Starting phenix.real_space_refine on Fri Mar 6 05:15:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dis_27441/03_2026/8dis_27441.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dis_27441/03_2026/8dis_27441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dis_27441/03_2026/8dis_27441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dis_27441/03_2026/8dis_27441.map" model { file = "/net/cci-nas-00/data/ceres_data/8dis_27441/03_2026/8dis_27441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dis_27441/03_2026/8dis_27441.cif" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14192 atoms to isotropic. 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 81 5.16 5 C 10704 2.51 5 N 2838 2.21 5 O 3421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17044 Number of models: 1 Model: "" Number of chains: 30 Chain: "D" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 18, 'TRANS': 306} Chain: "d" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1306 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 161} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 18, 'TRANS': 306} Chain: "e" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1306 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 161} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 18, 'TRANS': 306} Chain: "f" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1306 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 161} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "d" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "e" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "f" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 4.18, per 1000 atoms: 0.25 Number of scatterers: 17044 At special positions: 0 Unit cell: (136.35, 125.55, 143.775, 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 81 16.00 O 3421 8.00 N 2838 7.00 C 10704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS D 72 " - pdb=" SG CYS D 84 " distance=2.03 Simple disulfide: pdb=" SG CYS D 107 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 320 " distance=2.03 Simple disulfide: pdb=" SG CYS d 488 " - pdb=" SG CYS d 492 " distance=2.03 Simple disulfide: pdb=" SG CYS E 72 " - pdb=" SG CYS E 84 " distance=2.03 Simple disulfide: pdb=" SG CYS E 107 " - pdb=" SG CYS E 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 320 " distance=2.03 Simple disulfide: pdb=" SG CYS e 488 " - pdb=" SG CYS e 492 " distance=2.03 Simple disulfide: pdb=" SG CYS F 72 " - pdb=" SG CYS F 84 " distance=2.03 Simple disulfide: pdb=" SG CYS F 107 " - pdb=" SG CYS F 153 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 320 " distance=2.03 Simple disulfide: pdb=" SG CYS f 488 " - pdb=" SG CYS f 492 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG D 601 " - " ASN D 28 " " NAG D 602 " - " ASN D 304 " " NAG E 601 " - " ASN E 28 " " NAG E 602 " - " ASN E 304 " " NAG F 601 " - " ASN F 28 " " NAG F 602 " - " ASN F 304 " " NAG I 1 " - " ASN D 40 " " NAG J 1 " - " ASN D 104 " " NAG K 1 " - " ASN d 498 " " NAG M 1 " - " ASN E 40 " " NAG N 1 " - " ASN E 104 " " NAG O 1 " - " ASN e 498 " " NAG P 1 " - " ASN F 40 " " NAG Q 1 " - " ASN F 104 " " NAG R 1 " - " ASN f 498 " Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 746.1 milliseconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3912 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 48 sheets defined 18.0% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'D' and resid 73 through 80 Processing helix chain 'D' and resid 114 through 123 removed outlier: 3.548A pdb=" N LEU D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 removed outlier: 4.647A pdb=" N TRP D 140 " --> pdb=" O LYS D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 210 Processing helix chain 'd' and resid 381 through 402 Processing helix chain 'd' and resid 418 through 471 removed outlier: 3.996A pdb=" N GLU d 449 " --> pdb=" O LEU d 445 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG d 450 " --> pdb=" O LEU d 446 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS d 455 " --> pdb=" O THR d 451 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP d 456 " --> pdb=" O LEU d 452 " (cutoff:3.500A) Processing helix chain 'd' and resid 489 through 497 Processing helix chain 'd' and resid 503 through 507 Processing helix chain 'E' and resid 73 through 80 Processing helix chain 'E' and resid 114 through 123 removed outlier: 3.534A pdb=" N LEU E 118 " --> pdb=" O ASP E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 removed outlier: 4.642A pdb=" N TRP E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 210 Processing helix chain 'e' and resid 381 through 402 removed outlier: 3.508A pdb=" N THR e 385 " --> pdb=" O ASP e 381 " (cutoff:3.500A) Processing helix chain 'e' and resid 418 through 471 removed outlier: 4.019A pdb=" N GLU e 449 " --> pdb=" O LEU e 445 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG e 450 " --> pdb=" O LEU e 446 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS e 455 " --> pdb=" O THR e 451 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP e 456 " --> pdb=" O LEU e 452 " (cutoff:3.500A) Processing helix chain 'e' and resid 489 through 497 Processing helix chain 'e' and resid 503 through 507 Processing helix chain 'F' and resid 73 through 80 Processing helix chain 'F' and resid 114 through 123 removed outlier: 3.505A pdb=" N LEU F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 removed outlier: 4.644A pdb=" N TRP F 140 " --> pdb=" O LYS F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 210 Processing helix chain 'f' and resid 381 through 402 removed outlier: 3.553A pdb=" N THR f 385 " --> pdb=" O ASP f 381 " (cutoff:3.500A) Processing helix chain 'f' and resid 418 through 471 removed outlier: 4.012A pdb=" N GLU f 449 " --> pdb=" O LEU f 445 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG f 450 " --> pdb=" O LEU f 446 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS f 455 " --> pdb=" O THR f 451 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP f 456 " --> pdb=" O LEU f 452 " (cutoff:3.500A) Processing helix chain 'f' and resid 489 through 497 Processing helix chain 'f' and resid 503 through 507 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.726A pdb=" N ASN C 31 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP C 32 " --> pdb=" O ILE C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.715A pdb=" N ASP C 83 " --> pdb=" O GLN C 80 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU C 84 " --> pdb=" O THR C 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 80 through 84' Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.744A pdb=" N ASN L 31 " --> pdb=" O ASN L 28 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP L 32 " --> pdb=" O ILE L 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'd' and resid 376 through 380 Processing sheet with id=AA2, first strand: chain 'D' and resid 31 through 33 removed outlier: 4.585A pdb=" N ASP D 31 " --> pdb=" O VAL D 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 46 through 48 Processing sheet with id=AA4, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AA5, first strand: chain 'D' and resid 58 through 61 removed outlier: 6.188A pdb=" N LEU D 58 " --> pdb=" O HIS D 290 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N CYS D 292 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 67 through 68 removed outlier: 6.792A pdb=" N LEU D 67 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE D 96 " --> pdb=" O ILE D 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 125 through 132 removed outlier: 3.682A pdb=" N SER D 127 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR D 270 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU D 193 " --> pdb=" O TYR D 270 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU D 189 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEU D 193 " --> pdb=" O PRO D 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 125 through 132 removed outlier: 3.682A pdb=" N SER D 127 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR D 270 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU D 193 " --> pdb=" O TYR D 270 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU D 189 " --> pdb=" O LEU D 274 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 150 through 155 removed outlier: 7.703A pdb=" N ALA D 152 " --> pdb=" O LYS D 158 " (cutoff:3.500A) removed outlier: 10.630A pdb=" N LYS D 158 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 178 through 183 Processing sheet with id=AB2, first strand: chain 'D' and resid 301 through 303 removed outlier: 4.326A pdb=" N CYS D 296 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'e' and resid 376 through 380 Processing sheet with id=AB4, first strand: chain 'E' and resid 31 through 33 removed outlier: 4.569A pdb=" N ASP E 31 " --> pdb=" O VAL E 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 46 through 48 Processing sheet with id=AB6, first strand: chain 'E' and resid 50 through 51 Processing sheet with id=AB7, first strand: chain 'E' and resid 58 through 61 removed outlier: 6.176A pdb=" N LEU E 58 " --> pdb=" O HIS E 290 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N CYS E 292 " --> pdb=" O LEU E 58 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 67 through 68 removed outlier: 6.787A pdb=" N LEU E 67 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE E 96 " --> pdb=" O ILE E 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 125 through 132 removed outlier: 3.673A pdb=" N SER E 127 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR E 270 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU E 193 " --> pdb=" O TYR E 270 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE E 272 " --> pdb=" O LEU E 191 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU E 189 " --> pdb=" O LEU E 274 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU E 193 " --> pdb=" O PRO E 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 125 through 132 removed outlier: 3.673A pdb=" N SER E 127 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR E 270 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU E 193 " --> pdb=" O TYR E 270 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE E 272 " --> pdb=" O LEU E 191 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU E 189 " --> pdb=" O LEU E 274 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 150 through 155 removed outlier: 7.717A pdb=" N ALA E 152 " --> pdb=" O LYS E 158 " (cutoff:3.500A) removed outlier: 10.586A pdb=" N LYS E 158 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 178 through 183 Processing sheet with id=AC4, first strand: chain 'E' and resid 301 through 302 Processing sheet with id=AC5, first strand: chain 'f' and resid 376 through 380 Processing sheet with id=AC6, first strand: chain 'F' and resid 31 through 33 removed outlier: 4.564A pdb=" N ASP F 31 " --> pdb=" O VAL F 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 46 through 48 Processing sheet with id=AC8, first strand: chain 'F' and resid 50 through 51 Processing sheet with id=AC9, first strand: chain 'F' and resid 58 through 61 removed outlier: 6.186A pdb=" N LEU F 58 " --> pdb=" O HIS F 290 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N CYS F 292 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 67 through 68 removed outlier: 6.786A pdb=" N LEU F 67 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE F 96 " --> pdb=" O ILE F 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 125 through 132 removed outlier: 3.682A pdb=" N SER F 127 " --> pdb=" O SER F 275 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR F 270 " --> pdb=" O LEU F 193 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU F 193 " --> pdb=" O TYR F 270 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU F 189 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU F 193 " --> pdb=" O PRO F 268 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 125 through 132 removed outlier: 3.682A pdb=" N SER F 127 " --> pdb=" O SER F 275 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR F 270 " --> pdb=" O LEU F 193 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU F 193 " --> pdb=" O TYR F 270 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU F 189 " --> pdb=" O LEU F 274 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 150 through 155 removed outlier: 7.712A pdb=" N ALA F 152 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 10.608A pdb=" N LYS F 158 " --> pdb=" O ALA F 152 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 178 through 183 Processing sheet with id=AD6, first strand: chain 'F' and resid 301 through 302 Processing sheet with id=AD7, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AD8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.560A pdb=" N ALA H 92 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AE1, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.578A pdb=" N ALA A 92 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AE3, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.632A pdb=" N ALA B 92 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.268A pdb=" N VAL C 10 " --> pdb=" O THR C 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 17 through 23 Processing sheet with id=AE6, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.477A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.467A pdb=" N VAL G 10 " --> pdb=" O THR G 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'G' and resid 17 through 23 Processing sheet with id=AE9, first strand: chain 'G' and resid 46 through 49 removed outlier: 6.509A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.531A pdb=" N VAL L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AF3, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.479A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) 627 hydrogen bonds defined for protein. 1731 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.33 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 3 1.13 - 1.30: 2809 1.30 - 1.47: 7193 1.47 - 1.65: 7260 1.65 - 1.82: 114 Bond restraints: 17379 Sorted by residual: bond pdb=" CG PRO E 89 " pdb=" CD PRO E 89 " ideal model delta sigma weight residual 1.503 1.040 0.463 3.40e-02 8.65e+02 1.86e+02 bond pdb=" CG PRO D 89 " pdb=" CD PRO D 89 " ideal model delta sigma weight residual 1.503 1.043 0.460 3.40e-02 8.65e+02 1.83e+02 bond pdb=" CB PRO F 89 " pdb=" CG PRO F 89 " ideal model delta sigma weight residual 1.492 0.955 0.537 5.00e-02 4.00e+02 1.15e+02 bond pdb=" CG PRO F 89 " pdb=" CD PRO F 89 " ideal model delta sigma weight residual 1.503 1.183 0.320 3.40e-02 8.65e+02 8.86e+01 bond pdb=" N PRO E 89 " pdb=" CD PRO E 89 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.58e+01 ... (remaining 17374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.10: 23588 13.10 - 26.20: 5 26.20 - 39.29: 1 39.29 - 52.39: 0 52.39 - 65.49: 1 Bond angle restraints: 23595 Sorted by residual: angle pdb=" CB PRO F 89 " pdb=" CG PRO F 89 " pdb=" CD PRO F 89 " ideal model delta sigma weight residual 106.10 171.59 -65.49 3.20e+00 9.77e-02 4.19e+02 angle pdb=" N PRO F 89 " pdb=" CD PRO F 89 " pdb=" CG PRO F 89 " ideal model delta sigma weight residual 103.20 78.74 24.46 1.50e+00 4.44e-01 2.66e+02 angle pdb=" N PRO E 89 " pdb=" CD PRO E 89 " pdb=" CG PRO E 89 " ideal model delta sigma weight residual 103.20 79.25 23.95 1.50e+00 4.44e-01 2.55e+02 angle pdb=" N PRO D 89 " pdb=" CD PRO D 89 " pdb=" CG PRO D 89 " ideal model delta sigma weight residual 103.20 79.33 23.87 1.50e+00 4.44e-01 2.53e+02 angle pdb=" CA PRO F 89 " pdb=" CB PRO F 89 " pdb=" CG PRO F 89 " ideal model delta sigma weight residual 104.50 76.57 27.93 1.90e+00 2.77e-01 2.16e+02 ... (remaining 23590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.02: 9508 22.02 - 44.04: 889 44.04 - 66.07: 187 66.07 - 88.09: 44 88.09 - 110.11: 13 Dihedral angle restraints: 10641 sinusoidal: 4488 harmonic: 6153 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 89 " pdb=" CB CYS C 89 " ideal model delta sinusoidal sigma weight residual 93.00 51.44 41.56 1 1.00e+01 1.00e-02 2.42e+01 dihedral pdb=" N PRO F 89 " pdb=" CG PRO F 89 " pdb=" CD PRO F 89 " pdb=" CB PRO F 89 " ideal model delta sinusoidal sigma weight residual 30.00 91.43 -61.43 1 1.50e+01 4.44e-03 2.23e+01 dihedral pdb=" CB CYS E 72 " pdb=" SG CYS E 72 " pdb=" SG CYS E 84 " pdb=" CB CYS E 84 " ideal model delta sinusoidal sigma weight residual -86.00 -118.73 32.73 1 1.00e+01 1.00e-02 1.52e+01 ... (remaining 10638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2141 0.058 - 0.115: 428 0.115 - 0.173: 63 0.173 - 0.230: 4 0.230 - 0.288: 4 Chirality restraints: 2640 Sorted by residual: chirality pdb=" C1 NAG D 602 " pdb=" ND2 ASN D 304 " pdb=" C2 NAG D 602 " pdb=" O5 NAG D 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2637 not shown) Planarity restraints: 3027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG L 95 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO L 96 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 298 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO D 299 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 299 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 299 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 88 " 0.032 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO F 89 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO F 89 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 89 " 0.026 5.00e-02 4.00e+02 ... (remaining 3024 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2382 2.76 - 3.29: 14086 3.29 - 3.83: 26474 3.83 - 4.36: 32641 4.36 - 4.90: 58666 Nonbonded interactions: 134249 Sorted by model distance: nonbonded pdb=" N GLU G 84 " pdb=" OE1 GLU G 84 " model vdw 2.224 3.120 nonbonded pdb=" O THR F 146 " pdb=" OG1 THR F 146 " model vdw 2.269 3.040 nonbonded pdb=" O THR E 146 " pdb=" OG1 THR E 146 " model vdw 2.270 3.040 nonbonded pdb=" O THR D 146 " pdb=" OG1 THR D 146 " model vdw 2.271 3.040 nonbonded pdb=" O GLY d 356 " pdb=" O HOH d 701 " model vdw 2.282 3.040 ... (remaining 134244 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'J' selection = chain 'N' selection = chain 'Q' } ncs_group { reference = chain 'd' selection = chain 'e' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.390 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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:7.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 : 0.008 0.537 17424 Z= 0.275 Angle : 0.910 65.492 23712 Z= 0.476 Chirality : 0.048 0.288 2640 Planarity : 0.005 0.051 3012 Dihedral : 17.843 110.109 6675 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.67 % Favored : 95.90 % Rotamer: Outliers : 5.04 % Allowed : 22.81 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.17), residues: 2124 helix: 1.84 (0.29), residues: 369 sheet: -0.11 (0.21), residues: 597 loop : -2.30 (0.14), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 226 TYR 0.008 0.001 TYR f 501 PHE 0.016 0.002 PHE D 128 TRP 0.014 0.001 TRP G 92 HIS 0.005 0.001 HIS F 25 Details of bonding type rmsd covalent geometry : bond 0.00819 (17379) covalent geometry : angle 0.90569 (23595) SS BOND : bond 0.00277 ( 18) SS BOND : angle 1.36040 ( 36) hydrogen bonds : bond 0.14324 ( 604) hydrogen bonds : angle 6.36341 ( 1731) link_BETA1-4 : bond 0.00393 ( 12) link_BETA1-4 : angle 1.68248 ( 36) link_NAG-ASN : bond 0.00138 ( 15) link_NAG-ASN : angle 1.71354 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 231 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 82 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: C 108 LEU cc_start: 0.5197 (OUTLIER) cc_final: 0.4906 (tp) outliers start: 91 outliers final: 82 residues processed: 319 average time/residue: 0.5641 time to fit residues: 201.9780 Evaluate side-chains 307 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 223 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain d residue 355 GLU Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain e residue 394 ASN Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 288 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 355 GLU Chi-restraints excluded: chain f residue 362 ILE Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 27 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.0570 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 262 ASN F 300 GLN C 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.143394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.085054 restraints weight = 18790.608| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.55 r_work: 0.2820 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.0642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17424 Z= 0.180 Angle : 0.660 12.848 23712 Z= 0.341 Chirality : 0.049 0.228 2640 Planarity : 0.005 0.046 3012 Dihedral : 10.496 70.142 2978 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.95 % Favored : 95.62 % Rotamer: Outliers : 5.87 % Allowed : 20.54 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.17), residues: 2124 helix: 1.65 (0.28), residues: 375 sheet: 0.06 (0.22), residues: 600 loop : -2.11 (0.15), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 234 TYR 0.010 0.001 TYR C 99 PHE 0.017 0.002 PHE D 128 TRP 0.008 0.001 TRP G 92 HIS 0.006 0.001 HIS D 25 Details of bonding type rmsd covalent geometry : bond 0.00438 (17379) covalent geometry : angle 0.65290 (23595) SS BOND : bond 0.00340 ( 18) SS BOND : angle 0.78972 ( 36) hydrogen bonds : bond 0.07337 ( 604) hydrogen bonds : angle 5.21564 ( 1731) link_BETA1-4 : bond 0.00526 ( 12) link_BETA1-4 : angle 2.01070 ( 36) link_NAG-ASN : bond 0.00140 ( 15) link_NAG-ASN : angle 1.57159 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 240 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.7542 (tt0) REVERT: D 78 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7694 (mm) REVERT: D 137 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: E 137 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: e 381 ASP cc_start: 0.8543 (t70) cc_final: 0.8154 (t70) REVERT: F 113 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8823 (mp) REVERT: F 137 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: f 394 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8401 (t0) REVERT: f 498 ASN cc_start: 0.7962 (t0) cc_final: 0.7674 (t0) REVERT: B 82 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: G 79 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6241 (tt) REVERT: L 18 VAL cc_start: 0.5246 (OUTLIER) cc_final: 0.5008 (m) outliers start: 106 outliers final: 53 residues processed: 321 average time/residue: 0.6349 time to fit residues: 226.3128 Evaluate side-chains 298 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 235 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain e residue 394 ASN Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 288 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain f residue 366 TYR Chi-restraints excluded: chain f residue 394 ASN Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 71 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 3 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 180 optimal weight: 8.9990 chunk 50 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 105 optimal weight: 0.0170 chunk 67 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 300 GLN d 469 GLN e 469 GLN f 469 GLN H 39 GLN C 28 ASN L 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.146140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.088304 restraints weight = 19019.084| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.56 r_work: 0.2867 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17424 Z= 0.116 Angle : 0.553 6.873 23712 Z= 0.286 Chirality : 0.045 0.235 2640 Planarity : 0.004 0.046 3012 Dihedral : 8.277 59.200 2907 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.53 % Favored : 96.09 % Rotamer: Outliers : 4.54 % Allowed : 22.09 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.17), residues: 2124 helix: 1.83 (0.28), residues: 375 sheet: 0.50 (0.22), residues: 594 loop : -1.90 (0.15), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 60 TYR 0.009 0.001 TYR f 368 PHE 0.013 0.001 PHE e 353 TRP 0.008 0.001 TRP d 436 HIS 0.004 0.001 HIS e 370 Details of bonding type rmsd covalent geometry : bond 0.00251 (17379) covalent geometry : angle 0.54547 (23595) SS BOND : bond 0.00345 ( 18) SS BOND : angle 0.57191 ( 36) hydrogen bonds : bond 0.05940 ( 604) hydrogen bonds : angle 4.86452 ( 1731) link_BETA1-4 : bond 0.00606 ( 12) link_BETA1-4 : angle 1.79309 ( 36) link_NAG-ASN : bond 0.00190 ( 15) link_NAG-ASN : angle 1.48923 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 247 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 ILE cc_start: 0.8340 (mt) cc_final: 0.7920 (mp) REVERT: D 78 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7697 (mm) REVERT: d 487 LYS cc_start: 0.8236 (ttpp) cc_final: 0.7968 (ttmm) REVERT: e 381 ASP cc_start: 0.8488 (t70) cc_final: 0.8111 (t70) REVERT: F 137 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7215 (mp0) REVERT: f 394 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.8490 (t0) REVERT: f 498 ASN cc_start: 0.7970 (t0) cc_final: 0.7587 (t0) REVERT: B 82 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: G 79 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6247 (tt) REVERT: L 18 VAL cc_start: 0.5300 (OUTLIER) cc_final: 0.5051 (m) outliers start: 82 outliers final: 36 residues processed: 308 average time/residue: 0.6536 time to fit residues: 223.1441 Evaluate side-chains 277 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 235 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain e residue 394 ASN Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 366 TYR Chi-restraints excluded: chain f residue 394 ASN Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain L residue 18 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 103 optimal weight: 0.1980 chunk 60 optimal weight: 0.0770 chunk 154 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 185 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 overall best weight: 1.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 300 GLN d 469 GLN E 300 GLN e 390 ASN e 469 GLN f 390 ASN C 80 GLN G 80 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.143231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.084657 restraints weight = 18910.799| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.56 r_work: 0.2812 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17424 Z= 0.196 Angle : 0.640 6.521 23712 Z= 0.331 Chirality : 0.049 0.221 2640 Planarity : 0.005 0.046 3012 Dihedral : 7.484 59.985 2894 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.14 % Favored : 95.53 % Rotamer: Outliers : 6.04 % Allowed : 20.65 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.17), residues: 2124 helix: 1.75 (0.28), residues: 375 sheet: 0.50 (0.22), residues: 600 loop : -1.91 (0.15), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 234 TYR 0.010 0.002 TYR L 99 PHE 0.019 0.002 PHE D 128 TRP 0.008 0.001 TRP D 77 HIS 0.007 0.001 HIS F 25 Details of bonding type rmsd covalent geometry : bond 0.00485 (17379) covalent geometry : angle 0.63355 (23595) SS BOND : bond 0.00396 ( 18) SS BOND : angle 0.67309 ( 36) hydrogen bonds : bond 0.07402 ( 604) hydrogen bonds : angle 4.97540 ( 1731) link_BETA1-4 : bond 0.00510 ( 12) link_BETA1-4 : angle 1.82626 ( 36) link_NAG-ASN : bond 0.00111 ( 15) link_NAG-ASN : angle 1.44698 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 239 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.7513 (tt0) REVERT: D 78 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7675 (mm) REVERT: D 319 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: d 487 LYS cc_start: 0.8230 (ttpp) cc_final: 0.7954 (ttmm) REVERT: E 137 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: E 166 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8482 (tt) REVERT: F 68 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: F 113 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8763 (mp) REVERT: F 137 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: f 394 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8419 (t0) REVERT: f 498 ASN cc_start: 0.8026 (t0) cc_final: 0.7576 (t0) REVERT: B 82 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: G 80 GLN cc_start: 0.5379 (OUTLIER) cc_final: 0.5164 (mp10) REVERT: L 18 VAL cc_start: 0.5285 (OUTLIER) cc_final: 0.5048 (m) outliers start: 109 outliers final: 57 residues processed: 323 average time/residue: 0.6182 time to fit residues: 221.8980 Evaluate side-chains 305 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 236 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain e residue 394 ASN Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 366 TYR Chi-restraints excluded: chain f residue 394 ASN Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 80 GLN Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 18 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 10 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 131 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 469 GLN E 300 GLN e 469 GLN f 469 GLN L 80 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.145127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.086979 restraints weight = 18850.586| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.55 r_work: 0.2848 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17424 Z= 0.128 Angle : 0.561 6.450 23712 Z= 0.292 Chirality : 0.046 0.229 2640 Planarity : 0.004 0.044 3012 Dihedral : 7.118 58.387 2892 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.63 % Favored : 96.09 % Rotamer: Outliers : 5.04 % Allowed : 22.09 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.18), residues: 2124 helix: 1.83 (0.28), residues: 375 sheet: 0.72 (0.22), residues: 594 loop : -1.81 (0.15), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 234 TYR 0.009 0.001 TYR f 368 PHE 0.014 0.002 PHE f 353 TRP 0.008 0.001 TRP d 436 HIS 0.004 0.001 HIS E 25 Details of bonding type rmsd covalent geometry : bond 0.00290 (17379) covalent geometry : angle 0.55557 (23595) SS BOND : bond 0.00247 ( 18) SS BOND : angle 0.50955 ( 36) hydrogen bonds : bond 0.06298 ( 604) hydrogen bonds : angle 4.81293 ( 1731) link_BETA1-4 : bond 0.00525 ( 12) link_BETA1-4 : angle 1.58172 ( 36) link_NAG-ASN : bond 0.00158 ( 15) link_NAG-ASN : angle 1.41732 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 242 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 78 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7693 (mm) REVERT: E 166 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8459 (tt) REVERT: e 381 ASP cc_start: 0.8465 (t70) cc_final: 0.8116 (t70) REVERT: F 78 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7836 (mm) REVERT: F 137 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: F 189 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: F 234 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.7554 (mtt90) REVERT: f 394 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8525 (t0) REVERT: f 498 ASN cc_start: 0.8031 (t0) cc_final: 0.7566 (t0) REVERT: A 46 GLU cc_start: 0.8266 (tt0) cc_final: 0.7973 (tt0) REVERT: B 82 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: L 18 VAL cc_start: 0.5242 (OUTLIER) cc_final: 0.5036 (m) REVERT: L 80 GLN cc_start: 0.5398 (OUTLIER) cc_final: 0.5131 (mp10) outliers start: 91 outliers final: 53 residues processed: 310 average time/residue: 0.6744 time to fit residues: 231.5632 Evaluate side-chains 301 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 238 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain e residue 394 ASN Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 234 ARG Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 366 TYR Chi-restraints excluded: chain f residue 394 ASN Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 80 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 129 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 300 GLN d 469 GLN E 300 GLN e 469 GLN f 469 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.143080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.084729 restraints weight = 18695.363| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.54 r_work: 0.2810 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17424 Z= 0.206 Angle : 0.638 6.279 23712 Z= 0.331 Chirality : 0.049 0.218 2640 Planarity : 0.005 0.049 3012 Dihedral : 7.110 59.746 2889 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.05 % Favored : 95.67 % Rotamer: Outliers : 6.09 % Allowed : 21.10 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.18), residues: 2124 helix: 1.74 (0.28), residues: 375 sheet: 0.67 (0.22), residues: 600 loop : -1.83 (0.15), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 234 TYR 0.010 0.002 TYR L 99 PHE 0.019 0.002 PHE F 128 TRP 0.009 0.001 TRP D 77 HIS 0.007 0.001 HIS F 25 Details of bonding type rmsd covalent geometry : bond 0.00518 (17379) covalent geometry : angle 0.63300 (23595) SS BOND : bond 0.00379 ( 18) SS BOND : angle 0.57530 ( 36) hydrogen bonds : bond 0.07454 ( 604) hydrogen bonds : angle 4.93058 ( 1731) link_BETA1-4 : bond 0.00463 ( 12) link_BETA1-4 : angle 1.58745 ( 36) link_NAG-ASN : bond 0.00119 ( 15) link_NAG-ASN : angle 1.43482 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 237 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: D 78 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7661 (mm) REVERT: E 166 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8478 (tt) REVERT: e 381 ASP cc_start: 0.8533 (t70) cc_final: 0.8159 (t70) REVERT: F 39 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.7596 (mmtt) REVERT: F 64 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8147 (mp) REVERT: F 68 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: F 78 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7853 (mm) REVERT: F 113 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8765 (mp) REVERT: F 137 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: f 394 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8419 (t0) REVERT: f 498 ASN cc_start: 0.8031 (t0) cc_final: 0.7501 (t0) REVERT: A 46 GLU cc_start: 0.8328 (tt0) cc_final: 0.8031 (tt0) REVERT: B 82 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: L 18 VAL cc_start: 0.5269 (OUTLIER) cc_final: 0.5049 (m) outliers start: 110 outliers final: 63 residues processed: 322 average time/residue: 0.6578 time to fit residues: 235.2801 Evaluate side-chains 310 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 235 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain e residue 383 LYS Chi-restraints excluded: chain e residue 394 ASN Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 366 TYR Chi-restraints excluded: chain f residue 394 ASN Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 18 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 103 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 134 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 469 GLN E 300 GLN ** F 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 469 GLN L 80 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.144164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.085689 restraints weight = 18684.886| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.55 r_work: 0.2826 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17424 Z= 0.159 Angle : 0.590 6.235 23712 Z= 0.307 Chirality : 0.047 0.222 2640 Planarity : 0.005 0.047 3012 Dihedral : 7.032 59.372 2889 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.81 % Favored : 95.90 % Rotamer: Outliers : 5.32 % Allowed : 22.04 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.18), residues: 2124 helix: 1.81 (0.28), residues: 375 sheet: 0.77 (0.22), residues: 594 loop : -1.79 (0.15), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 234 TYR 0.009 0.001 TYR L 99 PHE 0.016 0.002 PHE D 128 TRP 0.007 0.001 TRP d 436 HIS 0.006 0.001 HIS D 25 Details of bonding type rmsd covalent geometry : bond 0.00386 (17379) covalent geometry : angle 0.58504 (23595) SS BOND : bond 0.00317 ( 18) SS BOND : angle 0.57916 ( 36) hydrogen bonds : bond 0.06822 ( 604) hydrogen bonds : angle 4.85394 ( 1731) link_BETA1-4 : bond 0.00506 ( 12) link_BETA1-4 : angle 1.50068 ( 36) link_NAG-ASN : bond 0.00150 ( 15) link_NAG-ASN : angle 1.42582 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 235 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 78 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7681 (mm) REVERT: E 137 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: E 226 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7874 (ttt90) REVERT: e 381 ASP cc_start: 0.8503 (t70) cc_final: 0.8116 (t70) REVERT: F 39 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.7555 (mmtt) REVERT: F 113 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8738 (mp) REVERT: F 137 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: F 234 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7578 (mtt90) REVERT: f 394 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8387 (t0) REVERT: f 498 ASN cc_start: 0.7991 (t0) cc_final: 0.7475 (t0) REVERT: A 46 GLU cc_start: 0.8293 (tt0) cc_final: 0.7907 (tt0) REVERT: B 82 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: L 18 VAL cc_start: 0.5258 (OUTLIER) cc_final: 0.5047 (m) REVERT: L 80 GLN cc_start: 0.5815 (OUTLIER) cc_final: 0.5424 (mp10) outliers start: 96 outliers final: 60 residues processed: 310 average time/residue: 0.6630 time to fit residues: 227.5918 Evaluate side-chains 306 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 235 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 226 ARG Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain e residue 394 ASN Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 234 ARG Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 366 TYR Chi-restraints excluded: chain f residue 394 ASN Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 80 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 176 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 198 optimal weight: 30.0000 chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 300 GLN d 469 GLN E 300 GLN e 469 GLN F 286 ASN ** F 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 469 GLN C 52 ASN L 80 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.142633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.084207 restraints weight = 18834.816| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.54 r_work: 0.2801 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 17424 Z= 0.230 Angle : 0.663 6.683 23712 Z= 0.344 Chirality : 0.050 0.214 2640 Planarity : 0.005 0.051 3012 Dihedral : 7.091 59.836 2889 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.24 % Favored : 95.48 % Rotamer: Outliers : 5.76 % Allowed : 21.71 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.18), residues: 2124 helix: 1.79 (0.28), residues: 372 sheet: 0.67 (0.22), residues: 600 loop : -1.84 (0.15), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 234 TYR 0.011 0.002 TYR L 99 PHE 0.019 0.002 PHE E 128 TRP 0.010 0.002 TRP D 77 HIS 0.008 0.001 HIS F 25 Details of bonding type rmsd covalent geometry : bond 0.00582 (17379) covalent geometry : angle 0.65867 (23595) SS BOND : bond 0.00421 ( 18) SS BOND : angle 0.66740 ( 36) hydrogen bonds : bond 0.07754 ( 604) hydrogen bonds : angle 4.96283 ( 1731) link_BETA1-4 : bond 0.00473 ( 12) link_BETA1-4 : angle 1.58434 ( 36) link_NAG-ASN : bond 0.00132 ( 15) link_NAG-ASN : angle 1.45287 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 235 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 78 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7634 (mm) REVERT: D 319 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: E 137 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: E 166 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8446 (tt) REVERT: E 226 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7980 (ttt90) REVERT: e 381 ASP cc_start: 0.8538 (t70) cc_final: 0.8113 (t70) REVERT: F 39 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.7602 (mmtt) REVERT: F 64 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8084 (mp) REVERT: F 78 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7914 (mm) REVERT: F 113 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8793 (mp) REVERT: F 137 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: F 234 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.7576 (mtt90) REVERT: f 498 ASN cc_start: 0.8004 (t0) cc_final: 0.7438 (t0) REVERT: A 46 GLU cc_start: 0.8314 (tt0) cc_final: 0.7950 (tt0) REVERT: B 82 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: L 80 GLN cc_start: 0.5576 (OUTLIER) cc_final: 0.5168 (mp10) outliers start: 104 outliers final: 65 residues processed: 315 average time/residue: 0.6692 time to fit residues: 233.6495 Evaluate side-chains 312 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 234 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 226 ARG Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain e residue 394 ASN Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 234 ARG Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 80 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 31 optimal weight: 0.6980 chunk 184 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 198 optimal weight: 30.0000 chunk 118 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 141 optimal weight: 0.0170 chunk 158 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 469 GLN e 469 GLN f 469 GLN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.146262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.088347 restraints weight = 18777.994| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.55 r_work: 0.2867 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17424 Z= 0.114 Angle : 0.534 6.180 23712 Z= 0.280 Chirality : 0.045 0.228 2640 Planarity : 0.004 0.042 3012 Dihedral : 6.844 57.909 2889 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.72 % Favored : 96.00 % Rotamer: Outliers : 3.77 % Allowed : 23.59 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.18), residues: 2124 helix: 1.93 (0.28), residues: 375 sheet: 0.89 (0.22), residues: 594 loop : -1.69 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 62 TYR 0.008 0.001 TYR d 368 PHE 0.011 0.001 PHE e 353 TRP 0.009 0.001 TRP d 436 HIS 0.003 0.001 HIS E 25 Details of bonding type rmsd covalent geometry : bond 0.00257 (17379) covalent geometry : angle 0.52891 (23595) SS BOND : bond 0.00239 ( 18) SS BOND : angle 0.48891 ( 36) hydrogen bonds : bond 0.05820 ( 604) hydrogen bonds : angle 4.70097 ( 1731) link_BETA1-4 : bond 0.00457 ( 12) link_BETA1-4 : angle 1.36007 ( 36) link_NAG-ASN : bond 0.00225 ( 15) link_NAG-ASN : angle 1.42187 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 242 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 78 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7689 (mm) REVERT: E 137 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: E 166 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8443 (tt) REVERT: e 381 ASP cc_start: 0.8455 (t70) cc_final: 0.8085 (t70) REVERT: F 78 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7814 (mm) REVERT: F 137 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: F 189 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: F 234 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.7588 (mtt90) REVERT: f 381 ASP cc_start: 0.8537 (t70) cc_final: 0.8102 (t70) REVERT: f 498 ASN cc_start: 0.7978 (t0) cc_final: 0.7428 (t0) REVERT: A 46 GLU cc_start: 0.8177 (tt0) cc_final: 0.7748 (tt0) REVERT: B 82 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8124 (tt0) outliers start: 68 outliers final: 48 residues processed: 293 average time/residue: 0.6735 time to fit residues: 218.2709 Evaluate side-chains 290 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 234 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain e residue 394 ASN Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 234 ARG Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 366 TYR Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain L residue 16 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 68 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 100 optimal weight: 0.0170 chunk 196 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 99 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 469 GLN E 300 GLN e 390 ASN e 469 GLN f 390 ASN f 469 GLN C 52 ASN L 80 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.146574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.088779 restraints weight = 18703.491| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.53 r_work: 0.2871 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17424 Z= 0.114 Angle : 0.530 6.128 23712 Z= 0.276 Chirality : 0.045 0.216 2640 Planarity : 0.004 0.043 3012 Dihedral : 6.746 58.290 2889 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.67 % Favored : 96.05 % Rotamer: Outliers : 3.49 % Allowed : 24.03 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.18), residues: 2124 helix: 2.04 (0.28), residues: 375 sheet: 0.93 (0.22), residues: 594 loop : -1.63 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 87 TYR 0.009 0.001 TYR f 368 PHE 0.012 0.001 PHE D 128 TRP 0.009 0.001 TRP d 436 HIS 0.004 0.001 HIS E 25 Details of bonding type rmsd covalent geometry : bond 0.00259 (17379) covalent geometry : angle 0.52537 (23595) SS BOND : bond 0.00234 ( 18) SS BOND : angle 0.49864 ( 36) hydrogen bonds : bond 0.05703 ( 604) hydrogen bonds : angle 4.61194 ( 1731) link_BETA1-4 : bond 0.00475 ( 12) link_BETA1-4 : angle 1.32803 ( 36) link_NAG-ASN : bond 0.00183 ( 15) link_NAG-ASN : angle 1.37188 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 234 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 ILE cc_start: 0.8147 (mt) cc_final: 0.7738 (mp) REVERT: D 78 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7682 (mm) REVERT: E 64 ILE cc_start: 0.8232 (mt) cc_final: 0.7852 (mp) REVERT: E 166 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8447 (tt) REVERT: F 137 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: F 234 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.7580 (mtt90) REVERT: f 498 ASN cc_start: 0.7934 (t0) cc_final: 0.7376 (t0) REVERT: A 46 GLU cc_start: 0.8095 (tt0) cc_final: 0.7685 (tt0) REVERT: L 80 GLN cc_start: 0.5358 (OUTLIER) cc_final: 0.4949 (mp10) outliers start: 63 outliers final: 49 residues processed: 282 average time/residue: 0.6889 time to fit residues: 214.8871 Evaluate side-chains 288 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 234 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain d residue 362 ILE Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain e residue 394 ASN Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 234 ARG Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 366 TYR Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 80 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 105 optimal weight: 0.8980 chunk 177 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 469 GLN E 300 GLN e 469 GLN f 469 GLN C 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.146465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.088530 restraints weight = 18738.382| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.54 r_work: 0.2870 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.299 17424 Z= 0.272 Angle : 0.895 65.896 23712 Z= 0.531 Chirality : 0.047 0.475 2640 Planarity : 0.007 0.260 3012 Dihedral : 6.760 58.289 2889 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.77 % Favored : 95.95 % Rotamer: Outliers : 3.32 % Allowed : 24.42 % Favored : 72.26 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.18), residues: 2124 helix: 2.05 (0.28), residues: 375 sheet: 0.93 (0.22), residues: 594 loop : -1.63 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 60 TYR 0.008 0.001 TYR d 368 PHE 0.013 0.001 PHE D 128 TRP 0.009 0.001 TRP d 436 HIS 0.004 0.001 HIS E 25 Details of bonding type rmsd covalent geometry : bond 0.00539 (17379) covalent geometry : angle 0.89374 (23595) SS BOND : bond 0.00278 ( 18) SS BOND : angle 0.47668 ( 36) hydrogen bonds : bond 0.05823 ( 604) hydrogen bonds : angle 4.60957 ( 1731) link_BETA1-4 : bond 0.00476 ( 12) link_BETA1-4 : angle 1.35270 ( 36) link_NAG-ASN : bond 0.00205 ( 15) link_NAG-ASN : angle 1.37033 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8881.92 seconds wall clock time: 151 minutes 19.92 seconds (9079.92 seconds total)