Starting phenix.real_space_refine on Fri Nov 15 18:02:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3u_36861/11_2024/8k3u_36861.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3u_36861/11_2024/8k3u_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3u_36861/11_2024/8k3u_36861.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3u_36861/11_2024/8k3u_36861.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3u_36861/11_2024/8k3u_36861.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3u_36861/11_2024/8k3u_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-5513/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: 5.62, per 1000 atoms: 0.63 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: 2.37 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: 1.09 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: 3.15 Time building geometry restraints manager: 2.72 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.910 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.420 ------------------------------------------------------------------------------- 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 : 1.011 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: 0.2165 time to fit residues: 54.1363 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 : 0.889 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 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 : 0.986 Fit side-chains revert: symmetry clash REVERT: A 476 MET cc_start: 0.7628 (mmm) cc_final: 0.7231 (mmt) REVERT: A 567 LEU cc_start: 0.7723 (mt) cc_final: 0.7510 (mt) REVERT: A 568 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7351 (mp) REVERT: A 580 ASN cc_start: 0.7485 (m110) cc_final: 0.7215 (m110) REVERT: A 772 PHE cc_start: 0.7140 (t80) cc_final: 0.6850 (t80) REVERT: A 1070 MET cc_start: 0.6157 (mtt) cc_final: 0.5646 (mtt) REVERT: A 1121 ILE cc_start: 0.8121 (mm) cc_final: 0.7897 (mm) REVERT: B 476 MET cc_start: 0.7709 (mmm) cc_final: 0.7290 (mmt) REVERT: B 519 TYR cc_start: 0.5919 (t80) cc_final: 0.5695 (t80) REVERT: B 580 ASN cc_start: 0.7530 (m110) cc_final: 0.7286 (m110) REVERT: B 665 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7141 (mt-10) REVERT: B 772 PHE cc_start: 0.7154 (t80) cc_final: 0.6839 (t80) REVERT: B 1070 MET cc_start: 0.6417 (mtt) cc_final: 0.5965 (mtt) REVERT: B 1121 ILE cc_start: 0.8142 (mm) cc_final: 0.7937 (mm) outliers start: 17 outliers final: 10 residues processed: 158 average time/residue: 0.1794 time to fit residues: 41.3924 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 : 0.943 ------------------------------------------------------------------------------- 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 59 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 937 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9104 Z= 0.239 Angle : 0.533 6.007 12391 Z= 0.291 Chirality : 0.042 0.176 1455 Planarity : 0.004 0.038 1516 Dihedral : 13.315 91.373 1456 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.53 % Favored : 96.30 % Rotamer: Outliers : 3.53 % Allowed : 12.42 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.02 (0.24), residues: 1162 helix: 0.93 (0.20), residues: 682 sheet: -1.18 (0.38), residues: 152 loop : -1.29 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 490 HIS 0.003 0.001 HIS A 536 PHE 0.016 0.002 PHE B 813 TYR 0.018 0.002 TYR A 842 ARG 0.005 0.001 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 166 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 476 MET cc_start: 0.7638 (mmm) cc_final: 0.7435 (mmt) REVERT: A 500 ASP cc_start: 0.6570 (t0) cc_final: 0.6291 (t0) REVERT: A 580 ASN cc_start: 0.7344 (m110) cc_final: 0.6846 (m110) REVERT: A 748 GLU cc_start: 0.3727 (pm20) cc_final: 0.3377 (tp30) REVERT: A 752 GLU cc_start: 0.5999 (OUTLIER) cc_final: 0.5668 (pm20) REVERT: A 772 PHE cc_start: 0.7154 (t80) cc_final: 0.6858 (t80) REVERT: A 938 MET cc_start: 0.6590 (ttm) cc_final: 0.6381 (tpp) REVERT: B 476 MET cc_start: 0.7810 (mmm) cc_final: 0.7486 (mmt) REVERT: B 568 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7558 (mp) REVERT: B 580 ASN cc_start: 0.7346 (m110) cc_final: 0.6954 (m110) REVERT: B 748 GLU cc_start: 0.3951 (OUTLIER) cc_final: 0.3449 (tm-30) REVERT: B 772 PHE cc_start: 0.7120 (t80) cc_final: 0.6825 (t80) REVERT: B 938 MET cc_start: 0.6615 (ttm) cc_final: 0.6393 (tpp) outliers start: 29 outliers final: 11 residues processed: 160 average time/residue: 0.1691 time to fit residues: 40.3152 Evaluate side-chains 138 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 A residue 865 TYR Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 748 GLU 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 1117 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 30.0000 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 667 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.3389 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= 0.184 Angle : 0.493 6.691 12391 Z= 0.271 Chirality : 0.040 0.175 1455 Planarity : 0.003 0.041 1516 Dihedral : 12.604 83.584 1452 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.10 % Favored : 96.73 % Rotamer: Outliers : 3.05 % Allowed : 14.25 % Favored : 82.70 % 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: 0.39 (0.24), residues: 1162 helix: 1.26 (0.20), residues: 686 sheet: -1.03 (0.39), residues: 152 loop : -1.13 (0.32), 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 0.031 0.002 PHE A 942 TYR 0.018 0.001 TYR A 455 ARG 0.004 0.001 ARG B 777 *********************** 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: 25 poor density : 128 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 476 MET cc_start: 0.7727 (mmm) cc_final: 0.7397 (mmt) REVERT: A 500 ASP cc_start: 0.6735 (t0) cc_final: 0.6391 (t0) REVERT: A 580 ASN cc_start: 0.7293 (m110) cc_final: 0.6769 (m110) REVERT: A 772 PHE cc_start: 0.7096 (t80) cc_final: 0.6783 (t80) REVERT: A 794 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6352 (tm-30) REVERT: A 1070 MET cc_start: 0.6487 (mtt) cc_final: 0.5931 (mtt) REVERT: B 476 MET cc_start: 0.7722 (mmm) cc_final: 0.7378 (mmt) REVERT: B 500 ASP cc_start: 0.6295 (t0) cc_final: 0.6088 (t0) REVERT: B 580 ASN cc_start: 0.7360 (m110) cc_final: 0.6944 (m110) REVERT: B 748 GLU cc_start: 0.3775 (OUTLIER) cc_final: 0.3363 (tm-30) REVERT: B 772 PHE cc_start: 0.7049 (t80) cc_final: 0.6734 (t80) REVERT: B 956 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7906 (mt) REVERT: B 1120 MET cc_start: 0.8033 (mmt) cc_final: 0.7404 (mmt) outliers start: 25 outliers final: 11 residues processed: 148 average time/residue: 0.1855 time to fit residues: 40.0449 Evaluate side-chains 132 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 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 B residue 426 ASN Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 748 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 956 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.3672 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= 0.174 Angle : 0.494 6.447 12391 Z= 0.268 Chirality : 0.040 0.170 1455 Planarity : 0.003 0.029 1516 Dihedral : 12.238 86.983 1452 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.93 % Favored : 96.90 % Rotamer: Outliers : 3.53 % Allowed : 14.98 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.51 (0.24), residues: 1162 helix: 1.31 (0.20), residues: 698 sheet: -0.92 (0.40), residues: 152 loop : -1.11 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 490 HIS 0.002 0.000 HIS A 536 PHE 0.016 0.001 PHE A 942 TYR 0.016 0.001 TYR B 455 ARG 0.002 0.000 ARG B 718 *********************** 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 157 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.975 Fit side-chains REVERT: A 500 ASP cc_start: 0.6596 (t0) cc_final: 0.6357 (t0) REVERT: A 580 ASN cc_start: 0.7280 (m110) cc_final: 0.6725 (m110) REVERT: A 772 PHE cc_start: 0.7061 (t80) cc_final: 0.6697 (t80) REVERT: A 794 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6332 (tm-30) REVERT: A 938 MET cc_start: 0.6798 (tpp) cc_final: 0.6525 (tpp) REVERT: A 1070 MET cc_start: 0.6358 (mtt) cc_final: 0.5825 (mtt) REVERT: B 580 ASN cc_start: 0.7324 (m110) cc_final: 0.6892 (m110) REVERT: B 748 GLU cc_start: 0.3736 (OUTLIER) cc_final: 0.3353 (tm-30) REVERT: B 772 PHE cc_start: 0.7029 (t80) cc_final: 0.6694 (t80) REVERT: B 956 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7903 (mt) REVERT: B 1120 MET cc_start: 0.7939 (mmt) cc_final: 0.7250 (mmt) outliers start: 29 outliers final: 18 residues processed: 149 average time/residue: 0.1793 time to fit residues: 39.1179 Evaluate side-chains 137 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 535 MET 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 454 MET Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 748 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 956 LEU 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 38 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 20.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9104 Z= 0.170 Angle : 0.487 6.348 12391 Z= 0.264 Chirality : 0.039 0.165 1455 Planarity : 0.003 0.030 1516 Dihedral : 11.763 86.780 1452 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.84 % Favored : 96.99 % Rotamer: Outliers : 2.92 % Allowed : 16.44 % Favored : 80.63 % 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: 0.63 (0.25), residues: 1162 helix: 1.39 (0.20), residues: 700 sheet: -0.83 (0.40), residues: 152 loop : -1.06 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 490 HIS 0.003 0.000 HIS A 536 PHE 0.015 0.001 PHE A 813 TYR 0.017 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 148 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.016 Fit side-chains REVERT: A 476 MET cc_start: 0.7183 (mmt) cc_final: 0.6549 (mmt) REVERT: A 500 ASP cc_start: 0.6544 (t0) cc_final: 0.6340 (t0) REVERT: A 580 ASN cc_start: 0.7225 (m110) cc_final: 0.6672 (m110) REVERT: A 772 PHE cc_start: 0.7043 (t80) cc_final: 0.6727 (t80) REVERT: A 794 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6305 (tm-30) REVERT: A 1070 MET cc_start: 0.6426 (mtt) cc_final: 0.5916 (mtt) REVERT: B 449 MET cc_start: 0.7382 (ttm) cc_final: 0.7174 (ttp) REVERT: B 476 MET cc_start: 0.7172 (mmt) cc_final: 0.6542 (mmt) REVERT: B 748 GLU cc_start: 0.3724 (OUTLIER) cc_final: 0.3355 (tm-30) REVERT: B 772 PHE cc_start: 0.7006 (t80) cc_final: 0.6653 (t80) REVERT: B 938 MET cc_start: 0.6513 (tpp) cc_final: 0.6159 (tpp) REVERT: B 1120 MET cc_start: 0.7926 (mmt) cc_final: 0.7375 (mmt) outliers start: 24 outliers final: 16 residues processed: 140 average time/residue: 0.1813 time to fit residues: 37.3702 Evaluate side-chains 134 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 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 640 VAL Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 777 ARG 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 110 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9104 Z= 0.251 Angle : 0.539 6.295 12391 Z= 0.293 Chirality : 0.041 0.147 1455 Planarity : 0.003 0.027 1516 Dihedral : 11.395 79.767 1452 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.84 % Favored : 96.99 % Rotamer: Outliers : 2.92 % Allowed : 17.66 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.39 (0.24), residues: 1162 helix: 1.16 (0.20), residues: 698 sheet: -0.81 (0.40), residues: 152 loop : -1.10 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 806 HIS 0.002 0.001 HIS A 536 PHE 0.023 0.002 PHE A 813 TYR 0.018 0.001 TYR B 455 ARG 0.002 0.000 ARG B 682 *********************** 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 146 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.027 Fit side-chains REVERT: A 772 PHE cc_start: 0.7142 (t80) cc_final: 0.6833 (t80) REVERT: A 794 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6896 (tm-30) REVERT: A 938 MET cc_start: 0.6716 (tpp) cc_final: 0.6409 (tpp) REVERT: A 1070 MET cc_start: 0.6594 (mtt) cc_final: 0.6143 (mtt) REVERT: B 449 MET cc_start: 0.7521 (ttm) cc_final: 0.7268 (ttp) REVERT: B 772 PHE cc_start: 0.7109 (t80) cc_final: 0.6793 (t80) REVERT: B 938 MET cc_start: 0.6494 (tpp) cc_final: 0.6129 (tpp) REVERT: B 1070 MET cc_start: 0.6679 (mtt) cc_final: 0.6287 (mtt) REVERT: B 1120 MET cc_start: 0.7684 (mmt) cc_final: 0.7363 (mmm) outliers start: 24 outliers final: 18 residues processed: 139 average time/residue: 0.1753 time to fit residues: 36.3614 Evaluate side-chains 133 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 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 777 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 77 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9104 Z= 0.160 Angle : 0.491 7.396 12391 Z= 0.263 Chirality : 0.040 0.154 1455 Planarity : 0.003 0.027 1516 Dihedral : 10.161 85.441 1452 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.67 % Favored : 97.16 % Rotamer: Outliers : 2.31 % Allowed : 19.00 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 690 sheet: -0.73 (0.41), residues: 152 loop : -0.93 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 806 HIS 0.002 0.000 HIS B 783 PHE 0.020 0.001 PHE A 812 TYR 0.018 0.001 TYR A 455 ARG 0.004 0.000 ARG B1040 *********************** 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 : 1.042 Fit side-chains REVERT: A 476 MET cc_start: 0.7144 (mmt) cc_final: 0.6673 (mmt) REVERT: A 772 PHE cc_start: 0.7031 (t80) cc_final: 0.6690 (t80) REVERT: A 794 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6892 (tm-30) REVERT: A 938 MET cc_start: 0.6640 (tpp) cc_final: 0.6389 (tpp) REVERT: A 1070 MET cc_start: 0.6466 (mtt) cc_final: 0.6005 (mtt) REVERT: B 476 MET cc_start: 0.7160 (mmt) cc_final: 0.6689 (mmt) REVERT: B 772 PHE cc_start: 0.6990 (t80) cc_final: 0.6609 (t80) REVERT: B 938 MET cc_start: 0.6513 (tpp) cc_final: 0.6191 (tpp) REVERT: B 1120 MET cc_start: 0.7658 (mmt) cc_final: 0.7392 (mmm) outliers start: 19 outliers final: 15 residues processed: 137 average time/residue: 0.1659 time to fit residues: 34.3065 Evaluate side-chains 132 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 802 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 100 optimal weight: 0.1980 chunk 69 optimal weight: 0.1980 chunk 112 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9104 Z= 0.149 Angle : 0.490 7.854 12391 Z= 0.261 Chirality : 0.039 0.152 1455 Planarity : 0.003 0.026 1516 Dihedral : 9.623 74.041 1452 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.58 % Favored : 97.25 % Rotamer: Outliers : 2.19 % Allowed : 19.00 % 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: 0.79 (0.25), residues: 1162 helix: 1.46 (0.20), residues: 692 sheet: -0.68 (0.40), residues: 152 loop : -0.84 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1047 HIS 0.003 0.001 HIS A 536 PHE 0.024 0.001 PHE A 812 TYR 0.020 0.001 TYR B 455 ARG 0.003 0.000 ARG A1040 *********************** 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 137 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.057 Fit side-chains REVERT: A 476 MET cc_start: 0.7160 (mmt) cc_final: 0.6730 (mmt) REVERT: A 565 ILE cc_start: 0.7011 (mm) cc_final: 0.6797 (mm) REVERT: A 772 PHE cc_start: 0.6979 (t80) cc_final: 0.6700 (t80) REVERT: A 794 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6903 (tm-30) REVERT: A 938 MET cc_start: 0.6392 (tpp) cc_final: 0.6114 (tpp) REVERT: A 1070 MET cc_start: 0.6440 (mtt) cc_final: 0.5943 (mtt) REVERT: B 476 MET cc_start: 0.7177 (mmt) cc_final: 0.6749 (mmt) REVERT: B 748 GLU cc_start: 0.3771 (OUTLIER) cc_final: 0.3261 (tm-30) REVERT: B 772 PHE cc_start: 0.6948 (t80) cc_final: 0.6601 (t80) REVERT: B 938 MET cc_start: 0.6668 (tpp) cc_final: 0.6326 (tpp) REVERT: B 1070 MET cc_start: 0.6586 (mtt) cc_final: 0.5995 (mtt) REVERT: B 1120 MET cc_start: 0.7632 (mmt) cc_final: 0.7310 (mmt) outliers start: 18 outliers final: 15 residues processed: 133 average time/residue: 0.1704 time to fit residues: 35.0791 Evaluate side-chains 130 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 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 748 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.4378 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= 0.171 Angle : 0.515 13.256 12391 Z= 0.270 Chirality : 0.039 0.148 1455 Planarity : 0.003 0.026 1516 Dihedral : 9.689 72.919 1452 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.41 % Favored : 97.42 % Rotamer: Outliers : 2.19 % Allowed : 19.37 % Favored : 78.44 % 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: 0.80 (0.25), residues: 1162 helix: 1.46 (0.20), residues: 690 sheet: -0.62 (0.40), residues: 152 loop : -0.83 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 806 HIS 0.003 0.001 HIS A 536 PHE 0.028 0.002 PHE A 812 TYR 0.017 0.001 TYR A 455 ARG 0.002 0.000 ARG A 718 ********************** 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 133 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.966 Fit side-chains REVERT: A 476 MET cc_start: 0.7181 (mmt) cc_final: 0.6813 (mmt) REVERT: A 565 ILE cc_start: 0.7027 (mm) cc_final: 0.6823 (mm) REVERT: A 772 PHE cc_start: 0.7078 (t80) cc_final: 0.6802 (t80) REVERT: A 794 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6804 (tm-30) REVERT: A 938 MET cc_start: 0.6305 (tpp) cc_final: 0.6000 (tpp) REVERT: A 1070 MET cc_start: 0.6441 (mtt) cc_final: 0.5962 (mtt) REVERT: B 476 MET cc_start: 0.7201 (mmt) cc_final: 0.6774 (mmt) REVERT: B 748 GLU cc_start: 0.3785 (OUTLIER) cc_final: 0.3267 (tm-30) REVERT: B 772 PHE cc_start: 0.6999 (t80) cc_final: 0.6684 (t80) REVERT: B 938 MET cc_start: 0.6650 (tpp) cc_final: 0.6294 (tpp) REVERT: B 1070 MET cc_start: 0.6613 (mtt) cc_final: 0.6056 (mtt) REVERT: B 1117 SER cc_start: 0.8640 (OUTLIER) cc_final: 0.8429 (p) REVERT: B 1120 MET cc_start: 0.7621 (mmt) cc_final: 0.7313 (mmt) outliers start: 18 outliers final: 14 residues processed: 129 average time/residue: 0.1685 time to fit residues: 32.8239 Evaluate side-chains 125 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 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 748 GLU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 865 TYR Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 11 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 82 optimal weight: 0.2980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4550 r_free = 0.4550 target = 0.224063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.180352 restraints weight = 9781.301| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 2.49 r_work: 0.4040 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6255 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9104 Z= 0.156 Angle : 0.507 13.194 12391 Z= 0.266 Chirality : 0.039 0.148 1455 Planarity : 0.002 0.026 1516 Dihedral : 9.585 69.608 1452 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.41 % Favored : 97.42 % Rotamer: Outliers : 2.19 % Allowed : 19.37 % Favored : 78.44 % 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: 0.86 (0.25), residues: 1162 helix: 1.47 (0.20), residues: 694 sheet: -0.59 (0.40), residues: 152 loop : -0.73 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1047 HIS 0.003 0.001 HIS A 536 PHE 0.033 0.002 PHE A 812 TYR 0.021 0.001 TYR B 842 ARG 0.002 0.000 ARG B 718 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1850.29 seconds wall clock time: 34 minutes 42.42 seconds (2082.42 seconds total)