (m110) cc_final: 0.6688 (m110) REVERT: B 772 PHE cc_start: 0.7416 (t80) cc_final: 0.7099 (t80) REVERT: B 938 MET cc_start: 0.6541 (ttm) cc_final: 0.6261 (tpp) REVERT: B 1120 MET cc_start: 0.7179 (mmt) cc_final: 0.6588 (mmt) outliers start: 23 outliers final: 13 residues processed: 152 average time/residue: 0.1649 time to fit residues: 37.1560 Evaluate side-chains 136 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain A residue 1117 SER 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 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: 1.9990 chunk 100 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4533 r_free = 0.4533 target = 0.222011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.177797 restraints weight = 9780.053| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 2.48 r_work: 0.4016 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 moved from start: 0.3540 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= 0.170 Angle : 0.482 6.495 12391 Z= 0.262 Chirality : 0.039 0.168 1455 Planarity : 0.003 0.046 1516 Dihedral : 12.148 89.961 1452 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.93 % Favored : 96.90 % Rotamer: Outliers : 3.41 % Allowed : 14.62 % Favored : 81.97 % 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: 0.69 (0.25), residues: 1162 helix: 1.47 (0.20), residues: 688 sheet: -0.86 (0.41), residues: 152 loop : -0.99 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 490 HIS 0.002 0.001 HIS A 536 PHE 0.018 0.001 PHE A 942 TYR 0.013 0.001 TYR A 681 ARG 0.004 0.000 ARG B 777 *********************** 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 159 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 449 MET cc_start: 0.7296 (ttm) cc_final: 0.6782 (ttp) REVERT: A 476 MET cc_start: 0.7608 (mmm) cc_final: 0.7214 (mmt) REVERT: A 580 ASN cc_start: 0.7165 (m110) cc_final: 0.6549 (m110) REVERT: A 748 GLU cc_start: 0.4330 (pm20) cc_final: 0.3462 (tp30) REVERT: A 772 PHE cc_start: 0.7452 (t80) cc_final: 0.7137 (t80) REVERT: A 794 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6269 (tm-30) REVERT: A 938 MET cc_start: 0.6349 (ttm) cc_final: 0.6047 (tpp) REVERT: A 1070 MET cc_start: 0.6033 (mtt) cc_final: 0.5655 (mtt) REVERT: A 1117 SER cc_start: 0.7995 (OUTLIER) cc_final: 0.7778 (p) REVERT: B 476 MET cc_start: 0.7612 (mmm) cc_final: 0.7229 (mmt) REVERT: B 500 ASP cc_start: 0.5639 (t0) cc_final: 0.5379 (t0) REVERT: B 580 ASN cc_start: 0.7188 (m110) cc_final: 0.6682 (m110) REVERT: B 772 PHE cc_start: 0.7410 (t80) cc_final: 0.7071 (t80) outliers start: 28 outliers final: 13 residues processed: 151 average time/residue: 0.1808 time to fit residues: 39.9541 Evaluate side-chains 136 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 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 A residue 1117 SER Chi-restraints excluded: chain B residue 426 ASN Chi-restraints excluded: chain B residue 454 MET Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 865 TYR Chi-restraints excluded: chain B residue 1066 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 96 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.4516 r_free = 0.4516 target = 0.219824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.175422 restraints weight = 9806.212| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 2.51 r_work: 0.3988 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.3747 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= 0.199 Angle : 0.501 6.349 12391 Z= 0.274 Chirality : 0.040 0.158 1455 Planarity : 0.003 0.024 1516 Dihedral : 11.770 83.597 1452 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.18 % Favored : 96.64 % Rotamer: Outliers : 3.41 % Allowed : 16.32 % Favored : 80.27 % 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: 0.65 (0.24), residues: 1162 helix: 1.41 (0.20), residues: 688 sheet: -0.77 (0.41), residues: 152 loop : -0.99 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 490 HIS 0.003 0.001 HIS A 536 PHE 0.018 0.001 PHE B 813 TYR 0.019 0.001 TYR A 455 ARG 0.002 0.000 ARG B 718 *********************** 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 156 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.998 Fit side-chains REVERT: A 449 MET cc_start: 0.7531 (ttm) cc_final: 0.7012 (ttp) REVERT: A 500 ASP cc_start: 0.6022 (t0) cc_final: 0.5679 (t0) REVERT: A 580 ASN cc_start: 0.7200 (m110) cc_final: 0.6576 (m110) REVERT: A 748 GLU cc_start: 0.4258 (pm20) cc_final: 0.3502 (tp30) REVERT: A 772 PHE cc_start: 0.7484 (t80) cc_final: 0.7165 (t80) REVERT: A 794 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6264 (tm-30) REVERT: A 1070 MET cc_start: 0.6238 (mtt) cc_final: 0.5918 (mtt) REVERT: A 1117 SER cc_start: 0.7957 (OUTLIER) cc_final: 0.7742 (p) REVERT: B 449 MET cc_start: 0.7374 (ttm) cc_final: 0.6959 (ttp) REVERT: B 500 ASP cc_start: 0.5737 (t0) cc_final: 0.5345 (t0) REVERT: B 772 PHE cc_start: 0.7484 (t80) cc_final: 0.7179 (t80) REVERT: B 1070 MET cc_start: 0.6365 (mtt) cc_final: 0.6061 (mtt) REVERT: B 1120 MET cc_start: 0.7045 (mmt) cc_final: 0.6368 (mmt) outliers start: 28 outliers final: 16 residues processed: 149 average time/residue: 0.1789 time to fit residues: 38.9602 Evaluate side-chains 136 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 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 A residue 1117 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 Chi-restraints excluded: chain B residue 948 LEU 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: 10.0000 chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 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 = 0.4519 r_free = 0.4519 target = 0.220397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.176105 restraints weight = 9942.884| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 2.54 r_work: 0.3994 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9104 Z= 0.195 Angle : 0.511 7.489 12391 Z= 0.275 Chirality : 0.040 0.153 1455 Planarity : 0.003 0.023 1516 Dihedral : 10.839 78.126 1452 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.58 % Favored : 97.25 % Rotamer: Outliers : 2.92 % Allowed : 17.42 % Favored : 79.66 % 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: 0.66 (0.24), residues: 1162 helix: 1.38 (0.20), residues: 688 sheet: -0.70 (0.41), residues: 152 loop : -0.93 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 806 HIS 0.002 0.001 HIS A 536 PHE 0.014 0.001 PHE B 813 TYR 0.015 0.001 TYR B 842 ARG 0.002 0.000 ARG B 777 *********************** 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 152 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.936 Fit side-chains REVERT: A 449 MET cc_start: 0.7403 (ttm) cc_final: 0.6877 (ttp) REVERT: A 500 ASP cc_start: 0.6027 (t0) cc_final: 0.5624 (t0) REVERT: A 580 ASN cc_start: 0.7181 (m110) cc_final: 0.6556 (m110) REVERT: A 748 GLU cc_start: 0.4140 (pm20) cc_final: 0.3430 (tp30) REVERT: A 772 PHE cc_start: 0.7468 (t80) cc_final: 0.7157 (t80) REVERT: A 794 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6282 (tm-30) REVERT: A 1070 MET cc_start: 0.6260 (mtt) cc_final: 0.5953 (mtt) REVERT: B 449 MET cc_start: 0.7406 (ttm) cc_final: 0.6891 (ttp) REVERT: B 500 ASP cc_start: 0.5774 (t0) cc_final: 0.5463 (t0) REVERT: B 772 PHE cc_start: 0.7456 (t80) cc_final: 0.7115 (t80) REVERT: B 938 MET cc_start: 0.6332 (tpp) cc_final: 0.5920 (tpp) REVERT: B 1120 MET cc_start: 0.6883 (mmt) cc_final: 0.6527 (mmm) outliers start: 24 outliers final: 20 residues processed: 147 average time/residue: 0.1675 time to fit residues: 37.1789 Evaluate side-chains 141 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 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 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 518 CYS Chi-restraints excluded: chain B residue 567 LEU 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 948 LEU 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: 7.9990 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 0.1980 chunk 80 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4537 r_free = 0.4537 target = 0.222653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.178218 restraints weight = 9988.334| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 2.54 r_work: 0.4017 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9104 Z= 0.163 Angle : 0.509 14.918 12391 Z= 0.267 Chirality : 0.040 0.153 1455 Planarity : 0.003 0.023 1516 Dihedral : 9.891 89.157 1452 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.75 % Favored : 97.07 % Rotamer: Outliers : 2.31 % Allowed : 18.64 % Favored : 79.05 % 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: 0.83 (0.25), residues: 1162 helix: 1.49 (0.20), residues: 692 sheet: -0.60 (0.42), residues: 152 loop : -0.85 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 840 HIS 0.002 0.001 HIS A 536 PHE 0.021 0.001 PHE B 812 TYR 0.019 0.001 TYR B 455 ARG 0.002 0.000 ARG A 718 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.908 Fit side-chains REVERT: A 449 MET cc_start: 0.7432 (ttm) cc_final: 0.6786 (ttp) REVERT: A 476 MET cc_start: 0.6889 (mmt) cc_final: 0.6493 (mmt) REVERT: A 580 ASN cc_start: 0.7166 (m110) cc_final: 0.6537 (m110) REVERT: A 748 GLU cc_start: 0.4106 (pm20) cc_final: 0.3384 (tp30) REVERT: A 772 PHE cc_start: 0.7410 (t80) cc_final: 0.7147 (t80) REVERT: A 794 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6228 (tm-30) REVERT: A 1070 MET cc_start: 0.6169 (mtt) cc_final: 0.5840 (mtt) REVERT: B 476 MET cc_start: 0.6996 (mmt) cc_final: 0.6605 (mmt) REVERT: B 772 PHE cc_start: 0.7396 (t80) cc_final: 0.7045 (t80) REVERT: B 938 MET cc_start: 0.6337 (tpp) cc_final: 0.5966 (tpp) REVERT: B 1120 MET cc_start: 0.6853 (mmt) cc_final: 0.6545 (mmm) outliers start: 19 outliers final: 17 residues processed: 140 average time/residue: 0.1640 time to fit residues: 34.5589 Evaluate side-chains 130 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 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 518 CYS Chi-restraints excluded: chain B residue 567 LEU 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 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: 0.6980 chunk 59 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.4481 r_free = 0.4481 target = 0.215975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.176643 restraints weight = 10058.589| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.46 r_work: 0.3923 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9104 Z= 0.320 Angle : 0.613 16.224 12391 Z= 0.322 Chirality : 0.044 0.140 1455 Planarity : 0.003 0.024 1516 Dihedral : 10.229 74.523 1452 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.44 % Favored : 96.39 % Rotamer: Outliers : 2.56 % Allowed : 18.51 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.23 (0.24), residues: 1162 helix: 0.99 (0.19), residues: 698 sheet: -0.84 (0.40), residues: 152 loop : -1.06 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 806 HIS 0.002 0.001 HIS B 783 PHE 0.023 0.002 PHE B 812 TYR 0.015 0.002 TYR A 925 ARG 0.002 0.000 ARG A 682 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.922 Fit side-chains REVERT: A 449 MET cc_start: 0.7485 (ttm) cc_final: 0.7149 (ttp) REVERT: A 476 MET cc_start: 0.7150 (mmt) cc_final: 0.6722 (mmt) REVERT: A 500 ASP cc_start: 0.5676 (t0) cc_final: 0.5313 (t0) REVERT: A 772 PHE cc_start: 0.7536 (t80) cc_final: 0.7261 (t80) REVERT: A 794 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6330 (tm-30) REVERT: A 864 PHE cc_start: 0.7452 (t80) cc_final: 0.7165 (t80) REVERT: A 1070 MET cc_start: 0.6602 (mtt) cc_final: 0.6401 (mtt) REVERT: A 1092 SER cc_start: 0.7719 (t) cc_final: 0.7435 (p) REVERT: B 449 MET cc_start: 0.7478 (ttm) cc_final: 0.7114 (ttp) REVERT: B 476 MET cc_start: 0.7379 (mmt) cc_final: 0.6935 (mmt) REVERT: B 500 ASP cc_start: 0.5701 (t0) cc_final: 0.5198 (t0) REVERT: B 772 PHE cc_start: 0.7575 (t80) cc_final: 0.7291 (t80) REVERT: B 1120 MET cc_start: 0.6829 (mmt) cc_final: 0.6475 (mmm) outliers start: 21 outliers final: 19 residues processed: 133 average time/residue: 0.1725 time to fit residues: 34.4292 Evaluate side-chains 134 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 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 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 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: 0.7980 chunk 51 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 114 optimal weight: 0.0270 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN A 580 ASN A 582 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.218948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.174478 restraints weight = 9970.406| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 2.52 r_work: 0.3971 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9104 Z= 0.207 Angle : 0.565 14.924 12391 Z= 0.291 Chirality : 0.041 0.144 1455 Planarity : 0.003 0.024 1516 Dihedral : 9.923 71.550 1452 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.75 % Favored : 97.07 % Rotamer: Outliers : 2.68 % Allowed : 18.76 % Favored : 78.56 % 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: 0.41 (0.24), residues: 1162 helix: 1.16 (0.20), residues: 688 sheet: -0.84 (0.40), residues: 152 loop : -0.96 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 806 HIS 0.003 0.001 HIS A 783 PHE 0.025 0.002 PHE B 812 TYR 0.014 0.001 TYR B1067 ARG 0.002 0.000 ARG A 682 ********************** 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 139 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.997 Fit side-chains REVERT: A 449 MET cc_start: 0.7447 (ttm) cc_final: 0.7020 (ttp) REVERT: A 476 MET cc_start: 0.7251 (mmt) cc_final: 0.6831 (mmt) REVERT: A 500 ASP cc_start: 0.5649 (t0) cc_final: 0.5263 (t0) REVERT: A 748 GLU cc_start: 0.4267 (pm20) cc_final: 0.3488 (tp30) REVERT: A 772 PHE cc_start: 0.7486 (t80) cc_final: 0.7155 (t80) REVERT: A 794 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6153 (tm-30) REVERT: A 1070 MET cc_start: 0.6401 (mtt) cc_final: 0.6152 (mtt) REVERT: A 1092 SER cc_start: 0.7629 (t) cc_final: 0.7344 (p) REVERT: B 449 MET cc_start: 0.7463 (ttm) cc_final: 0.7077 (ttp) REVERT: B 476 MET cc_start: 0.7255 (mmt) cc_final: 0.6846 (mmt) REVERT: B 500 ASP cc_start: 0.5679 (t0) cc_final: 0.5235 (t0) REVERT: B 535 MET cc_start: 0.5889 (ttt) cc_final: 0.5564 (mmm) REVERT: B 772 PHE cc_start: 0.7445 (t80) cc_final: 0.7149 (t80) REVERT: B 1120 MET cc_start: 0.6762 (mmt) cc_final: 0.6429 (mmm) outliers start: 22 outliers final: 19 residues processed: 133 average time/residue: 0.1627 time to fit residues: 32.6681 Evaluate side-chains 136 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 13 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 11 optimal weight: 0.0050 chunk 38 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- 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 = 0.4500 r_free = 0.4500 target = 0.218182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.173415 restraints weight = 10014.715| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 2.55 r_work: 0.3959 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9104 Z= 0.230 Angle : 0.576 15.174 12391 Z= 0.297 Chirality : 0.042 0.145 1455 Planarity : 0.003 0.024 1516 Dihedral : 9.914 69.715 1452 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.10 % Favored : 96.73 % Rotamer: Outliers : 2.68 % Allowed : 18.51 % 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: 0.33 (0.24), residues: 1162 helix: 1.11 (0.20), residues: 688 sheet: -0.89 (0.39), residues: 152 loop : -1.00 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 806 HIS 0.003 0.001 HIS B 536 PHE 0.029 0.002 PHE B 812 TYR 0.019 0.001 TYR B 455 ARG 0.002 0.000 ARG B 777 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4039.79 seconds wall clock time: 72 minutes 33.50 seconds (4353.50 seconds total)