Starting phenix.real_space_refine on Sat Oct 24 15:08:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oem_70402/10_2026/9oem_70402.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oem_70402/10_2026/9oem_70402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oem_70402/10_2026/9oem_70402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oem_70402/10_2026/9oem_70402.map" model { file = "/net/cci-nas-00/data/ceres_data/9oem_70402/10_2026/9oem_70402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oem_70402/10_2026/9oem_70402.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 Br 2 7.06 5 P 2 5.49 5 S 93 5.16 5 C 8807 2.51 5 N 2182 2.21 5 O 2425 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13511 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3224 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 405} Chain breaks: 2 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 6, 'ASN:plan1': 4, 'ARG:plan': 5, 'GLU:plan': 6, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3345 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 412} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 5, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 3174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3174 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 403} Chain breaks: 2 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 6, 'ASN:plan1': 5, 'ARG:plan': 8, 'GLU:plan': 8, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 119 Chain: "D" Number of atoms: 3338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3338 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {'J86': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 133 Unusual residues: {'NAG': 2, 'Y01': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'J86': 1, 'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 98 Unusual residues: {'NAG': 2, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.94, per 1000 atoms: 0.22 Number of scatterers: 13511 At special positions: 0 Unit cell: (137.24, 102.46, 128.78, 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) Br 2 34.99 S 93 16.00 P 2 15.00 O 2425 8.00 N 2182 7.00 C 8807 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 575 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 859 " - pdb=" SG CYS B 913 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 537 " - pdb=" SG CYS D 575 " distance=2.03 Simple disulfide: pdb=" SG CYS D 543 " - pdb=" SG CYS D 576 " distance=2.03 Simple disulfide: pdb=" SG CYS D 859 " - pdb=" SG CYS D 913 " distance=2.03 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 902 " - " ASN A 771 " " NAG B1002 " - " ASN B 886 " " NAG C 902 " - " ASN C 771 " " NAG D1002 " - " ASN D 886 " " NAG D1003 " - " ASN D 565 " " NAG E 1 " - " ASN B 549 " " NAG F 1 " - " ASN D 549 " Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 468.8 milliseconds 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3194 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 20 sheets defined 51.3% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.538A pdb=" N GLY A 503 " --> pdb=" O ASN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 527 Processing helix chain 'A' and resid 555 through 559 removed outlier: 3.670A pdb=" N PHE A 558 " --> pdb=" O MET A 555 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A 559 " --> pdb=" O GLN A 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 555 through 559' Processing helix chain 'A' and resid 561 through 584 Processing helix chain 'A' and resid 602 through 615 Processing helix chain 'A' and resid 626 through 657 Processing helix chain 'A' and resid 669 through 674 removed outlier: 3.532A pdb=" N ARG A 673 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 669 through 674' Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.755A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 710 removed outlier: 3.609A pdb=" N HIS A 709 " --> pdb=" O HIS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 768 through 783 removed outlier: 3.753A pdb=" N GLY A 783 " --> pdb=" O SER A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 809 through 834 removed outlier: 3.516A pdb=" N MET A 813 " --> pdb=" O THR A 809 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLY A 815 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE A 817 " --> pdb=" O MET A 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 563 removed outlier: 3.604A pdb=" N HIS B 562 " --> pdb=" O PHE B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 592 Processing helix chain 'B' and resid 614 through 622 Processing helix chain 'B' and resid 636 through 642 removed outlier: 3.745A pdb=" N VAL B 641 " --> pdb=" O ALA B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.919A pdb=" N MET B 670 " --> pdb=" O GLY B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 698 Processing helix chain 'B' and resid 715 through 729 removed outlier: 3.587A pdb=" N GLY B 729 " --> pdb=" O ALA B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 768 Processing helix chain 'B' and resid 782 through 787 Processing helix chain 'B' and resid 800 through 810 Processing helix chain 'B' and resid 810 through 820 removed outlier: 3.579A pdb=" N HIS B 814 " --> pdb=" O PHE B 810 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU B 815 " --> pdb=" O PRO B 811 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N TYR B 816 " --> pdb=" O GLU B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 834 Processing helix chain 'B' and resid 846 through 855 Processing helix chain 'B' and resid 883 through 897 Processing helix chain 'B' and resid 898 through 908 Processing helix chain 'B' and resid 912 through 916 Processing helix chain 'B' and resid 927 through 930 Processing helix chain 'B' and resid 931 through 957 Processing helix chain 'C' and resid 457 through 471 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.687A pdb=" N GLN C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 559 removed outlier: 3.745A pdb=" N PHE C 558 " --> pdb=" O MET C 555 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN C 559 " --> pdb=" O GLN C 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 555 through 559' Processing helix chain 'C' and resid 561 through 583 Processing helix chain 'C' and resid 602 through 615 Processing helix chain 'C' and resid 627 through 657 removed outlier: 3.610A pdb=" N ILE C 631 " --> pdb=" O PHE C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 removed outlier: 3.531A pdb=" N ASN C 674 " --> pdb=" O PRO C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.903A pdb=" N GLN C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 710 removed outlier: 3.608A pdb=" N HIS C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 768 through 782 Processing helix chain 'C' and resid 783 through 792 Processing helix chain 'C' and resid 809 through 834 removed outlier: 7.091A pdb=" N GLY C 815 " --> pdb=" O GLU C 811 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL C 816 " --> pdb=" O ASN C 812 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE C 817 " --> pdb=" O MET C 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 563 removed outlier: 3.624A pdb=" N LEU D 554 " --> pdb=" O ASP D 550 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS D 562 " --> pdb=" O PHE D 558 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER D 563 " --> pdb=" O SER D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 592 Processing helix chain 'D' and resid 614 through 622 Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 667 through 671 removed outlier: 3.877A pdb=" N MET D 670 " --> pdb=" O GLY D 667 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP D 671 " --> pdb=" O ALA D 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 667 through 671' Processing helix chain 'D' and resid 674 through 699 Processing helix chain 'D' and resid 715 through 729 Processing helix chain 'D' and resid 740 through 768 Processing helix chain 'D' and resid 782 through 787 Processing helix chain 'D' and resid 800 through 810 Processing helix chain 'D' and resid 810 through 818 Processing helix chain 'D' and resid 824 through 834 removed outlier: 3.676A pdb=" N GLY D 828 " --> pdb=" O ALA D 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 856 Processing helix chain 'D' and resid 883 through 898 Processing helix chain 'D' and resid 898 through 908 Processing helix chain 'D' and resid 912 through 917 removed outlier: 4.038A pdb=" N SER D 917 " --> pdb=" O CYS D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 927 through 930 Processing helix chain 'D' and resid 931 through 960 Processing sheet with id=AA1, first strand: chain 'A' and resid 475 through 478 removed outlier: 4.020A pdb=" N MET A 512 " --> pdb=" O LYS A 399 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 410 through 412 removed outlier: 3.575A pdb=" N GLY A 438 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488 removed outlier: 3.995A pdb=" N GLU A 488 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU A 497 " --> pdb=" O GLU A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AA5, first strand: chain 'A' and resid 681 through 682 removed outlier: 11.839A pdb=" N LYS A 534 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N ARG A 755 " --> pdb=" O LYS A 534 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N GLN A 536 " --> pdb=" O PHE A 753 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE A 753 " --> pdb=" O GLN A 536 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 538 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLU A 751 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 514 through 515 Processing sheet with id=AA7, first strand: chain 'B' and resid 527 through 529 removed outlier: 3.790A pdb=" N TYR B 577 " --> pdb=" O PHE B 527 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AA9, first strand: chain 'B' and resid 628 through 633 removed outlier: 7.954A pdb=" N THR B 630 " --> pdb=" O GLY B 876 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY B 876 " --> pdb=" O THR B 630 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE B 632 " --> pdb=" O GLY B 874 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 628 through 633 removed outlier: 7.954A pdb=" N THR B 630 " --> pdb=" O GLY B 876 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY B 876 " --> pdb=" O THR B 630 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE B 632 " --> pdb=" O GLY B 874 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N GLY B 865 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 10.623A pdb=" N VAL B 657 " --> pdb=" O GLY B 865 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N ILE B 655 " --> pdb=" O PRO B 867 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ALA B 869 " --> pdb=" O LEU B 653 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 653 " --> pdb=" O ALA B 869 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE B 649 " --> pdb=" O TYR B 873 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY B 795 " --> pdb=" O ILE B 843 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N ASP B 845 " --> pdb=" O GLY B 795 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 662 through 663 Processing sheet with id=AB3, first strand: chain 'C' and resid 473 through 478 removed outlier: 5.129A pdb=" N ALA C 515 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY C 759 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LEU C 517 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLY C 757 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLU C 751 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU C 538 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE C 753 " --> pdb=" O GLN C 536 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N GLN C 536 " --> pdb=" O PHE C 753 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N ARG C 755 " --> pdb=" O LYS C 534 " (cutoff:3.500A) removed outlier: 11.644A pdb=" N LYS C 534 " --> pdb=" O ARG C 755 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AB5, first strand: chain 'C' and resid 438 through 439 removed outlier: 3.818A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 487 through 488 removed outlier: 3.562A pdb=" N GLU C 488 " --> pdb=" O GLU C 497 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C 497 " --> pdb=" O GLU C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 594 through 599 removed outlier: 3.817A pdb=" N MET D 627 " --> pdb=" O ARG D 516 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 527 through 530 removed outlier: 3.638A pdb=" N TYR D 577 " --> pdb=" O PHE D 527 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 608 through 609 Processing sheet with id=AC1, first strand: chain 'D' and resid 643 through 644 removed outlier: 3.507A pdb=" N ASP D 643 " --> pdb=" O LEU D 877 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 794 through 795 removed outlier: 6.615A pdb=" N GLY D 795 " --> pdb=" O ILE D 843 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N ASP D 845 " --> pdb=" O GLY D 795 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE D 649 " --> pdb=" O TYR D 873 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU D 653 " --> pdb=" O ALA D 869 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ALA D 869 " --> pdb=" O LEU D 653 " (cutoff:3.500A) removed outlier: 9.378A pdb=" N ILE D 655 " --> pdb=" O PRO D 867 " (cutoff:3.500A) removed outlier: 10.906A pdb=" N VAL D 657 " --> pdb=" O GLY D 865 " (cutoff:3.500A) removed outlier: 9.902A pdb=" N GLY D 865 " --> pdb=" O VAL D 657 " (cutoff:3.500A) 676 hydrogen bonds defined for protein. 1965 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 3268 1.33 - 1.48: 4590 1.48 - 1.64: 5860 1.64 - 1.79: 15 1.79 - 1.94: 139 Bond restraints: 13872 Sorted by residual: bond pdb=" C4 J86 A 903 " pdb=" N2 J86 A 903 " ideal model delta sigma weight residual 1.383 1.489 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C4 J86 C 903 " pdb=" N2 J86 C 903 " ideal model delta sigma weight residual 1.383 1.489 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C5 J86 C 903 " pdb=" N3 J86 C 903 " ideal model delta sigma weight residual 1.384 1.488 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C5 J86 A 903 " pdb=" N3 J86 A 903 " ideal model delta sigma weight residual 1.384 1.488 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C10 J86 A 903 " pdb=" N2 J86 A 903 " ideal model delta sigma weight residual 1.346 1.430 -0.084 2.00e-02 2.50e+03 1.75e+01 ... (remaining 13867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 18835 3.47 - 6.94: 65 6.94 - 10.41: 2 10.41 - 13.88: 0 13.88 - 17.35: 4 Bond angle restraints: 18906 Sorted by residual: angle pdb=" C2 J86 A 903 " pdb=" C3 J86 A 903 " pdb=" C7 J86 A 903 " ideal model delta sigma weight residual 120.09 102.74 17.35 3.00e+00 1.11e-01 3.35e+01 angle pdb=" C2 J86 C 903 " pdb=" C3 J86 C 903 " pdb=" C7 J86 C 903 " ideal model delta sigma weight residual 120.09 103.73 16.36 3.00e+00 1.11e-01 2.97e+01 angle pdb=" C2 J86 A 903 " pdb=" C3 J86 A 903 " pdb=" C4 J86 A 903 " ideal model delta sigma weight residual 121.16 137.26 -16.10 3.00e+00 1.11e-01 2.88e+01 angle pdb=" C2 J86 C 903 " pdb=" C3 J86 C 903 " pdb=" C4 J86 C 903 " ideal model delta sigma weight residual 121.16 136.22 -15.06 3.00e+00 1.11e-01 2.52e+01 angle pdb=" N TYR A 795 " pdb=" CA TYR A 795 " pdb=" C TYR A 795 " ideal model delta sigma weight residual 111.28 107.68 3.60 1.09e+00 8.42e-01 1.09e+01 ... (remaining 18901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 7964 17.55 - 35.10: 444 35.10 - 52.66: 133 52.66 - 70.21: 29 70.21 - 87.76: 6 Dihedral angle restraints: 8576 sinusoidal: 3623 harmonic: 4953 Sorted by residual: dihedral pdb=" CB CYS B 537 " pdb=" SG CYS B 537 " pdb=" SG CYS B 575 " pdb=" CB CYS B 575 " ideal model delta sinusoidal sigma weight residual 93.00 135.53 -42.53 1 1.00e+01 1.00e-02 2.53e+01 dihedral pdb=" CA PHE A 472 " pdb=" C PHE A 472 " pdb=" N THR A 473 " pdb=" CA THR A 473 " ideal model delta harmonic sigma weight residual 180.00 163.11 16.89 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA PHE C 558 " pdb=" C PHE C 558 " pdb=" N GLN C 559 " pdb=" CA GLN C 559 " ideal model delta harmonic sigma weight residual 180.00 164.15 15.85 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 8573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2011 0.082 - 0.163: 163 0.163 - 0.245: 2 0.245 - 0.327: 0 0.327 - 0.409: 1 Chirality restraints: 2177 Sorted by residual: chirality pdb=" C1 NAG D1002 " pdb=" ND2 ASN D 886 " pdb=" C2 NAG D1002 " pdb=" O5 NAG D1002 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 771 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 549 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 2174 not shown) Planarity restraints: 2336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 822 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO B 823 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 823 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 823 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 881 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO D 882 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 882 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 882 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 793 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.06e+00 pdb=" C VAL A 793 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL A 793 " 0.009 2.00e-02 2.50e+03 pdb=" N ARG A 794 " 0.008 2.00e-02 2.50e+03 ... (remaining 2333 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 217 2.68 - 3.23: 12935 3.23 - 3.79: 20228 3.79 - 4.34: 26827 4.34 - 4.90: 46381 Nonbonded interactions: 106588 Sorted by model distance: nonbonded pdb=" O THR A 396 " pdb=" OG1 THR A 473 " model vdw 2.120 3.040 nonbonded pdb=" O ASP B 596 " pdb=" OD1 ASP B 596 " model vdw 2.209 3.040 nonbonded pdb=" O LEU C 580 " pdb=" OG SER C 584 " model vdw 2.209 3.040 nonbonded pdb=" O THR C 396 " pdb=" OG1 THR C 473 " model vdw 2.233 3.040 nonbonded pdb=" O PRO D 672 " pdb=" ND2 ASN D 763 " model vdw 2.248 3.120 ... (remaining 106583 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 396 through 441 or (resid 446 and (name N or name CA or na \ me C or name O or name CB )) or resid 447 or (resid 448 and (name N or name CA o \ r name C or name O or name CB )) or resid 449 through 491 or (resid 492 and (nam \ e N or name CA or name C or name O or name CB )) or resid 493 through 527 or (re \ sid 528 and (name N or name CA or name C or name O or name CB )) or resid 529 th \ rough 535 or (resid 536 and (name N or name CA or name C or name O or name CB )) \ or resid 537 through 581 or (resid 582 and (name N or name CA or name C or name \ O or name CB )) or resid 583 through 625 or (resid 626 and (name N or name CA o \ r name C or name O or name CB )) or resid 627 through 662 or (resid 663 and (nam \ e N or name CA or name C or name O or name CB )) or resid 664 through 785 or (re \ sid 786 and (name N or name CA or name C or name O or name CB )) or resid 787 th \ rough 795 or (resid 796 and (name N or name CA or name C or name O or name CB )) \ or resid 797 through 833 or (resid 834 and (name N or name CA or name C or name \ O or name CB )) or resid 901)) selection = (chain 'C' and (resid 396 through 544 or (resid 545 through 546 and (name N or n \ ame CA or name C or name O or name CB )) or resid 547 through 583 or (resid 584 \ and (name N or name CA or name C or name O or name CB )) or resid 585 through 83 \ 4 or resid 902)) } ncs_group { reference = (chain 'B' and (resid 513 through 551 or (resid 552 and (name N or name CA or na \ me C or name O or name CB )) or resid 553 through 565 or (resid 566 through 567 \ and (name N or name CA or name C or name O or name CB )) or resid 568 through 59 \ 1 or (resid 592 and (name N or name CA or name C or name O or name CB )) or resi \ d 593 through 660 or (resid 661 and (name N or name CA or name C or name O or na \ me CB )) or resid 662 through 697 or (resid 698 through 699 and (name N or name \ CA or name C or name O or name CB )) or resid 700 or resid 714 through 740 or (r \ esid 741 and (name N or name CA or name C or name O or name CB )) or resid 742 t \ hrough 797 or (resid 798 and (name N or name CA or name C or name O or name CB ) \ ) or resid 799 through 857 or (resid 858 and (name N or name CA or name C or nam \ e O or name CB )) or resid 859 through 916 or (resid 917 and (name N or name CA \ or name C or name O or name CB )) or resid 918 through 921 or (resid 922 and (na \ me N or name CA or name C or name O or name CB )) or resid 923 through 955 or (r \ esid 956 through 957 and (name N or name CA or name C or name O or name CB )) or \ resid 1003 or resid 1005 through 1006)) selection = (chain 'D' and (resid 513 through 546 or (resid 547 through 548 and (name N or n \ ame CA or name C or name O or name CB )) or resid 549 through 695 or (resid 696 \ and (name N or name CA or name C or name O or name CB )) or resid 697 through 77 \ 2 or (resid 773 and (name N or name CA or name C or name O or name CB )) or resi \ d 774 through 836 or (resid 837 and (name N or name CA or name C or name O or na \ me CB )) or resid 838 through 951 or (resid 952 and (name N or name CA or name C \ or name O or name CB )) or resid 953 through 957 or resid 1002 or resid 1004 th \ rough 1005)) } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 4.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.840 Find NCS groups from input model: 0.380 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 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 : 0.004 0.106 13893 Z= 0.209 Angle : 0.619 17.355 18957 Z= 0.296 Chirality : 0.042 0.409 2177 Planarity : 0.004 0.043 2329 Dihedral : 12.332 87.759 5346 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.60 % Allowed : 7.69 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.21), residues: 1693 helix: 1.81 (0.18), residues: 802 sheet: -1.83 (0.46), residues: 147 loop : -1.26 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 818 TYR 0.021 0.001 TYR D 579 PHE 0.017 0.001 PHE A 458 TRP 0.008 0.001 TRP D 749 HIS 0.004 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.21 (13872) covalent geometry : angle 0.61541 / 0.30 (18906) SS BOND : bond 0.00281 / 0.17 ( 12) SS BOND : angle 0.49945 / 0.31 ( 24) hydrogen bonds : bond 0.15961 / 9.90 ( 675) hydrogen bonds : angle 5.90730 / 4.13 ( 1965) link_BETA1-4 : bond 0.00327 / 0.16 ( 2) link_BETA1-4 : angle 1.53501 / 0.76 ( 6) link_NAG-ASN : bond 0.00297 / 0.10 ( 7) link_NAG-ASN : angle 2.00352 / 1.58 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 206 time to evaluate : 0.533 Fit side-chains REVERT: A 398 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7759 (mt) REVERT: A 769 LYS cc_start: 0.7792 (tttm) cc_final: 0.7257 (tttm) REVERT: A 795 TYR cc_start: 0.6242 (OUTLIER) cc_final: 0.5487 (m-80) REVERT: B 660 ARG cc_start: 0.7901 (tpp-160) cc_final: 0.7543 (mmm160) REVERT: B 694 LEU cc_start: 0.8537 (tt) cc_final: 0.8286 (tp) REVERT: B 746 MET cc_start: 0.6825 (ttp) cc_final: 0.6617 (ttt) REVERT: C 555 MET cc_start: 0.8754 (mtm) cc_final: 0.8459 (mtt) REVERT: D 671 TRP cc_start: 0.8685 (m-10) cc_final: 0.8402 (m-10) REVERT: D 939 CYS cc_start: 0.7139 (m) cc_final: 0.6814 (m) outliers start: 8 outliers final: 2 residues processed: 214 average time/residue: 0.1128 time to fit residues: 35.8668 Evaluate side-chains 151 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 147 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain C residue 780 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 ASN A 705 HIS A 812 ASN B 747 ASN B 930 HIS ** C 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 HIS D 523 HIS D 586 GLN D 610 ASN D 893 GLN D 930 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.131312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.096663 restraints weight = 18759.306| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.63 r_work: 0.3169 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 13893 Z= 0.247 Angle : 0.614 6.690 18957 Z= 0.318 Chirality : 0.046 0.226 2177 Planarity : 0.004 0.050 2329 Dihedral : 10.068 88.194 2536 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.17 % Allowed : 11.35 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.21), residues: 1693 helix: 1.82 (0.18), residues: 813 sheet: -2.02 (0.44), residues: 155 loop : -1.29 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 807 TYR 0.026 0.002 TYR D 579 PHE 0.030 0.002 PHE C 533 TRP 0.008 0.001 TRP A 563 HIS 0.006 0.001 HIS D 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.25 (13872) covalent geometry : angle 0.60718 / 0.32 (18906) SS BOND : bond 0.00578 / 0.37 ( 12) SS BOND : angle 1.93612 / 1.59 ( 24) hydrogen bonds : bond 0.05402 / 3.61 ( 675) hydrogen bonds : angle 4.90408 / 3.43 ( 1965) link_BETA1-4 : bond 0.00399 / 0.19 ( 2) link_BETA1-4 : angle 1.35919 / 0.70 ( 6) link_NAG-ASN : bond 0.00151 / 0.08 ( 7) link_NAG-ASN : angle 1.98031 / 1.61 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.505 Fit side-chains REVERT: A 398 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7421 (mt) REVERT: A 509 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8038 (mt0) REVERT: A 627 PHE cc_start: 0.6605 (t80) cc_final: 0.6094 (t80) REVERT: B 596 ASP cc_start: 0.8620 (p0) cc_final: 0.8234 (p0) REVERT: B 660 ARG cc_start: 0.7993 (tpp-160) cc_final: 0.7115 (mmm160) REVERT: C 526 TYR cc_start: 0.8611 (m-80) cc_final: 0.8224 (m-80) REVERT: C 555 MET cc_start: 0.8743 (mtm) cc_final: 0.8398 (mtt) REVERT: C 578 TYR cc_start: 0.7382 (t80) cc_final: 0.6946 (t80) REVERT: C 813 MET cc_start: 0.7514 (mtp) cc_final: 0.7313 (mtp) REVERT: D 671 TRP cc_start: 0.8617 (m-10) cc_final: 0.8299 (m-10) REVERT: D 908 TYR cc_start: 0.8665 (m-80) cc_final: 0.8429 (m-80) REVERT: D 939 CYS cc_start: 0.7259 (m) cc_final: 0.6960 (t) outliers start: 29 outliers final: 14 residues processed: 176 average time/residue: 0.0989 time to fit residues: 26.9635 Evaluate side-chains 156 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 819 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: [164, 145, 81, 132, 74, 37, 100, 116, 30, 45, 66] chunk 164 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 132 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 100 optimal weight: 0.2980 chunk 116 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 449 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 = 0.3797 r_free = 0.3797 target = 0.135201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.100514 restraints weight = 18714.357| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.64 r_work: 0.3222 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13893 Z= 0.111 Angle : 0.501 5.833 18957 Z= 0.259 Chirality : 0.041 0.242 2177 Planarity : 0.004 0.042 2329 Dihedral : 9.580 80.144 2536 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.39 % Allowed : 12.25 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.21), residues: 1693 helix: 2.12 (0.18), residues: 816 sheet: -1.97 (0.43), residues: 159 loop : -1.19 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 807 TYR 0.015 0.001 TYR D 579 PHE 0.012 0.001 PHE A 458 TRP 0.008 0.001 TRP A 563 HIS 0.004 0.000 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (13872) covalent geometry : angle 0.49551 / 0.26 (18906) SS BOND : bond 0.00565 / 0.35 ( 12) SS BOND : angle 1.26874 / 1.01 ( 24) hydrogen bonds : bond 0.04075 / 2.75 ( 675) hydrogen bonds : angle 4.56831 / 3.19 ( 1965) link_BETA1-4 : bond 0.00284 / 0.14 ( 2) link_BETA1-4 : angle 1.34478 / 0.71 ( 6) link_NAG-ASN : bond 0.00399 / 0.16 ( 7) link_NAG-ASN : angle 1.80269 / 1.55 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.547 Fit side-chains REVERT: A 749 THR cc_start: 0.8979 (p) cc_final: 0.8732 (t) REVERT: A 769 LYS cc_start: 0.7401 (tttm) cc_final: 0.7125 (tptt) REVERT: B 596 ASP cc_start: 0.8494 (p0) cc_final: 0.8118 (p0) REVERT: B 660 ARG cc_start: 0.8082 (tpp-160) cc_final: 0.7157 (mmm160) REVERT: C 526 TYR cc_start: 0.8562 (m-80) cc_final: 0.8123 (m-80) REVERT: C 555 MET cc_start: 0.8705 (mtm) cc_final: 0.8374 (mtt) REVERT: C 578 TYR cc_start: 0.7318 (t80) cc_final: 0.6874 (t80) REVERT: C 813 MET cc_start: 0.7604 (mtp) cc_final: 0.7234 (mtp) REVERT: D 609 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7725 (mttp) REVERT: D 671 TRP cc_start: 0.8594 (m-10) cc_final: 0.8255 (m-10) REVERT: D 908 TYR cc_start: 0.8533 (m-80) cc_final: 0.8330 (m-80) REVERT: D 939 CYS cc_start: 0.7243 (m) cc_final: 0.6967 (t) outliers start: 32 outliers final: 19 residues processed: 171 average time/residue: 0.0973 time to fit residues: 26.3970 Evaluate side-chains 160 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 609 LYS Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 773 ILE Chi-restraints excluded: chain D residue 819 ARG Chi-restraints excluded: chain D residue 944 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: [134, 128, 105, 85, 145, 60, 152, 158, 78, 28, 24] chunk 134 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 158 optimal weight: 0.0270 chunk 78 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 449 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 = 0.3759 r_free = 0.3759 target = 0.131890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.097129 restraints weight = 18746.602| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.64 r_work: 0.3173 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13893 Z= 0.222 Angle : 0.575 7.861 18957 Z= 0.295 Chirality : 0.044 0.215 2177 Planarity : 0.004 0.046 2329 Dihedral : 9.303 73.955 2534 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.44 % Allowed : 12.32 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.21), residues: 1693 helix: 1.99 (0.18), residues: 817 sheet: -2.06 (0.43), residues: 157 loop : -1.21 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 556 TYR 0.025 0.002 TYR B 724 PHE 0.028 0.002 PHE C 533 TRP 0.008 0.001 TRP A 563 HIS 0.007 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.22 (13872) covalent geometry : angle 0.56861 / 0.29 (18906) SS BOND : bond 0.00422 / 0.24 ( 12) SS BOND : angle 1.75708 / 1.38 ( 24) hydrogen bonds : bond 0.04817 / 3.25 ( 675) hydrogen bonds : angle 4.57945 / 3.18 ( 1965) link_BETA1-4 : bond 0.00307 / 0.15 ( 2) link_BETA1-4 : angle 1.48434 / 0.78 ( 6) link_NAG-ASN : bond 0.00130 / 0.06 ( 7) link_NAG-ASN : angle 1.92367 / 1.54 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7566 (mt) REVERT: A 483 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8048 (mtpp) REVERT: A 627 PHE cc_start: 0.6436 (t80) cc_final: 0.6151 (t80) REVERT: B 596 ASP cc_start: 0.8564 (p0) cc_final: 0.8172 (p0) REVERT: B 660 ARG cc_start: 0.8078 (tpp-160) cc_final: 0.7118 (mmm160) REVERT: C 526 TYR cc_start: 0.8647 (m-80) cc_final: 0.8234 (m-80) REVERT: C 555 MET cc_start: 0.8694 (mtm) cc_final: 0.8402 (mtt) REVERT: C 578 TYR cc_start: 0.7443 (t80) cc_final: 0.7008 (t80) REVERT: D 609 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7629 (mttp) REVERT: D 671 TRP cc_start: 0.8645 (m-10) cc_final: 0.8342 (m-10) REVERT: D 830 GLN cc_start: 0.6827 (OUTLIER) cc_final: 0.6488 (tp40) REVERT: D 939 CYS cc_start: 0.7349 (m) cc_final: 0.7064 (t) outliers start: 46 outliers final: 28 residues processed: 174 average time/residue: 0.0917 time to fit residues: 25.2636 Evaluate side-chains 169 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 808 GLN Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 553 MET Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 609 LYS Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 773 ILE Chi-restraints excluded: chain D residue 819 ARG Chi-restraints excluded: chain D residue 830 GLN Chi-restraints excluded: chain D residue 905 ASP Chi-restraints excluded: chain D residue 944 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: [16, 14, 144, 136, 50, 129, 61, 114, 15, 31, 13] chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 136 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 449 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 = 0.3793 r_free = 0.3793 target = 0.134838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.100113 restraints weight = 18754.068| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.66 r_work: 0.3215 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13893 Z= 0.116 Angle : 0.495 7.685 18957 Z= 0.255 Chirality : 0.041 0.233 2177 Planarity : 0.003 0.041 2329 Dihedral : 8.902 75.356 2534 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.39 % Allowed : 13.89 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.21), residues: 1693 helix: 2.19 (0.18), residues: 817 sheet: -2.07 (0.41), residues: 165 loop : -1.18 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 807 TYR 0.016 0.001 TYR D 579 PHE 0.028 0.001 PHE B 716 TRP 0.007 0.001 TRP A 563 HIS 0.004 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (13872) covalent geometry : angle 0.49053 / 0.25 (18906) SS BOND : bond 0.00246 / 0.15 ( 12) SS BOND : angle 1.07323 / 0.83 ( 24) hydrogen bonds : bond 0.03830 / 2.60 ( 675) hydrogen bonds : angle 4.40609 / 3.07 ( 1965) link_BETA1-4 : bond 0.00258 / 0.13 ( 2) link_BETA1-4 : angle 1.35428 / 0.72 ( 6) link_NAG-ASN : bond 0.00361 / 0.15 ( 7) link_NAG-ASN : angle 1.77555 / 1.49 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 725 LYS cc_start: 0.7977 (mtpp) cc_final: 0.7701 (mtpp) REVERT: B 553 MET cc_start: 0.7752 (ttt) cc_final: 0.7397 (ttp) REVERT: B 596 ASP cc_start: 0.8523 (p0) cc_final: 0.8100 (p0) REVERT: B 660 ARG cc_start: 0.8060 (tpp-160) cc_final: 0.7141 (mmm160) REVERT: C 526 TYR cc_start: 0.8584 (m-80) cc_final: 0.8210 (m-80) REVERT: C 555 MET cc_start: 0.8748 (mtm) cc_final: 0.8434 (mtt) REVERT: C 578 TYR cc_start: 0.7471 (t80) cc_final: 0.7066 (t80) REVERT: C 813 MET cc_start: 0.7679 (mtp) cc_final: 0.7448 (mtp) REVERT: D 609 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7760 (mttp) REVERT: D 671 TRP cc_start: 0.8611 (m-10) cc_final: 0.8295 (m-10) REVERT: D 844 MET cc_start: 0.8853 (tpt) cc_final: 0.8548 (tpt) REVERT: D 939 CYS cc_start: 0.7284 (m) cc_final: 0.7003 (t) outliers start: 32 outliers final: 21 residues processed: 165 average time/residue: 0.0928 time to fit residues: 24.0407 Evaluate side-chains 160 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 609 LYS Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 773 ILE Chi-restraints excluded: chain D residue 819 ARG Chi-restraints excluded: chain D residue 944 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: [98, 50, 107, 126, 80, 77, 72, 141, 87, 59, 66] chunk 98 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 80 optimal weight: 0.0870 chunk 77 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 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 = 0.3753 r_free = 0.3753 target = 0.131714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.096698 restraints weight = 18788.233| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.65 r_work: 0.3166 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13893 Z= 0.227 Angle : 0.580 9.280 18957 Z= 0.296 Chirality : 0.044 0.213 2177 Planarity : 0.004 0.049 2329 Dihedral : 8.887 75.041 2534 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.76 % Allowed : 14.56 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.21), residues: 1693 helix: 1.98 (0.18), residues: 820 sheet: -2.08 (0.43), residues: 157 loop : -1.22 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 638 TYR 0.024 0.002 TYR D 579 PHE 0.030 0.002 PHE C 533 TRP 0.008 0.001 TRP A 563 HIS 0.008 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.23 (13872) covalent geometry : angle 0.57441 / 0.29 (18906) SS BOND : bond 0.00446 / 0.25 ( 12) SS BOND : angle 1.42361 / 1.17 ( 24) hydrogen bonds : bond 0.04800 / 3.25 ( 675) hydrogen bonds : angle 4.51342 / 3.13 ( 1965) link_BETA1-4 : bond 0.00259 / 0.12 ( 2) link_BETA1-4 : angle 1.52480 / 0.79 ( 6) link_NAG-ASN : bond 0.00094 / 0.05 ( 7) link_NAG-ASN : angle 1.93208 / 1.48 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.374 Fit side-chains REVERT: A 483 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8034 (mtpp) REVERT: A 719 GLN cc_start: 0.7354 (tp40) cc_final: 0.7116 (tp-100) REVERT: B 596 ASP cc_start: 0.8516 (p0) cc_final: 0.8106 (p0) REVERT: B 660 ARG cc_start: 0.8050 (tpp-160) cc_final: 0.7128 (mmm160) REVERT: B 812 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7760 (pm20) REVERT: C 526 TYR cc_start: 0.8642 (m-80) cc_final: 0.8271 (m-80) REVERT: C 555 MET cc_start: 0.8700 (mtm) cc_final: 0.8418 (mtt) REVERT: C 578 TYR cc_start: 0.7558 (t80) cc_final: 0.7085 (t80) REVERT: D 609 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7631 (mttp) REVERT: D 671 TRP cc_start: 0.8641 (m-10) cc_final: 0.8350 (m-10) REVERT: D 830 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6570 (tp40) REVERT: D 939 CYS cc_start: 0.7320 (m) cc_final: 0.7042 (t) outliers start: 37 outliers final: 26 residues processed: 167 average time/residue: 0.0971 time to fit residues: 25.3137 Evaluate side-chains 164 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 808 GLN Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 553 MET Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 609 LYS Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 773 ILE Chi-restraints excluded: chain D residue 819 ARG Chi-restraints excluded: chain D residue 830 GLN Chi-restraints excluded: chain D residue 905 ASP Chi-restraints excluded: chain D residue 944 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: [33, 109, 25, 60, 149, 138, 83, 50, 157, 120, 136] chunk 33 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 157 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 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 = 0.3788 r_free = 0.3788 target = 0.134525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.099824 restraints weight = 18536.369| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.64 r_work: 0.3208 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13893 Z= 0.117 Angle : 0.500 5.822 18957 Z= 0.257 Chirality : 0.041 0.224 2177 Planarity : 0.003 0.044 2329 Dihedral : 8.695 77.215 2534 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.99 % Allowed : 14.79 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.21), residues: 1693 helix: 2.19 (0.18), residues: 822 sheet: -2.15 (0.41), residues: 165 loop : -1.17 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 523 TYR 0.017 0.001 TYR D 579 PHE 0.024 0.001 PHE B 716 TRP 0.007 0.001 TRP A 563 HIS 0.005 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (13872) covalent geometry : angle 0.49497 / 0.26 (18906) SS BOND : bond 0.00259 / 0.15 ( 12) SS BOND : angle 1.21872 / 0.87 ( 24) hydrogen bonds : bond 0.03881 / 2.63 ( 675) hydrogen bonds : angle 4.35301 / 3.02 ( 1965) link_BETA1-4 : bond 0.00287 / 0.14 ( 2) link_BETA1-4 : angle 1.39040 / 0.73 ( 6) link_NAG-ASN : bond 0.00319 / 0.13 ( 7) link_NAG-ASN : angle 1.74645 / 1.42 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.543 Fit side-chains REVERT: A 398 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7512 (mt) REVERT: A 509 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8136 (mt0) REVERT: B 553 MET cc_start: 0.7734 (ttt) cc_final: 0.7426 (ttp) REVERT: B 596 ASP cc_start: 0.8447 (p0) cc_final: 0.8012 (p0) REVERT: B 660 ARG cc_start: 0.8054 (tpp-160) cc_final: 0.7143 (mmm160) REVERT: C 526 TYR cc_start: 0.8626 (m-80) cc_final: 0.8190 (m-80) REVERT: C 555 MET cc_start: 0.8753 (mtm) cc_final: 0.8453 (mtt) REVERT: C 578 TYR cc_start: 0.7611 (t80) cc_final: 0.7155 (t80) REVERT: D 609 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7763 (mttp) REVERT: D 671 TRP cc_start: 0.8621 (m-10) cc_final: 0.8327 (m-10) REVERT: D 830 GLN cc_start: 0.6790 (OUTLIER) cc_final: 0.6576 (tm-30) REVERT: D 855 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7398 (tp) REVERT: D 939 CYS cc_start: 0.7295 (m) cc_final: 0.7021 (t) outliers start: 40 outliers final: 25 residues processed: 170 average time/residue: 0.0973 time to fit residues: 26.1550 Evaluate side-chains 167 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 609 LYS Chi-restraints excluded: chain D residue 659 THR Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 773 ILE Chi-restraints excluded: chain D residue 819 ARG Chi-restraints excluded: chain D residue 830 GLN Chi-restraints excluded: chain D residue 855 ILE Chi-restraints excluded: chain D residue 944 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: [114, 59, 157, 115, 160, 108, 152, 55, 112, 167, 61] chunk 114 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 160 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 449 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 = 0.3787 r_free = 0.3787 target = 0.134606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.099264 restraints weight = 18618.477| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.70 r_work: 0.3195 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13893 Z= 0.145 Angle : 0.519 8.628 18957 Z= 0.264 Chirality : 0.042 0.210 2177 Planarity : 0.003 0.043 2329 Dihedral : 8.590 77.397 2534 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.69 % Allowed : 15.38 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.21), residues: 1693 helix: 2.20 (0.18), residues: 824 sheet: -2.08 (0.42), residues: 159 loop : -1.16 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 807 TYR 0.019 0.001 TYR D 579 PHE 0.021 0.001 PHE B 716 TRP 0.006 0.001 TRP A 563 HIS 0.006 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.14 (13872) covalent geometry : angle 0.51374 / 0.26 (18906) SS BOND : bond 0.00287 / 0.17 ( 12) SS BOND : angle 1.15533 / 0.89 ( 24) hydrogen bonds : bond 0.04057 / 2.76 ( 675) hydrogen bonds : angle 4.32589 / 3.00 ( 1965) link_BETA1-4 : bond 0.00285 / 0.14 ( 2) link_BETA1-4 : angle 1.42618 / 0.75 ( 6) link_NAG-ASN : bond 0.00200 / 0.09 ( 7) link_NAG-ASN : angle 1.73327 / 1.37 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 398 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7503 (mt) REVERT: A 509 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8113 (mt0) REVERT: B 553 MET cc_start: 0.7756 (ttt) cc_final: 0.7429 (ttp) REVERT: B 596 ASP cc_start: 0.8497 (p0) cc_final: 0.8072 (p0) REVERT: B 660 ARG cc_start: 0.8048 (tpp-160) cc_final: 0.7150 (mmm160) REVERT: C 526 TYR cc_start: 0.8661 (m-80) cc_final: 0.8221 (m-80) REVERT: C 555 MET cc_start: 0.8703 (mtm) cc_final: 0.8399 (mtt) REVERT: C 578 TYR cc_start: 0.7616 (t80) cc_final: 0.7174 (t80) REVERT: D 609 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7760 (mttp) REVERT: D 671 TRP cc_start: 0.8620 (m-10) cc_final: 0.8325 (m-10) REVERT: D 830 GLN cc_start: 0.6851 (OUTLIER) cc_final: 0.6640 (tm-30) REVERT: D 855 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7369 (tp) REVERT: D 939 CYS cc_start: 0.7227 (m) cc_final: 0.6943 (t) outliers start: 36 outliers final: 26 residues processed: 162 average time/residue: 0.0957 time to fit residues: 24.4804 Evaluate side-chains 166 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 808 GLN Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 609 LYS Chi-restraints excluded: chain D residue 659 THR Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 773 ILE Chi-restraints excluded: chain D residue 819 ARG Chi-restraints excluded: chain D residue 830 GLN Chi-restraints excluded: chain D residue 855 ILE Chi-restraints excluded: chain D residue 905 ASP Chi-restraints excluded: chain D residue 944 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: [71, 131, 29, 115, 140, 78, 68, 69, 41, 109, 127] chunk 71 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 449 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 = 0.3786 r_free = 0.3786 target = 0.134703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.099241 restraints weight = 18912.343| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.72 r_work: 0.3195 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13893 Z= 0.143 Angle : 0.513 5.781 18957 Z= 0.262 Chirality : 0.042 0.210 2177 Planarity : 0.003 0.043 2329 Dihedral : 8.512 77.874 2534 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.84 % Allowed : 15.38 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.21), residues: 1693 helix: 2.22 (0.18), residues: 824 sheet: -2.09 (0.42), residues: 160 loop : -1.17 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 807 TYR 0.022 0.001 TYR B 695 PHE 0.020 0.001 PHE B 716 TRP 0.007 0.001 TRP A 563 HIS 0.006 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 (13872) covalent geometry : angle 0.50799 / 0.26 (18906) SS BOND : bond 0.00271 / 0.16 ( 12) SS BOND : angle 1.05471 / 0.82 ( 24) hydrogen bonds : bond 0.04001 / 2.72 ( 675) hydrogen bonds : angle 4.30504 / 2.98 ( 1965) link_BETA1-4 : bond 0.00295 / 0.14 ( 2) link_BETA1-4 : angle 1.42554 / 0.75 ( 6) link_NAG-ASN : bond 0.00208 / 0.09 ( 7) link_NAG-ASN : angle 1.71456 / 1.34 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.513 Fit side-chains REVERT: A 398 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7434 (mt) REVERT: A 509 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8101 (mt0) REVERT: B 553 MET cc_start: 0.7739 (ttt) cc_final: 0.7428 (ttp) REVERT: B 596 ASP cc_start: 0.8486 (p0) cc_final: 0.8064 (p0) REVERT: B 660 ARG cc_start: 0.8030 (tpp-160) cc_final: 0.7143 (mmm160) REVERT: C 526 TYR cc_start: 0.8661 (m-80) cc_final: 0.8222 (m-80) REVERT: C 555 MET cc_start: 0.8719 (mtm) cc_final: 0.8421 (mtt) REVERT: C 578 TYR cc_start: 0.7616 (t80) cc_final: 0.7158 (t80) REVERT: D 609 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7747 (mttp) REVERT: D 671 TRP cc_start: 0.8609 (m-10) cc_final: 0.8313 (m-10) REVERT: D 674 HIS cc_start: 0.6561 (OUTLIER) cc_final: 0.6334 (t-90) REVERT: D 830 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6649 (tm-30) REVERT: D 855 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7368 (tp) REVERT: D 939 CYS cc_start: 0.7224 (m) cc_final: 0.6942 (t) outliers start: 38 outliers final: 27 residues processed: 163 average time/residue: 0.0899 time to fit residues: 23.4332 Evaluate side-chains 168 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 808 GLN Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 553 MET Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 609 LYS Chi-restraints excluded: chain D residue 659 THR Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 674 HIS Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 773 ILE Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 819 ARG Chi-restraints excluded: chain D residue 830 GLN Chi-restraints excluded: chain D residue 855 ILE Chi-restraints excluded: chain D residue 905 ASP Chi-restraints excluded: chain D residue 944 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: [139, 99, 17, 62, 2, 151, 16, 103, 20, 149, 140] chunk 139 optimal weight: 0.0770 chunk 99 optimal weight: 0.0980 chunk 17 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 149 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 520 ASN ** C 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.135863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.101143 restraints weight = 18503.927| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.65 r_work: 0.3228 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13893 Z= 0.105 Angle : 0.493 11.041 18957 Z= 0.251 Chirality : 0.041 0.215 2177 Planarity : 0.003 0.041 2329 Dihedral : 8.383 79.360 2533 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.69 % Allowed : 15.76 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.21), residues: 1693 helix: 2.33 (0.18), residues: 825 sheet: -2.05 (0.41), residues: 166 loop : -1.09 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 807 TYR 0.023 0.001 TYR B 695 PHE 0.020 0.001 PHE B 716 TRP 0.007 0.001 TRP C 498 HIS 0.005 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (13872) covalent geometry : angle 0.48881 / 0.25 (18906) SS BOND : bond 0.00312 / 0.19 ( 12) SS BOND : angle 0.81264 / 0.64 ( 24) hydrogen bonds : bond 0.03575 / 2.45 ( 675) hydrogen bonds : angle 4.24298 / 2.94 ( 1965) link_BETA1-4 : bond 0.00467 / 0.23 ( 2) link_BETA1-4 : angle 1.39624 / 0.74 ( 6) link_NAG-ASN : bond 0.00302 / 0.13 ( 7) link_NAG-ASN : angle 1.60320 / 1.28 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 398 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7446 (mt) REVERT: A 509 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8208 (mt0) REVERT: A 749 THR cc_start: 0.9020 (p) cc_final: 0.8773 (t) REVERT: B 553 MET cc_start: 0.7693 (ttt) cc_final: 0.7382 (ttp) REVERT: B 596 ASP cc_start: 0.8431 (p0) cc_final: 0.8013 (p0) REVERT: B 660 ARG cc_start: 0.8042 (tpp-160) cc_final: 0.7164 (mmm160) REVERT: C 526 TYR cc_start: 0.8664 (m-80) cc_final: 0.8254 (m-80) REVERT: C 555 MET cc_start: 0.8756 (mtm) cc_final: 0.8451 (mtt) REVERT: C 578 TYR cc_start: 0.7609 (t80) cc_final: 0.7175 (t80) REVERT: C 813 MET cc_start: 0.7148 (mtm) cc_final: 0.6323 (mtp) REVERT: D 609 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7773 (mttp) REVERT: D 671 TRP cc_start: 0.8630 (m-10) cc_final: 0.8358 (m-10) REVERT: D 830 GLN cc_start: 0.6844 (OUTLIER) cc_final: 0.6624 (tm-30) REVERT: D 939 CYS cc_start: 0.7216 (m) cc_final: 0.6940 (t) outliers start: 36 outliers final: 25 residues processed: 165 average time/residue: 0.0910 time to fit residues: 23.7445 Evaluate side-chains 163 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 808 GLN Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 553 MET Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 609 LYS Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 773 ILE Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 819 ARG Chi-restraints excluded: chain D residue 830 GLN Chi-restraints excluded: chain D residue 944 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: [33, 65, 111, 121, 37, 164, 6, 66, 163, 110, 123] chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 123 optimal weight: 8.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 449 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 = 0.3778 r_free = 0.3778 target = 0.133784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.098864 restraints weight = 18638.650| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.66 r_work: 0.3195 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13893 Z= 0.167 Angle : 0.529 5.963 18957 Z= 0.270 Chirality : 0.042 0.211 2177 Planarity : 0.003 0.045 2329 Dihedral : 8.381 78.018 2533 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.39 % Allowed : 15.68 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.21), residues: 1693 helix: 2.26 (0.18), residues: 824 sheet: -2.08 (0.41), residues: 164 loop : -1.10 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 807 TYR 0.020 0.001 TYR D 579 PHE 0.022 0.002 PHE C 533 TRP 0.007 0.001 TRP A 563 HIS 0.006 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (13872) covalent geometry : angle 0.52501 / 0.27 (18906) SS BOND : bond 0.00437 / 0.26 ( 12) SS BOND : angle 1.09498 / 0.86 ( 24) hydrogen bonds : bond 0.04109 / 2.79 ( 675) hydrogen bonds : angle 4.29790 / 2.97 ( 1965) link_BETA1-4 : bond 0.00303 / 0.15 ( 2) link_BETA1-4 : angle 1.45566 / 0.77 ( 6) link_NAG-ASN : bond 0.00148 / 0.07 ( 7) link_NAG-ASN : angle 1.69114 / 1.28 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3813.61 seconds wall clock time: 65 minutes 44.64 seconds (3944.64 seconds total)