Starting phenix.real_space_refine on Sat Sep 12 04:27:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6y5r_10703/09_2026/6y5r_10703.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5r_10703/09_2026/6y5r_10703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6y5r_10703/09_2026/6y5r_10703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5r_10703/09_2026/6y5r_10703.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6y5r_10703/09_2026/6y5r_10703.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6y5r_10703/09_2026/6y5r_10703.cif" model { file = "/net/cci-nas-00/data/ceres_data/6y5r_10703/09_2026/6y5r_10703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5r_10703/09_2026/6y5r_10703.cif" } resolution = 3.76 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= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 93 5.16 5 C 8825 2.51 5 N 2257 2.21 5 O 2417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13592 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6723 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 879, 6636 Classifications: {'peptide': 879} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 32, 'TRANS': 846} Chain breaks: 4 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 5, 'PHE:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 100 Conformer: "B" Number of residues, atoms: 879, 6636 Classifications: {'peptide': 879} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 32, 'TRANS': 846} Chain breaks: 4 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 5, 'PHE:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 100 bond proxies already assigned to first conformer: 6699 Chain: "B" Number of atoms: 6763 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 879, 6666 Classifications: {'peptide': 879} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 32, 'TRANS': 846} Chain breaks: 4 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 11, 'ASP:plan': 3, 'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 879, 6666 Classifications: {'peptide': 879} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 32, 'TRANS': 846} Chain breaks: 4 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 11, 'ASP:plan': 3, 'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 6720 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 28 residue: pdb=" N AMET A 905 " occ=0.50 ... (8 atoms not shown) pdb=" CB BMET A 905 " occ=0.50 residue: pdb=" N ALYS A 906 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLYS A 906 " occ=0.50 residue: pdb=" N ALYS A 907 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLYS A 907 " occ=0.50 residue: pdb=" N AASP A 908 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP A 908 " occ=0.50 residue: pdb=" N ALEU A 909 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLEU A 909 " occ=0.50 residue: pdb=" N AALA A 910 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 910 " occ=0.50 residue: pdb=" N ATHR A 911 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTHR A 911 " occ=0.50 residue: pdb=" N APHE A 912 " occ=0.50 ... (8 atoms not shown) pdb=" CB BPHE A 912 " occ=0.50 residue: pdb=" N ALEU A 913 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLEU A 913 " occ=0.50 residue: pdb=" N ATYR A 914 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTYR A 914 " occ=0.50 residue: pdb=" N AHIS A 915 " occ=0.50 ... (8 atoms not shown) pdb=" CB BHIS A 915 " occ=0.50 residue: pdb=" N ALEU A 916 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLEU A 916 " occ=0.50 ... (remaining 16 not shown) Time building chain proxies: 4.51, per 1000 atoms: 0.33 Number of scatterers: 13592 At special positions: 0 Unit cell: (107.415, 106.764, 147.126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 93 16.00 O 2417 8.00 N 2257 7.00 C 8825 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 640 " distance=2.03 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 359 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 640 " distance=2.04 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 359 " - pdb=" SG CYS B 369 " 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 C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A1104 " - " ASN A 377 " " NAG B1104 " - " ASN B 377 " " NAG C 1 " - " ASN A 328 " " NAG D 1 " - " ASN B 328 " Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 968.1 milliseconds 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3292 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 6 sheets defined 62.4% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 111 through 121 removed outlier: 3.777A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 156 through 193 removed outlier: 6.462A pdb=" N VAL A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N LEU A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 243 removed outlier: 3.646A pdb=" N MET A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 211 - end of helix Processing helix chain 'A' and resid 261 through 284 Processing helix chain 'A' and resid 285 through 314 removed outlier: 3.594A pdb=" N VAL A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N SER A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LEU A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 removed outlier: 3.922A pdb=" N GLY A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.530A pdb=" N VAL A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HIS A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 376' Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 433 through 442 removed outlier: 3.775A pdb=" N GLY A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 447 through 453 removed outlier: 3.635A pdb=" N SER A 452 " --> pdb=" O MET A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 491 Proline residue: A 466 - end of helix removed outlier: 3.762A pdb=" N VAL A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 517 through 550 removed outlier: 4.322A pdb=" N ILE A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Proline residue: A 541 - end of helix removed outlier: 3.504A pdb=" N ASP A 550 " --> pdb=" O ALA A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 561 removed outlier: 3.959A pdb=" N VAL A 558 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 584 removed outlier: 3.526A pdb=" N LEU A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 616 Proline residue: A 593 - end of helix removed outlier: 3.807A pdb=" N CYS A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 675 removed outlier: 3.605A pdb=" N SER A 633 " --> pdb=" O HIS A 629 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N TYR A 650 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 654 " --> pdb=" O TYR A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 696 removed outlier: 3.792A pdb=" N GLU A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 734 removed outlier: 4.192A pdb=" N LEU A 726 " --> pdb=" O HIS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 751 Processing helix chain 'A' and resid 752 through 770 Processing helix chain 'A' and resid 783 through 795 removed outlier: 3.882A pdb=" N GLN A 793 " --> pdb=" O SER A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 835 Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'A' and resid 868 through 881 removed outlier: 3.507A pdb=" N LEU A 872 " --> pdb=" O ASP A 868 " (cutoff:3.500A) Proline residue: A 876 - end of helix Processing helix chain 'A' and resid 906 through 919 Processing helix chain 'A' and resid 929 through 931 No H-bonds generated for 'chain 'A' and resid 929 through 931' Processing helix chain 'A' and resid 932 through 946 removed outlier: 4.046A pdb=" N GLU A 938 " --> pdb=" O ALA A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1048 removed outlier: 3.840A pdb=" N LYS A1038 " --> pdb=" O HIS A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1066 through 1078 Processing helix chain 'B' and resid 111 through 121 removed outlier: 3.733A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 149 Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 156 through 193 removed outlier: 6.319A pdb=" N VAL B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N LEU B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 243 removed outlier: 3.611A pdb=" N MET B 204 " --> pdb=" O GLY B 200 " (cutoff:3.500A) Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 261 through 284 Processing helix chain 'B' and resid 285 through 314 removed outlier: 3.563A pdb=" N VAL B 289 " --> pdb=" O GLY B 285 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N SER B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 370 through 376 removed outlier: 3.811A pdb=" N VAL B 374 " --> pdb=" O ASP B 370 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N HIS B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN B 376 " --> pdb=" O TYR B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 370 through 376' Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 433 through 442 removed outlier: 3.753A pdb=" N GLY B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 445 No H-bonds generated for 'chain 'B' and resid 443 through 445' Processing helix chain 'B' and resid 447 through 453 Processing helix chain 'B' and resid 460 through 489 Proline residue: B 466 - end of helix removed outlier: 3.668A pdb=" N VAL B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 517 through 550 removed outlier: 4.256A pdb=" N ILE B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Proline residue: B 541 - end of helix removed outlier: 3.571A pdb=" N ASP B 550 " --> pdb=" O ALA B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 561 removed outlier: 4.043A pdb=" N VAL B 558 " --> pdb=" O PHE B 555 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS B 561 " --> pdb=" O VAL B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 584 Processing helix chain 'B' and resid 587 through 616 Proline residue: B 593 - end of helix removed outlier: 3.856A pdb=" N CYS B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 675 removed outlier: 3.790A pdb=" N SER B 633 " --> pdb=" O HIS B 629 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N TYR B 650 " --> pdb=" O ILE B 646 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N TYR B 651 " --> pdb=" O SER B 647 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 654 " --> pdb=" O TYR B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 696 removed outlier: 3.688A pdb=" N GLU B 696 " --> pdb=" O LEU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 734 removed outlier: 4.057A pdb=" N LEU B 726 " --> pdb=" O HIS B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 751 Processing helix chain 'B' and resid 752 through 770 Processing helix chain 'B' and resid 783 through 795 removed outlier: 3.826A pdb=" N GLN B 793 " --> pdb=" O SER B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 835 removed outlier: 3.932A pdb=" N LYS B 823 " --> pdb=" O ALA B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 Processing helix chain 'B' and resid 868 through 881 removed outlier: 4.182A pdb=" N LEU B 872 " --> pdb=" O ASP B 868 " (cutoff:3.500A) Proline residue: B 876 - end of helix Processing helix chain 'B' and resid 884 through 888 removed outlier: 4.452A pdb=" N LYS B 887 " --> pdb=" O VAL B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 919 removed outlier: 3.761A pdb=" N AALA B 910 " --> pdb=" O ALYS B 906 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N BTHR B 911 " --> pdb=" O BLYS B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 931 No H-bonds generated for 'chain 'B' and resid 929 through 931' Processing helix chain 'B' and resid 932 through 946 removed outlier: 3.945A pdb=" N GLU B 938 " --> pdb=" O ALA B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1048 removed outlier: 4.078A pdb=" N LYS B1038 " --> pdb=" O HIS B1034 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1078 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA3, first strand: chain 'A' and resid 775 through 781 removed outlier: 6.491A pdb=" N LEU A 708 " --> pdb=" O ILE A 740 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N GLY A 742 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL A 710 " --> pdb=" O GLY A 742 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL A 744 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLY A 808 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 805 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ALA A 842 " --> pdb=" O VAL A 805 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET A 807 " --> pdb=" O ALA A 842 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A1053 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL A1087 " --> pdb=" O VAL A1053 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU A1055 " --> pdb=" O VAL A1087 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASN A 859 " --> pdb=" O LEU A1052 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU A1054 " --> pdb=" O ASN A 859 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP A 861 " --> pdb=" O LEU A1054 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ASN A1056 " --> pdb=" O ASP A 861 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N TRP A 863 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 921 " --> pdb=" O ILE A 890 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 329 through 330 Processing sheet with id=AA5, first strand: chain 'B' and resid 342 through 344 Processing sheet with id=AA6, first strand: chain 'B' and resid 775 through 781 removed outlier: 6.523A pdb=" N LEU B 708 " --> pdb=" O ILE B 740 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLY B 742 " --> pdb=" O LEU B 708 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL B 710 " --> pdb=" O GLY B 742 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL B 744 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY B 808 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 805 " --> pdb=" O LEU B 840 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ALA B 842 " --> pdb=" O VAL B 805 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N MET B 807 " --> pdb=" O ALA B 842 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B1084 " --> pdb=" O LYS B 843 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B1053 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL B1087 " --> pdb=" O VAL B1053 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU B1055 " --> pdb=" O VAL B1087 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN B1056 " --> pdb=" O TRP B 863 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 921 " --> pdb=" O ILE B 890 " (cutoff:3.500A) 823 hydrogen bonds defined for protein. 2367 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: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4284 1.35 - 1.48: 3541 1.48 - 1.60: 5922 1.60 - 1.73: 0 1.73 - 1.86: 148 Bond restraints: 13895 Sorted by residual: bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.71e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.51e+00 bond pdb=" CB CYS B 640 " pdb=" SG CYS B 640 " ideal model delta sigma weight residual 1.808 1.758 0.050 3.30e-02 9.18e+02 2.29e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" CB CYS B 179 " pdb=" SG CYS B 179 " ideal model delta sigma weight residual 1.808 1.857 -0.049 3.30e-02 9.18e+02 2.17e+00 ... (remaining 13890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 18432 1.72 - 3.45: 408 3.45 - 5.17: 56 5.17 - 6.90: 9 6.90 - 8.62: 3 Bond angle restraints: 18908 Sorted by residual: angle pdb=" N BGLU A 919 " pdb=" CA BGLU A 919 " pdb=" C BGLU A 919 " ideal model delta sigma weight residual 110.91 115.72 -4.81 1.17e+00 7.31e-01 1.69e+01 angle pdb=" C ILE B 639 " pdb=" N CYS B 640 " pdb=" CA CYS B 640 " ideal model delta sigma weight residual 122.38 115.92 6.46 1.81e+00 3.05e-01 1.27e+01 angle pdb=" N VAL B 494 " pdb=" CA VAL B 494 " pdb=" C VAL B 494 " ideal model delta sigma weight residual 111.90 109.28 2.62 8.10e-01 1.52e+00 1.04e+01 angle pdb=" CA CYS B 640 " pdb=" CB CYS B 640 " pdb=" SG CYS B 640 " ideal model delta sigma weight residual 114.40 121.67 -7.27 2.30e+00 1.89e-01 1.00e+01 angle pdb=" N ARG A 454 " pdb=" CA ARG A 454 " pdb=" C ARG A 454 " ideal model delta sigma weight residual 110.44 106.95 3.49 1.20e+00 6.94e-01 8.48e+00 ... (remaining 18903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 7457 16.49 - 32.98: 505 32.98 - 49.46: 84 49.46 - 65.95: 15 65.95 - 82.44: 4 Dihedral angle restraints: 8065 sinusoidal: 2945 harmonic: 5120 Sorted by residual: dihedral pdb=" CB CYS B 179 " pdb=" SG CYS B 179 " pdb=" SG CYS B 640 " pdb=" CB CYS B 640 " ideal model delta sinusoidal sigma weight residual 93.00 48.74 44.26 1 1.00e+01 1.00e-02 2.72e+01 dihedral pdb=" CA CYS B 640 " pdb=" C CYS B 640 " pdb=" N LEU B 641 " pdb=" CA LEU B 641 " ideal model delta harmonic sigma weight residual 180.00 154.20 25.80 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA GLN B 707 " pdb=" C GLN B 707 " pdb=" N LEU B 708 " pdb=" CA LEU B 708 " ideal model delta harmonic sigma weight residual -180.00 -155.81 -24.19 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 8062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1860 0.054 - 0.107: 342 0.107 - 0.161: 46 0.161 - 0.214: 1 0.214 - 0.268: 3 Chirality restraints: 2252 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA CYS B 640 " pdb=" N CYS B 640 " pdb=" C CYS B 640 " pdb=" CB CYS B 640 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 2249 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 640 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C CYS B 640 " -0.046 2.00e-02 2.50e+03 pdb=" O CYS B 640 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU B 641 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 142 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO B 143 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 143 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 143 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 442 " -0.027 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO B 443 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 443 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 443 " -0.023 5.00e-02 4.00e+02 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2124 2.76 - 3.29: 14024 3.29 - 3.83: 22822 3.83 - 4.36: 26503 4.36 - 4.90: 45833 Nonbonded interactions: 111306 Sorted by model distance: nonbonded pdb=" OD1 ASN A 859 " pdb=" OG SER A 889 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR B 308 " pdb=" OG SER B 482 " model vdw 2.240 3.040 nonbonded pdb=" ND2 ASN B1040 " pdb=" O VAL B1076 " model vdw 2.248 3.120 nonbonded pdb=" O PRO B1058 " pdb=" OH TYR B1070 " model vdw 2.260 3.040 nonbonded pdb=" O ILE A1043 " pdb=" OG SER A1047 " model vdw 2.288 3.040 ... (remaining 111301 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 102 through 312 or (resid 313 and (name N or name CA or na \ me C or name O or name CB )) or resid 314 through 341 or (resid 342 and (name N \ or name CA or name C or name O or name CB )) or resid 343 through 393 or (resid \ 394 and (name N or name CA or name C or name O or name CB )) or resid 395 throug \ h 407 or (resid 408 and (name N or name CA or name C or name O or name CB )) or \ resid 409 through 428 or (resid 429 and (name N or name CA or name C or name O o \ r name CB )) or resid 430 through 491 or (resid 492 and (name N or name CA or na \ me C or name O or name CB )) or resid 493 through 504 or (resid 505 and (name N \ or name CA or name C or name O or name CB )) or resid 506 through 715 or (resid \ 716 and (name N or name CA or name C or name O or name CB )) or resid 717 throug \ h 856 or (resid 857 and (name N or name CA or name C or name O or name CB )) or \ resid 858 through 882 or (resid 883 and (name N or name CA or name C or name O o \ r name CB )) or resid 884 through 896 or resid 920 through 928 or (resid 929 and \ (name N or name CA or name C or name O or name CB )) or resid 930 or (resid 931 \ and (name N or name CA or name C or name O or name CB )) or resid 932 through 9 \ 37 or (resid 938 through 939 and (name N or name CA or name C or name O or name \ CB )) or resid 940 or (resid 941 and (name N or name CA or name C or name O or n \ ame CB )) or resid 942 through 1045 or (resid 1046 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1047 through 1078 or (resid 1079 and (name \ N or name CA or name C or name O or name CB )) or resid 1080 through 1081 or (re \ sid 1082 and (name N or name CA or name C or name O or name CB )) or resid 1083 \ through 1104)) selection = (chain 'B' and (resid 102 through 112 or (resid 113 through 114 and (name N or n \ ame CA or name C or name O or name CB )) or resid 115 through 118 or (resid 119 \ through 121 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 3 through 211 or (resid 212 and (name N or name CA or name C or name O or name C \ B )) or resid 213 through 286 or (resid 287 and (name N or name CA or name C or \ name O or name CB )) or resid 288 through 290 or (resid 291 and (name N or name \ CA or name C or name O or name CB )) or resid 292 through 352 or (resid 353 and \ (name N or name CA or name C or name O or name CB )) or resid 354 through 364 or \ (resid 365 through 367 and (name N or name CA or name C or name O or name CB )) \ or resid 368 through 417 or (resid 418 and (name N or name CA or name C or name \ O or name CB )) or resid 419 through 420 or (resid 421 and (name N or name CA o \ r name C or name O or name CB )) or resid 422 through 462 or (resid 463 and (nam \ e N or name CA or name C or name O or name CB )) or resid 464 through 616 or (re \ sid 617 and (name N or name CA or name C or name O or name CB )) or resid 618 th \ rough 634 or (resid 635 and (name N or name CA or name C or name O or name CB )) \ or resid 636 through 814 or (resid 815 and (name N or name CA or name C or name \ O or name CB )) or resid 816 or (resid 817 and (name N or name CA or name C or \ name O or name CB )) or resid 818 through 872 or (resid 873 and (name N or name \ CA or name C or name O or name CB )) or resid 874 through 896 or resid 920 throu \ gh 942 or (resid 943 through 946 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1028 through 1030 or (resid 1031 and (name N or name CA or na \ me C or name O or name CB )) or resid 1032 through 1071 or (resid 1072 and (name \ N or name CA or name C or name O or name CB )) or resid 1073 through 1104)) } ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.260 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 0.054 13909 Z= 0.173 Angle : 0.645 8.623 18944 Z= 0.380 Chirality : 0.042 0.268 2252 Planarity : 0.004 0.042 2348 Dihedral : 11.470 82.440 4755 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.07 % Allowed : 2.15 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.18), residues: 1768 helix: -0.81 (0.15), residues: 960 sheet: -1.87 (0.45), residues: 92 loop : -2.34 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 814 TYR 0.009 0.001 TYR B 628 PHE 0.014 0.001 PHE B1073 TRP 0.012 0.001 TRP A 630 HIS 0.002 0.001 HIS B 790 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (13895) covalent geometry : angle 0.64012 / 0.38 (18908) SS BOND : bond 0.00489 / 0.24 ( 6) SS BOND : angle 2.11970 / 1.22 ( 12) hydrogen bonds : bond 0.13755 / 8.70 ( 823) hydrogen bonds : angle 5.90778 / 4.15 ( 2367) link_BETA1-4 : bond 0.00369 / 0.18 ( 4) link_BETA1-4 : angle 1.21891 / 0.66 ( 12) link_NAG-ASN : bond 0.00236 / 0.11 ( 4) link_NAG-ASN : angle 2.34151 / 1.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.8363 (tpp) cc_final: 0.7904 (tpp) REVERT: A 892 ILE cc_start: 0.8991 (mm) cc_final: 0.8763 (mt) REVERT: A 937 TYR cc_start: 0.8298 (t80) cc_final: 0.7928 (t80) REVERT: B 597 MET cc_start: 0.8442 (tpp) cc_final: 0.7876 (tpp) REVERT: B 601 MET cc_start: 0.8404 (tpp) cc_final: 0.8164 (tpp) REVERT: B 843 LYS cc_start: 0.8444 (tttm) cc_final: 0.8208 (tttm) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.0997 time to fit residues: 27.3294 Evaluate side-chains 116 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 GLN A 290 ASN A 867 HIS A 882 HIS ** A1040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 483 ASN B 629 HIS ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.102753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.080860 restraints weight = 35334.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.083346 restraints weight = 20213.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.085033 restraints weight = 12599.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.085178 restraints weight = 9463.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.085433 restraints weight = 9569.309| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13909 Z= 0.142 Angle : 0.587 9.324 18944 Z= 0.302 Chirality : 0.042 0.268 2252 Planarity : 0.004 0.033 2348 Dihedral : 4.370 24.725 1889 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.72 % Allowed : 7.10 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.20), residues: 1768 helix: 0.51 (0.16), residues: 994 sheet: -1.52 (0.50), residues: 96 loop : -1.71 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1062 TYR 0.017 0.001 TYR A 628 PHE 0.017 0.001 PHE B 877 TRP 0.021 0.001 TRP A 630 HIS 0.004 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (13895) covalent geometry : angle 0.58255 / 0.30 (18908) SS BOND : bond 0.00388 / 0.19 ( 6) SS BOND : angle 1.68791 / 0.97 ( 12) hydrogen bonds : bond 0.04419 / 2.92 ( 823) hydrogen bonds : angle 4.83911 / 3.41 ( 2367) link_BETA1-4 : bond 0.00243 / 0.12 ( 4) link_BETA1-4 : angle 1.59660 / 0.84 ( 12) link_NAG-ASN : bond 0.00308 / 0.16 ( 4) link_NAG-ASN : angle 1.77720 / 0.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.8171 (mtp) cc_final: 0.7902 (mtp) REVERT: A 601 MET cc_start: 0.8379 (tpp) cc_final: 0.7948 (tpp) REVERT: A 937 TYR cc_start: 0.7950 (t80) cc_final: 0.7682 (t80) REVERT: A 1071 MET cc_start: 0.8699 (mmm) cc_final: 0.8432 (mmm) REVERT: B 444 SER cc_start: 0.9049 (p) cc_final: 0.8657 (t) REVERT: B 597 MET cc_start: 0.8507 (tpp) cc_final: 0.7920 (tpp) REVERT: B 601 MET cc_start: 0.8556 (tpp) cc_final: 0.8192 (tpp) outliers start: 9 outliers final: 7 residues processed: 133 average time/residue: 0.0890 time to fit residues: 19.3856 Evaluate side-chains 113 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 653 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 30 optimal weight: 0.8980 chunk 170 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 172 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 169 optimal weight: 0.2980 chunk 48 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1040 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.102838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.081609 restraints weight = 32466.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.083666 restraints weight = 18664.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.084822 restraints weight = 12426.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.085494 restraints weight = 9954.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.085872 restraints weight = 9634.557| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13909 Z= 0.148 Angle : 0.561 9.111 18944 Z= 0.287 Chirality : 0.042 0.257 2252 Planarity : 0.003 0.036 2348 Dihedral : 4.260 23.249 1889 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.00 % Allowed : 8.24 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.20), residues: 1768 helix: 1.01 (0.17), residues: 982 sheet: -1.30 (0.53), residues: 96 loop : -1.42 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1062 TYR 0.024 0.001 TYR A 628 PHE 0.027 0.001 PHE B 877 TRP 0.015 0.001 TRP B 809 HIS 0.003 0.001 HIS B 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (13895) covalent geometry : angle 0.55708 / 0.29 (18908) SS BOND : bond 0.00387 / 0.19 ( 6) SS BOND : angle 1.58247 / 0.91 ( 12) hydrogen bonds : bond 0.04161 / 2.75 ( 823) hydrogen bonds : angle 4.66397 / 3.27 ( 2367) link_BETA1-4 : bond 0.00382 / 0.19 ( 4) link_BETA1-4 : angle 1.44454 / 0.78 ( 12) link_NAG-ASN : bond 0.00106 / 0.05 ( 4) link_NAG-ASN : angle 1.60591 / 0.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.8160 (mtp) cc_final: 0.7890 (mtp) REVERT: A 601 MET cc_start: 0.8365 (tpp) cc_final: 0.7986 (tpp) REVERT: A 628 TYR cc_start: 0.7836 (t80) cc_final: 0.7552 (t80) REVERT: A 937 TYR cc_start: 0.7924 (t80) cc_final: 0.7721 (t80) REVERT: A 1071 MET cc_start: 0.8819 (mmm) cc_final: 0.8598 (mmm) REVERT: B 263 MET cc_start: 0.8468 (tpp) cc_final: 0.8228 (tpp) REVERT: B 444 SER cc_start: 0.9084 (p) cc_final: 0.8702 (t) REVERT: B 597 MET cc_start: 0.8516 (tpp) cc_final: 0.7992 (tpp) REVERT: B 601 MET cc_start: 0.8553 (tpp) cc_final: 0.8222 (tpp) REVERT: B 767 MET cc_start: 0.9200 (mtp) cc_final: 0.8974 (mtm) outliers start: 13 outliers final: 6 residues processed: 119 average time/residue: 0.0883 time to fit residues: 17.4407 Evaluate side-chains 108 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain B residue 485 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 43 optimal weight: 1.9990 chunk 163 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 156 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1040 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.102578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.079929 restraints weight = 34607.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.082877 restraints weight = 19978.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.084486 restraints weight = 12027.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.084572 restraints weight = 9474.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.084902 restraints weight = 9594.411| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13909 Z= 0.150 Angle : 0.561 8.927 18944 Z= 0.284 Chirality : 0.042 0.288 2252 Planarity : 0.003 0.038 2348 Dihedral : 4.207 29.762 1889 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.15 % Allowed : 8.96 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1768 helix: 1.22 (0.17), residues: 980 sheet: -1.26 (0.55), residues: 96 loop : -1.30 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1062 TYR 0.030 0.001 TYR B 628 PHE 0.016 0.001 PHE B 555 TRP 0.024 0.001 TRP A 630 HIS 0.003 0.001 HIS B 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (13895) covalent geometry : angle 0.55715 / 0.28 (18908) SS BOND : bond 0.00644 / 0.32 ( 6) SS BOND : angle 1.88264 / 1.10 ( 12) hydrogen bonds : bond 0.03994 / 2.63 ( 823) hydrogen bonds : angle 4.57564 / 3.20 ( 2367) link_BETA1-4 : bond 0.00359 / 0.18 ( 4) link_BETA1-4 : angle 1.36676 / 0.74 ( 12) link_NAG-ASN : bond 0.00118 / 0.06 ( 4) link_NAG-ASN : angle 1.62065 / 0.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.8206 (mtp) cc_final: 0.7950 (mtp) REVERT: A 601 MET cc_start: 0.8428 (tpp) cc_final: 0.8052 (tpp) REVERT: A 628 TYR cc_start: 0.7832 (t80) cc_final: 0.7397 (t80) REVERT: A 1071 MET cc_start: 0.8922 (mmm) cc_final: 0.8685 (mmm) REVERT: B 444 SER cc_start: 0.9140 (p) cc_final: 0.8774 (t) REVERT: B 597 MET cc_start: 0.8585 (tpp) cc_final: 0.8071 (tpp) REVERT: B 601 MET cc_start: 0.8555 (tpp) cc_final: 0.8198 (tpp) REVERT: B 628 TYR cc_start: 0.8233 (t80) cc_final: 0.8027 (t80) REVERT: B 1071 MET cc_start: 0.8934 (tpp) cc_final: 0.8201 (tpt) outliers start: 15 outliers final: 10 residues processed: 120 average time/residue: 0.0803 time to fit residues: 15.9342 Evaluate side-chains 117 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 653 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 135 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 106 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 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 = 0.3409 r_free = 0.3409 target = 0.102583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.080436 restraints weight = 29871.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.082598 restraints weight = 18246.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.083828 restraints weight = 12403.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.084111 restraints weight = 10024.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.084282 restraints weight = 9632.177| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13909 Z= 0.129 Angle : 0.538 8.835 18944 Z= 0.272 Chirality : 0.041 0.269 2252 Planarity : 0.003 0.036 2348 Dihedral : 4.072 28.516 1889 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.00 % Allowed : 9.89 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.20), residues: 1768 helix: 1.43 (0.17), residues: 982 sheet: -1.12 (0.56), residues: 96 loop : -1.19 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1062 TYR 0.019 0.001 TYR A 628 PHE 0.014 0.001 PHE B 555 TRP 0.020 0.001 TRP A 630 HIS 0.005 0.001 HIS B 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (13895) covalent geometry : angle 0.53451 / 0.27 (18908) SS BOND : bond 0.00572 / 0.29 ( 6) SS BOND : angle 1.82515 / 1.07 ( 12) hydrogen bonds : bond 0.03786 / 2.51 ( 823) hydrogen bonds : angle 4.43948 / 3.10 ( 2367) link_BETA1-4 : bond 0.00434 / 0.22 ( 4) link_BETA1-4 : angle 1.27912 / 0.70 ( 12) link_NAG-ASN : bond 0.00053 / 0.03 ( 4) link_NAG-ASN : angle 1.60978 / 0.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.8434 (tpp) cc_final: 0.7774 (tpp) REVERT: A 1071 MET cc_start: 0.9027 (mmm) cc_final: 0.8775 (mmm) REVERT: B 263 MET cc_start: 0.8546 (tpp) cc_final: 0.8232 (tpp) REVERT: B 444 SER cc_start: 0.9174 (p) cc_final: 0.8865 (t) REVERT: B 597 MET cc_start: 0.8537 (tpp) cc_final: 0.8053 (tpp) REVERT: B 601 MET cc_start: 0.8608 (tpp) cc_final: 0.8291 (tpp) REVERT: B 1071 MET cc_start: 0.9016 (tpp) cc_final: 0.8329 (tpt) outliers start: 12 outliers final: 7 residues processed: 132 average time/residue: 0.0895 time to fit residues: 19.3338 Evaluate side-chains 119 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 485 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 15 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 164 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 123 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 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 = 0.3455 r_free = 0.3455 target = 0.105584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.084299 restraints weight = 30004.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.086374 restraints weight = 17958.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.087576 restraints weight = 12866.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.087929 restraints weight = 10683.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.088010 restraints weight = 9852.723| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13909 Z= 0.120 Angle : 0.539 8.871 18944 Z= 0.271 Chirality : 0.041 0.273 2252 Planarity : 0.003 0.038 2348 Dihedral : 4.050 28.996 1889 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.00 % Allowed : 10.54 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.60 (0.21), residues: 1768 helix: 1.55 (0.17), residues: 984 sheet: -1.04 (0.56), residues: 96 loop : -1.08 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1088 TYR 0.026 0.001 TYR B 628 PHE 0.039 0.001 PHE B 877 TRP 0.018 0.001 TRP A 630 HIS 0.003 0.001 HIS B 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (13895) covalent geometry : angle 0.53521 / 0.27 (18908) SS BOND : bond 0.00488 / 0.24 ( 6) SS BOND : angle 1.63734 / 0.96 ( 12) hydrogen bonds : bond 0.03688 / 2.45 ( 823) hydrogen bonds : angle 4.35775 / 3.04 ( 2367) link_BETA1-4 : bond 0.00426 / 0.21 ( 4) link_BETA1-4 : angle 1.25938 / 0.69 ( 12) link_NAG-ASN : bond 0.00049 / 0.03 ( 4) link_NAG-ASN : angle 1.62998 / 0.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.8372 (tpp) cc_final: 0.7740 (tpp) REVERT: A 1071 MET cc_start: 0.8900 (mmm) cc_final: 0.8659 (mmm) REVERT: B 444 SER cc_start: 0.9158 (p) cc_final: 0.8790 (t) REVERT: B 597 MET cc_start: 0.8543 (tpp) cc_final: 0.8051 (tpp) REVERT: B 601 MET cc_start: 0.8508 (tpp) cc_final: 0.8221 (tpp) outliers start: 11 outliers final: 6 residues processed: 129 average time/residue: 0.0836 time to fit residues: 17.9182 Evaluate side-chains 119 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain B residue 392 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 57 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 173 optimal weight: 0.2980 chunk 126 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 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 = 0.3461 r_free = 0.3461 target = 0.105873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.084399 restraints weight = 29881.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.086678 restraints weight = 18110.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.087812 restraints weight = 12657.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.088037 restraints weight = 10459.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088083 restraints weight = 10017.536| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13909 Z= 0.113 Angle : 0.536 9.923 18944 Z= 0.268 Chirality : 0.041 0.255 2252 Planarity : 0.003 0.035 2348 Dihedral : 3.969 26.803 1889 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.00 % Allowed : 11.61 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.21), residues: 1768 helix: 1.71 (0.17), residues: 982 sheet: -1.13 (0.53), residues: 104 loop : -1.06 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1088 TYR 0.017 0.001 TYR A 628 PHE 0.012 0.001 PHE B 555 TRP 0.017 0.001 TRP A 630 HIS 0.005 0.001 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (13895) covalent geometry : angle 0.53276 / 0.27 (18908) SS BOND : bond 0.00445 / 0.22 ( 6) SS BOND : angle 1.55083 / 0.92 ( 12) hydrogen bonds : bond 0.03622 / 2.41 ( 823) hydrogen bonds : angle 4.28141 / 2.98 ( 2367) link_BETA1-4 : bond 0.00466 / 0.23 ( 4) link_BETA1-4 : angle 1.21926 / 0.67 ( 12) link_NAG-ASN : bond 0.00070 / 0.04 ( 4) link_NAG-ASN : angle 1.62513 / 0.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.8344 (tpp) cc_final: 0.7764 (tpp) REVERT: B 263 MET cc_start: 0.8492 (tpp) cc_final: 0.8198 (tpp) REVERT: B 444 SER cc_start: 0.9169 (p) cc_final: 0.8830 (t) REVERT: B 597 MET cc_start: 0.8512 (tpp) cc_final: 0.8021 (tpp) REVERT: B 601 MET cc_start: 0.8520 (tpp) cc_final: 0.8255 (tpp) REVERT: B 942 MET cc_start: 0.6946 (mmm) cc_final: 0.6500 (mpp) outliers start: 11 outliers final: 9 residues processed: 127 average time/residue: 0.0808 time to fit residues: 17.1913 Evaluate side-chains 122 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 867 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 70 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 139 optimal weight: 6.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 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 = 0.3468 r_free = 0.3468 target = 0.106251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.085009 restraints weight = 30352.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.087562 restraints weight = 18813.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.088514 restraints weight = 12548.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.088597 restraints weight = 10415.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.088769 restraints weight = 10148.480| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13909 Z= 0.117 Angle : 0.535 9.574 18944 Z= 0.270 Chirality : 0.041 0.258 2252 Planarity : 0.003 0.034 2348 Dihedral : 3.939 26.395 1889 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.36 % Allowed : 11.76 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.21), residues: 1768 helix: 1.73 (0.17), residues: 984 sheet: -1.09 (0.53), residues: 104 loop : -1.00 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1088 TYR 0.019 0.001 TYR A 628 PHE 0.024 0.001 PHE B 877 TRP 0.025 0.001 TRP A 355 HIS 0.007 0.001 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (13895) covalent geometry : angle 0.53211 / 0.27 (18908) SS BOND : bond 0.00429 / 0.21 ( 6) SS BOND : angle 1.53110 / 0.91 ( 12) hydrogen bonds : bond 0.03616 / 2.41 ( 823) hydrogen bonds : angle 4.25823 / 2.97 ( 2367) link_BETA1-4 : bond 0.00430 / 0.22 ( 4) link_BETA1-4 : angle 1.19816 / 0.65 ( 12) link_NAG-ASN : bond 0.00051 / 0.03 ( 4) link_NAG-ASN : angle 1.64105 / 0.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.8334 (tpp) cc_final: 0.7765 (tpp) REVERT: B 263 MET cc_start: 0.8494 (tpp) cc_final: 0.8224 (tpp) REVERT: B 444 SER cc_start: 0.9181 (p) cc_final: 0.8821 (t) REVERT: B 597 MET cc_start: 0.8476 (tpp) cc_final: 0.8014 (tpp) REVERT: B 601 MET cc_start: 0.8510 (tpp) cc_final: 0.8241 (tpp) REVERT: B 942 MET cc_start: 0.6892 (mmm) cc_final: 0.6455 (mpp) outliers start: 16 outliers final: 12 residues processed: 124 average time/residue: 0.0853 time to fit residues: 17.8527 Evaluate side-chains 122 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 867 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 112 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 144 optimal weight: 0.0070 chunk 8 optimal weight: 0.0570 chunk 107 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 60 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 867 HIS ** A1040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 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 = 0.3492 r_free = 0.3492 target = 0.107908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.087091 restraints weight = 29798.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.088975 restraints weight = 18369.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.090711 restraints weight = 12708.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.090921 restraints weight = 10095.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.091042 restraints weight = 9350.996| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13909 Z= 0.103 Angle : 0.538 9.668 18944 Z= 0.270 Chirality : 0.041 0.245 2252 Planarity : 0.003 0.033 2348 Dihedral : 3.896 25.598 1889 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.36 % Allowed : 12.11 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.21), residues: 1768 helix: 1.78 (0.16), residues: 998 sheet: -1.00 (0.53), residues: 104 loop : -0.96 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1088 TYR 0.016 0.001 TYR A 628 PHE 0.014 0.001 PHE B 877 TRP 0.033 0.001 TRP A 864 HIS 0.007 0.001 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (13895) covalent geometry : angle 0.53497 / 0.27 (18908) SS BOND : bond 0.00380 / 0.19 ( 6) SS BOND : angle 1.43941 / 0.86 ( 12) hydrogen bonds : bond 0.03517 / 2.35 ( 823) hydrogen bonds : angle 4.18075 / 2.91 ( 2367) link_BETA1-4 : bond 0.00476 / 0.24 ( 4) link_BETA1-4 : angle 1.14408 / 0.62 ( 12) link_NAG-ASN : bond 0.00133 / 0.07 ( 4) link_NAG-ASN : angle 1.64097 / 0.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.7793 (ttm) cc_final: 0.7362 (ttp) REVERT: A 601 MET cc_start: 0.8295 (tpp) cc_final: 0.7751 (tpp) REVERT: B 263 MET cc_start: 0.8445 (tpp) cc_final: 0.8243 (tpp) REVERT: B 444 SER cc_start: 0.9171 (p) cc_final: 0.8844 (t) REVERT: B 597 MET cc_start: 0.8415 (tpp) cc_final: 0.8004 (tpp) REVERT: B 601 MET cc_start: 0.8479 (tpp) cc_final: 0.8231 (tpp) REVERT: B 942 MET cc_start: 0.6909 (mmm) cc_final: 0.6476 (mpp) outliers start: 15 outliers final: 12 residues processed: 134 average time/residue: 0.0831 time to fit residues: 18.7880 Evaluate side-chains 124 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 867 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 110 optimal weight: 20.0000 chunk 56 optimal weight: 0.3980 chunk 99 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 chunk 41 optimal weight: 0.0000 chunk 27 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 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 = 0.3477 r_free = 0.3477 target = 0.106868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.085652 restraints weight = 29173.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.087870 restraints weight = 17289.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.088693 restraints weight = 12905.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.089698 restraints weight = 10409.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.089823 restraints weight = 9467.101| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13909 Z= 0.113 Angle : 0.545 9.810 18944 Z= 0.270 Chirality : 0.041 0.250 2252 Planarity : 0.003 0.034 2348 Dihedral : 3.866 25.576 1889 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.15 % Allowed : 12.47 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.21), residues: 1768 helix: 1.82 (0.16), residues: 998 sheet: -0.99 (0.52), residues: 104 loop : -0.92 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1088 TYR 0.020 0.001 TYR A 628 PHE 0.012 0.001 PHE B 555 TRP 0.048 0.001 TRP B 515 HIS 0.006 0.001 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (13895) covalent geometry : angle 0.54120 / 0.27 (18908) SS BOND : bond 0.00419 / 0.21 ( 6) SS BOND : angle 1.57081 / 0.93 ( 12) hydrogen bonds : bond 0.03499 / 2.33 ( 823) hydrogen bonds : angle 4.15448 / 2.90 ( 2367) link_BETA1-4 : bond 0.00500 / 0.25 ( 4) link_BETA1-4 : angle 1.20040 / 0.65 ( 12) link_NAG-ASN : bond 0.00061 / 0.03 ( 4) link_NAG-ASN : angle 1.64625 / 0.86 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.7803 (ttm) cc_final: 0.7384 (ttp) REVERT: A 601 MET cc_start: 0.8310 (tpp) cc_final: 0.7760 (tpp) REVERT: B 114 GLU cc_start: 0.7860 (mp0) cc_final: 0.7296 (mp0) REVERT: B 263 MET cc_start: 0.8457 (tpp) cc_final: 0.8257 (tpp) REVERT: B 444 SER cc_start: 0.9177 (p) cc_final: 0.8816 (t) REVERT: B 597 MET cc_start: 0.8422 (tpp) cc_final: 0.8036 (tpp) REVERT: B 601 MET cc_start: 0.8471 (tpp) cc_final: 0.8205 (tpp) REVERT: B 942 MET cc_start: 0.6925 (mmm) cc_final: 0.6493 (mpp) outliers start: 12 outliers final: 12 residues processed: 128 average time/residue: 0.0828 time to fit residues: 17.8549 Evaluate side-chains 129 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 867 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 0.9990 chunk 113 optimal weight: 0.0050 chunk 132 optimal weight: 0.8980 chunk 142 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 26 optimal weight: 0.0470 chunk 49 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 96 optimal weight: 0.2980 chunk 20 optimal weight: 8.9990 overall best weight: 0.3892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 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 = 0.3505 r_free = 0.3505 target = 0.108700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.087332 restraints weight = 29100.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.089256 restraints weight = 18034.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.090250 restraints weight = 13779.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.091819 restraints weight = 10847.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.091846 restraints weight = 9550.259| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13909 Z= 0.101 Angle : 0.542 11.248 18944 Z= 0.267 Chirality : 0.041 0.373 2252 Planarity : 0.003 0.033 2348 Dihedral : 3.796 24.747 1889 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.08 % Allowed : 12.40 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.21), residues: 1768 helix: 1.92 (0.16), residues: 1000 sheet: -1.00 (0.47), residues: 136 loop : -0.80 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1088 TYR 0.016 0.001 TYR A 628 PHE 0.013 0.001 PHE B 442 TRP 0.039 0.001 TRP B 515 HIS 0.006 0.001 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (13895) covalent geometry : angle 0.53882 / 0.27 (18908) SS BOND : bond 0.00397 / 0.20 ( 6) SS BOND : angle 1.47810 / 0.88 ( 12) hydrogen bonds : bond 0.03378 / 2.26 ( 823) hydrogen bonds : angle 4.08364 / 2.84 ( 2367) link_BETA1-4 : bond 0.00528 / 0.26 ( 4) link_BETA1-4 : angle 1.14459 / 0.62 ( 12) link_NAG-ASN : bond 0.00141 / 0.07 ( 4) link_NAG-ASN : angle 1.63025 / 0.85 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2246.65 seconds wall clock time: 39 minutes 37.36 seconds (2377.36 seconds total)