Starting phenix.real_space_refine on Thu Jul 31 18:28:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y5r_10703/07_2025/6y5r_10703.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5r_10703/07_2025/6y5r_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_10703/07_2025/6y5r_10703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5r_10703/07_2025/6y5r_10703.map" model { file = "/net/cci-nas-00/data/ceres_data/6y5r_10703/07_2025/6y5r_10703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5r_10703/07_2025/6y5r_10703.cif" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} 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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} 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: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 2} 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: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 2} 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 3 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 dihedrals: 3 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: 15.16, per 1000 atoms: 1.12 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: 3.51 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 1.37 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: 4.65 Time building geometry restraints manager: 4.13 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 - 21.80: 7856 21.80 - 43.60: 318 43.60 - 65.40: 30 65.40 - 87.20: 17 87.20 - 109.00: 8 Dihedral angle restraints: 8229 sinusoidal: 3109 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 8226 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 1093 or resid 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 1093 or re \ sid 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: 8.040 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: 0.770 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 42.060 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 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 : 12.766 108.996 4919 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.90 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.012 0.001 TRP A 630 HIS 0.002 0.001 HIS B 790 PHE 0.014 0.001 PHE B1073 TYR 0.009 0.001 TYR B 628 ARG 0.003 0.000 ARG A 814 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 4) link_NAG-ASN : angle 2.34151 ( 12) link_BETA1-4 : bond 0.00369 ( 4) link_BETA1-4 : angle 1.21891 ( 12) hydrogen bonds : bond 0.13755 ( 823) hydrogen bonds : angle 5.90778 ( 2367) SS BOND : bond 0.00489 ( 6) SS BOND : angle 2.11970 ( 12) covalent geometry : bond 0.00356 (13895) covalent geometry : angle 0.64012 (18908) *********************** 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 : 1.460 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: 0.2600 time to fit residues: 70.1178 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 : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 45 optimal weight: 0.0370 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 0.0770 chunk 136 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3420 r_free = 0.3420 target = 0.103360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.081475 restraints weight = 36695.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.083549 restraints weight = 20636.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.085830 restraints weight = 13400.060| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 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 = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13909 Z= 0.133 Angle : 0.591 8.852 18944 Z= 0.302 Chirality : 0.042 0.268 2252 Planarity : 0.004 0.032 2348 Dihedral : 6.830 63.648 2053 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.49 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.20), residues: 1768 helix: 0.55 (0.16), residues: 1004 sheet: -1.94 (0.45), residues: 132 loop : -1.63 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 630 HIS 0.004 0.001 HIS B 802 PHE 0.020 0.001 PHE A 357 TYR 0.015 0.001 TYR A 628 ARG 0.004 0.000 ARG A1062 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 4) link_NAG-ASN : angle 1.68333 ( 12) link_BETA1-4 : bond 0.00390 ( 4) link_BETA1-4 : angle 2.20452 ( 12) hydrogen bonds : bond 0.04315 ( 823) hydrogen bonds : angle 4.81048 ( 2367) SS BOND : bond 0.00371 ( 6) SS BOND : angle 1.62320 ( 12) covalent geometry : bond 0.00291 (13895) covalent geometry : angle 0.58597 (18908) *********************** 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 140 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 453 ASN cc_start: 0.8337 (m110) cc_final: 0.8123 (m110) REVERT: A 601 MET cc_start: 0.8386 (tpp) cc_final: 0.7982 (tpp) REVERT: A 937 TYR cc_start: 0.7918 (t80) cc_final: 0.7673 (t80) REVERT: A 1071 MET cc_start: 0.8717 (mmm) cc_final: 0.8441 (mmm) REVERT: B 597 MET cc_start: 0.8457 (tpp) cc_final: 0.7880 (tpp) REVERT: B 601 MET cc_start: 0.8527 (tpp) cc_final: 0.8164 (tpp) REVERT: B 843 LYS cc_start: 0.8435 (tttm) cc_final: 0.8154 (tttm) outliers start: 9 outliers final: 6 residues processed: 136 average time/residue: 0.2037 time to fit residues: 45.0442 Evaluate side-chains 113 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 128 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 126 optimal weight: 0.0060 chunk 35 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** A1040 ASN ** 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 = 0.3426 r_free = 0.3426 target = 0.103598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.082025 restraints weight = 32334.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.084168 restraints weight = 19020.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.086110 restraints weight = 12481.801| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 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 = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13909 Z= 0.129 Angle : 0.555 8.840 18944 Z= 0.281 Chirality : 0.042 0.254 2252 Planarity : 0.003 0.034 2348 Dihedral : 5.383 41.085 2053 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.79 % Allowed : 8.60 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.20), residues: 1768 helix: 1.13 (0.17), residues: 980 sheet: -1.16 (0.54), residues: 96 loop : -1.42 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 630 HIS 0.003 0.000 HIS B 802 PHE 0.023 0.001 PHE B 877 TYR 0.026 0.001 TYR A 628 ARG 0.003 0.000 ARG A1062 Details of bonding type rmsd link_NAG-ASN : bond 0.00099 ( 4) link_NAG-ASN : angle 1.62583 ( 12) link_BETA1-4 : bond 0.00349 ( 4) link_BETA1-4 : angle 2.03264 ( 12) hydrogen bonds : bond 0.04037 ( 823) hydrogen bonds : angle 4.59963 ( 2367) SS BOND : bond 0.00353 ( 6) SS BOND : angle 1.52924 ( 12) covalent geometry : bond 0.00285 (13895) covalent geometry : angle 0.55049 (18908) *********************** 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 129 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.8442 (tpp) cc_final: 0.8048 (tpp) REVERT: A 1071 MET cc_start: 0.8848 (mmm) cc_final: 0.8615 (mmm) REVERT: B 263 MET cc_start: 0.8508 (tpp) cc_final: 0.8214 (tpp) REVERT: B 444 SER cc_start: 0.9063 (p) cc_final: 0.8685 (t) REVERT: B 597 MET cc_start: 0.8462 (tpp) cc_final: 0.7961 (tpp) REVERT: B 601 MET cc_start: 0.8554 (tpp) cc_final: 0.8231 (tpp) REVERT: B 1071 MET cc_start: 0.8769 (tpt) cc_final: 0.8534 (tpt) outliers start: 10 outliers final: 5 residues processed: 125 average time/residue: 0.2054 time to fit residues: 42.0860 Evaluate side-chains 112 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 ILE 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 163 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3404 r_free = 0.3404 target = 0.102377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.080789 restraints weight = 31971.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.083405 restraints weight = 18691.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.084742 restraints weight = 11710.313| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 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 = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1753 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= 0.162 Angle : 0.570 9.660 18944 Z= 0.287 Chirality : 0.042 0.288 2252 Planarity : 0.003 0.036 2348 Dihedral : 4.590 29.691 2053 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.15 % Allowed : 8.89 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.20), residues: 1768 helix: 1.25 (0.17), residues: 980 sheet: -1.12 (0.55), residues: 96 loop : -1.26 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 630 HIS 0.005 0.001 HIS B 928 PHE 0.031 0.001 PHE B 877 TYR 0.029 0.001 TYR B 628 ARG 0.003 0.000 ARG A 497 Details of bonding type rmsd link_NAG-ASN : bond 0.00095 ( 4) link_NAG-ASN : angle 1.66056 ( 12) link_BETA1-4 : bond 0.00404 ( 4) link_BETA1-4 : angle 1.98850 ( 12) hydrogen bonds : bond 0.04001 ( 823) hydrogen bonds : angle 4.55663 ( 2367) SS BOND : bond 0.00362 ( 6) SS BOND : angle 1.61708 ( 12) covalent geometry : bond 0.00377 (13895) covalent geometry : angle 0.56537 (18908) *********************** 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 131 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.8453 (tpp) cc_final: 0.8068 (tpp) REVERT: A 1071 MET cc_start: 0.8916 (mmm) cc_final: 0.8658 (mmm) REVERT: B 444 SER cc_start: 0.9127 (p) cc_final: 0.8742 (t) REVERT: B 597 MET cc_start: 0.8573 (tpp) cc_final: 0.8078 (tpp) REVERT: B 601 MET cc_start: 0.8576 (tpp) cc_final: 0.8217 (tpp) REVERT: B 628 TYR cc_start: 0.8231 (t80) cc_final: 0.7915 (t80) outliers start: 14 outliers final: 10 residues processed: 125 average time/residue: 0.2009 time to fit residues: 41.0399 Evaluate side-chains 120 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 304 ILE 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 Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 1057 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 145 optimal weight: 1.9990 chunk 72 optimal weight: 0.0050 chunk 91 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 116 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 chunk 55 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 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 = 0.3420 r_free = 0.3420 target = 0.103288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.080903 restraints weight = 32691.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.083912 restraints weight = 18834.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.085056 restraints weight = 11487.465| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13909 Z= 0.116 Angle : 0.535 9.678 18944 Z= 0.270 Chirality : 0.041 0.264 2252 Planarity : 0.003 0.035 2348 Dihedral : 4.316 28.254 2053 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.93 % Allowed : 10.11 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.21), residues: 1768 helix: 1.48 (0.17), residues: 984 sheet: -1.17 (0.52), residues: 104 loop : -1.18 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 630 HIS 0.003 0.000 HIS B 802 PHE 0.030 0.001 PHE B 877 TYR 0.020 0.001 TYR B 628 ARG 0.003 0.000 ARG A1062 Details of bonding type rmsd link_NAG-ASN : bond 0.00101 ( 4) link_NAG-ASN : angle 1.60290 ( 12) link_BETA1-4 : bond 0.00487 ( 4) link_BETA1-4 : angle 1.58086 ( 12) hydrogen bonds : bond 0.03752 ( 823) hydrogen bonds : angle 4.41791 ( 2367) SS BOND : bond 0.00523 ( 6) SS BOND : angle 1.68740 ( 12) covalent geometry : bond 0.00256 (13895) covalent geometry : angle 0.53089 (18908) *********************** 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 137 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.8437 (tpp) cc_final: 0.7789 (tpp) REVERT: A 1071 MET cc_start: 0.9013 (mmm) cc_final: 0.8755 (mmm) REVERT: B 114 GLU cc_start: 0.7988 (mp0) cc_final: 0.7288 (mp0) REVERT: B 263 MET cc_start: 0.8569 (tpp) cc_final: 0.8265 (tpp) REVERT: B 444 SER cc_start: 0.9147 (p) cc_final: 0.8834 (t) REVERT: B 597 MET cc_start: 0.8500 (tpp) cc_final: 0.8025 (tpp) REVERT: B 601 MET cc_start: 0.8578 (tpp) cc_final: 0.8289 (tpp) REVERT: B 628 TYR cc_start: 0.8214 (t80) cc_final: 0.7926 (t80) outliers start: 10 outliers final: 5 residues processed: 133 average time/residue: 0.2061 time to fit residues: 44.3085 Evaluate side-chains 123 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 86 optimal weight: 2.9990 chunk 155 optimal weight: 0.0670 chunk 25 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 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 = 0.3458 r_free = 0.3458 target = 0.105764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.084742 restraints weight = 31395.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.085929 restraints weight = 21559.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.087045 restraints weight = 15671.736| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 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 = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13909 Z= 0.120 Angle : 0.535 9.733 18944 Z= 0.270 Chirality : 0.041 0.269 2252 Planarity : 0.003 0.035 2348 Dihedral : 4.269 27.436 2053 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.36 % Allowed : 10.47 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.21), residues: 1768 helix: 1.60 (0.17), residues: 982 sheet: -1.08 (0.52), residues: 104 loop : -1.11 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 630 HIS 0.003 0.000 HIS B 802 PHE 0.031 0.001 PHE B 877 TYR 0.019 0.001 TYR A 628 ARG 0.004 0.000 ARG A 497 Details of bonding type rmsd link_NAG-ASN : bond 0.00036 ( 4) link_NAG-ASN : angle 1.62647 ( 12) link_BETA1-4 : bond 0.00413 ( 4) link_BETA1-4 : angle 1.48784 ( 12) hydrogen bonds : bond 0.03693 ( 823) hydrogen bonds : angle 4.34382 ( 2367) SS BOND : bond 0.00458 ( 6) SS BOND : angle 1.58341 ( 12) covalent geometry : bond 0.00270 (13895) covalent geometry : angle 0.53072 (18908) *********************** 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 142 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.8379 (tpp) cc_final: 0.7750 (tpp) REVERT: A 1071 MET cc_start: 0.8875 (mmm) cc_final: 0.8630 (mmm) REVERT: B 114 GLU cc_start: 0.7974 (mp0) cc_final: 0.7332 (mp0) REVERT: B 444 SER cc_start: 0.9143 (p) cc_final: 0.8794 (t) REVERT: B 597 MET cc_start: 0.8511 (tpp) cc_final: 0.8005 (tpp) REVERT: B 601 MET cc_start: 0.8498 (tpp) cc_final: 0.8214 (tpp) REVERT: B 628 TYR cc_start: 0.8120 (t80) cc_final: 0.7840 (t80) outliers start: 16 outliers final: 13 residues processed: 136 average time/residue: 0.1983 time to fit residues: 43.9721 Evaluate side-chains 125 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 237 ILE 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 138 MET Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 1057 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 53 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 79 optimal weight: 0.0010 chunk 91 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 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 = 0.3456 r_free = 0.3456 target = 0.105463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.084323 restraints weight = 34001.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.086381 restraints weight = 21372.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.087909 restraints weight = 14385.307| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2305 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 : 0.552 11.708 18944 Z= 0.273 Chirality : 0.041 0.255 2252 Planarity : 0.003 0.034 2348 Dihedral : 4.207 26.659 2053 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.43 % Allowed : 11.33 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.21), residues: 1768 helix: 1.72 (0.17), residues: 982 sheet: -1.01 (0.52), residues: 104 loop : -1.04 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 630 HIS 0.003 0.000 HIS B 802 PHE 0.012 0.001 PHE B 877 TYR 0.018 0.001 TYR A 628 ARG 0.003 0.000 ARG A 497 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 4) link_NAG-ASN : angle 1.61993 ( 12) link_BETA1-4 : bond 0.00444 ( 4) link_BETA1-4 : angle 1.39193 ( 12) hydrogen bonds : bond 0.03628 ( 823) hydrogen bonds : angle 4.24859 ( 2367) SS BOND : bond 0.00440 ( 6) SS BOND : angle 1.59686 ( 12) covalent geometry : bond 0.00249 (13895) covalent geometry : angle 0.54860 (18908) *********************** 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 141 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.8351 (tpp) cc_final: 0.7752 (tpp) REVERT: B 114 GLU cc_start: 0.7927 (mp0) cc_final: 0.7362 (mp0) REVERT: B 263 MET cc_start: 0.8506 (tpp) cc_final: 0.8246 (tpp) REVERT: B 444 SER cc_start: 0.9143 (p) cc_final: 0.8810 (t) REVERT: B 597 MET cc_start: 0.8458 (tpp) cc_final: 0.8013 (tpp) REVERT: B 601 MET cc_start: 0.8479 (tpp) cc_final: 0.8217 (tpp) REVERT: B 942 MET cc_start: 0.6850 (mmm) cc_final: 0.6434 (mpp) outliers start: 16 outliers final: 12 residues processed: 136 average time/residue: 0.2016 time to fit residues: 44.8118 Evaluate side-chains 126 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 1.514 ------------------------------------------------------------------------------- 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 138 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 867 HIS Chi-restraints excluded: chain B residue 1057 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 64 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 155 optimal weight: 0.0060 chunk 66 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 114 optimal weight: 0.0870 chunk 157 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 135 optimal weight: 0.0970 overall best weight: 0.3772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 HIS ** A1040 ASN ** 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 = 0.3488 r_free = 0.3488 target = 0.107682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.086731 restraints weight = 29151.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.088895 restraints weight = 17534.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.090088 restraints weight = 12945.266| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 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 = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13909 Z= 0.106 Angle : 0.558 13.978 18944 Z= 0.276 Chirality : 0.041 0.246 2252 Planarity : 0.003 0.033 2348 Dihedral : 4.119 25.999 2053 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.36 % Allowed : 11.68 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.21), residues: 1768 helix: 1.82 (0.17), residues: 984 sheet: -0.90 (0.53), residues: 104 loop : -0.99 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 355 HIS 0.003 0.000 HIS B 802 PHE 0.012 0.001 PHE B 442 TYR 0.016 0.001 TYR A 628 ARG 0.002 0.000 ARG A 497 Details of bonding type rmsd link_NAG-ASN : bond 0.00128 ( 4) link_NAG-ASN : angle 1.63251 ( 12) link_BETA1-4 : bond 0.00448 ( 4) link_BETA1-4 : angle 1.30242 ( 12) hydrogen bonds : bond 0.03553 ( 823) hydrogen bonds : angle 4.18864 ( 2367) SS BOND : bond 0.00395 ( 6) SS BOND : angle 1.51807 ( 12) covalent geometry : bond 0.00225 (13895) covalent geometry : angle 0.55439 (18908) *********************** 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 135 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.8329 (tpp) cc_final: 0.7778 (tpp) REVERT: A 871 MET cc_start: 0.7563 (mtm) cc_final: 0.7339 (mtt) REVERT: B 114 GLU cc_start: 0.7902 (mp0) cc_final: 0.7366 (mp0) REVERT: B 263 MET cc_start: 0.8457 (tpp) cc_final: 0.8245 (tpp) REVERT: B 444 SER cc_start: 0.9148 (p) cc_final: 0.8821 (t) REVERT: B 597 MET cc_start: 0.8416 (tpp) cc_final: 0.8030 (tpp) REVERT: B 601 MET cc_start: 0.8477 (tpp) cc_final: 0.8241 (tpp) REVERT: B 942 MET cc_start: 0.6901 (mmm) cc_final: 0.6459 (mpp) outliers start: 15 outliers final: 11 residues processed: 130 average time/residue: 0.1961 time to fit residues: 41.7545 Evaluate side-chains 127 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.412 ------------------------------------------------------------------------------- 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 392 ILE Chi-restraints excluded: chain B residue 746 VAL 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 77 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 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 = 0.3443 r_free = 0.3443 target = 0.104743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.083944 restraints weight = 31413.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.086153 restraints weight = 20354.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.087126 restraints weight = 14146.139| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13909 Z= 0.160 Angle : 0.585 14.032 18944 Z= 0.290 Chirality : 0.043 0.272 2252 Planarity : 0.003 0.035 2348 Dihedral : 4.213 26.382 2053 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.86 % Favored : 96.09 % Rotamer: Outliers : 1.51 % Allowed : 11.90 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1768 helix: 1.71 (0.16), residues: 984 sheet: -1.02 (0.52), residues: 104 loop : -0.94 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 515 HIS 0.006 0.001 HIS B 928 PHE 0.016 0.001 PHE B 555 TYR 0.022 0.001 TYR A 628 ARG 0.003 0.000 ARG A 497 Details of bonding type rmsd link_NAG-ASN : bond 0.00133 ( 4) link_NAG-ASN : angle 1.66986 ( 12) link_BETA1-4 : bond 0.00360 ( 4) link_BETA1-4 : angle 1.47802 ( 12) hydrogen bonds : bond 0.03704 ( 823) hydrogen bonds : angle 4.24015 ( 2367) SS BOND : bond 0.00504 ( 6) SS BOND : angle 1.79446 ( 12) covalent geometry : bond 0.00370 (13895) covalent geometry : angle 0.58075 (18908) *********************** 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 136 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 871 MET cc_start: 0.7597 (mtm) cc_final: 0.7342 (mtt) REVERT: B 114 GLU cc_start: 0.7942 (mp0) cc_final: 0.7289 (mp0) REVERT: B 444 SER cc_start: 0.9196 (p) cc_final: 0.8812 (t) REVERT: B 597 MET cc_start: 0.8525 (tpp) cc_final: 0.7602 (tpp) REVERT: B 601 MET cc_start: 0.8492 (tpp) cc_final: 0.8122 (tpp) REVERT: B 942 MET cc_start: 0.6874 (mmm) cc_final: 0.6453 (mpp) outliers start: 17 outliers final: 14 residues processed: 132 average time/residue: 0.2003 time to fit residues: 43.4315 Evaluate side-chains 129 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 237 ILE 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 653 ILE 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 29 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 128 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 131 optimal weight: 0.0570 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 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 = 0.3468 r_free = 0.3468 target = 0.106421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.085383 restraints weight = 30723.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.087463 restraints weight = 19404.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.088689 restraints weight = 13254.905| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 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 : 0.003 0.040 13909 Z= 0.116 Angle : 0.557 13.824 18944 Z= 0.275 Chirality : 0.041 0.253 2252 Planarity : 0.003 0.036 2348 Dihedral : 4.137 25.892 2053 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.15 % Allowed : 12.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.21), residues: 1768 helix: 1.75 (0.16), residues: 994 sheet: -1.00 (0.52), residues: 104 loop : -0.90 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 515 HIS 0.003 0.000 HIS B 802 PHE 0.012 0.001 PHE B 555 TYR 0.019 0.001 TYR A 628 ARG 0.002 0.000 ARG A 497 Details of bonding type rmsd link_NAG-ASN : bond 0.00066 ( 4) link_NAG-ASN : angle 1.57319 ( 12) link_BETA1-4 : bond 0.00441 ( 4) link_BETA1-4 : angle 1.37674 ( 12) hydrogen bonds : bond 0.03569 ( 823) hydrogen bonds : angle 4.19338 ( 2367) SS BOND : bond 0.00437 ( 6) SS BOND : angle 1.60498 ( 12) covalent geometry : bond 0.00260 (13895) covalent geometry : angle 0.55335 (18908) ********************** 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 131 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.7851 (ttm) cc_final: 0.7516 (ttp) REVERT: A 601 MET cc_start: 0.8239 (tpp) cc_final: 0.7907 (tpp) REVERT: A 871 MET cc_start: 0.7603 (mtm) cc_final: 0.7358 (mtt) REVERT: B 114 GLU cc_start: 0.7938 (mp0) cc_final: 0.7351 (mp0) REVERT: B 263 MET cc_start: 0.8503 (tpp) cc_final: 0.8287 (tpp) REVERT: B 444 SER cc_start: 0.9196 (p) cc_final: 0.8854 (t) REVERT: B 597 MET cc_start: 0.8474 (tpp) cc_final: 0.7598 (tpp) REVERT: B 601 MET cc_start: 0.8474 (tpp) cc_final: 0.8162 (tpp) REVERT: B 942 MET cc_start: 0.6951 (mmm) cc_final: 0.6508 (mpp) outliers start: 12 outliers final: 11 residues processed: 129 average time/residue: 0.2195 time to fit residues: 47.1206 Evaluate side-chains 128 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 746 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 43 optimal weight: 0.0030 chunk 113 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 95 optimal weight: 0.0050 chunk 1 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN ** A1040 ASN ** 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 = 0.3493 r_free = 0.3493 target = 0.107991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.086977 restraints weight = 30406.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.089471 restraints weight = 18681.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.090196 restraints weight = 13014.115| |-----------------------------------------------------------------------------| 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 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13909 Z= 0.104 Angle : 0.547 13.312 18944 Z= 0.269 Chirality : 0.041 0.241 2252 Planarity : 0.003 0.036 2348 Dihedral : 4.001 25.273 2053 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.08 % Allowed : 12.47 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.21), residues: 1768 helix: 1.90 (0.16), residues: 994 sheet: -0.88 (0.53), residues: 104 loop : -0.85 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 515 HIS 0.004 0.000 HIS B 802 PHE 0.018 0.001 PHE B 877 TYR 0.017 0.001 TYR A 628 ARG 0.002 0.000 ARG A1062 Details of bonding type rmsd link_NAG-ASN : bond 0.00097 ( 4) link_NAG-ASN : angle 1.57961 ( 12) link_BETA1-4 : bond 0.00501 ( 4) link_BETA1-4 : angle 1.26056 ( 12) hydrogen bonds : bond 0.03434 ( 823) hydrogen bonds : angle 4.10364 ( 2367) SS BOND : bond 0.00366 ( 6) SS BOND : angle 1.50693 ( 12) covalent geometry : bond 0.00229 (13895) covalent geometry : angle 0.54365 (18908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4606.40 seconds wall clock time: 80 minutes 34.24 seconds (4834.24 seconds total)