Starting phenix.real_space_refine on Sun Jul 5 14:11:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dis_27441/07_2026/8dis_27441.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dis_27441/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8dis_27441/07_2026/8dis_27441.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dis_27441/07_2026/8dis_27441.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dis_27441/07_2026/8dis_27441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dis_27441/07_2026/8dis_27441.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dis_27441/07_2026/8dis_27441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dis_27441/07_2026/8dis_27441.map" } 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-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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: 3.68, per 1000 atoms: 0.22 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: 1.58 Conformation dependent library (CDL) restraints added in 737.2 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: 0.70 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: 3.02 Time building geometry restraints manager: 2.09 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 - 17.74: 8668 17.74 - 35.47: 1034 35.47 - 53.21: 287 53.21 - 70.94: 73 70.94 - 88.68: 18 Dihedral angle restraints: 10080 sinusoidal: 3927 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 10077 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: 11.850 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: 0.360 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.500 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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 : 17.035 88.675 6114 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/Z covalent geometry : bond 0.00819 / 0.28 (17379) covalent geometry : angle 0.90569 / 0.48 (23595) SS BOND : bond 0.00277 / 0.18 ( 18) SS BOND : angle 1.36040 / 0.80 ( 36) hydrogen bonds : bond 0.14324 / 9.75 ( 604) hydrogen bonds : angle 6.36341 / 4.45 ( 1731) link_BETA1-4 : bond 0.00393 / 0.25 ( 12) link_BETA1-4 : angle 1.68248 / 1.09 ( 36) link_NAG-ASN : bond 0.00138 / 0.09 ( 15) link_NAG-ASN : angle 1.71354 / 1.08 ( 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 : 0.539 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: 0.5276 time to fit residues: 189.6873 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 : 0.689 ------------------------------------------------------------------------------- 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... D 262 ASN ** F 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.143481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.085105 restraints weight = 18792.134| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.55 r_work: 0.2819 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.0618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17424 Z= 0.179 Angle : 0.647 11.012 23712 Z= 0.338 Chirality : 0.048 0.231 2640 Planarity : 0.005 0.047 3012 Dihedral : 7.740 58.679 2417 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.00 % Favored : 95.57 % Rotamer: Outliers : 5.70 % Allowed : 20.82 % Favored : 73.48 % 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: -1.11 (0.17), residues: 2124 helix: 1.66 (0.28), residues: 375 sheet: 0.04 (0.22), residues: 600 loop : -2.10 (0.15), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 234 TYR 0.009 0.001 TYR C 99 PHE 0.017 0.002 PHE D 128 TRP 0.008 0.001 TRP d 436 HIS 0.006 0.001 HIS F 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (17379) covalent geometry : angle 0.64119 / 0.34 (23595) SS BOND : bond 0.00339 / 0.22 ( 18) SS BOND : angle 0.81478 / 0.53 ( 36) hydrogen bonds : bond 0.07390 / 5.05 ( 604) hydrogen bonds : angle 5.24478 / 3.66 ( 1731) link_BETA1-4 : bond 0.00417 / 0.27 ( 12) link_BETA1-4 : angle 1.60754 / 1.08 ( 36) link_NAG-ASN : bond 0.00123 / 0.08 ( 15) link_NAG-ASN : angle 1.63575 / 1.02 ( 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 343 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 240 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: D 78 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7708 (mm) REVERT: D 137 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: E 137 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: E 145 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8310 (m) REVERT: F 68 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: F 137 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: f 394 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8376 (t0) REVERT: B 82 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8145 (tt0) REVERT: G 79 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6242 (tt) REVERT: L 18 VAL cc_start: 0.5257 (OUTLIER) cc_final: 0.5018 (m) outliers start: 103 outliers final: 50 residues processed: 319 average time/residue: 0.5826 time to fit residues: 207.2536 Evaluate side-chains 297 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 236 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 145 THR 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 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 68 GLN 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 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 L residue 18 VAL 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: 5.9990 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 15 optimal weight: 4.9990 chunk 105 optimal weight: 0.0060 chunk 67 optimal weight: 4.9990 chunk 152 optimal weight: 0.0000 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 300 GLN d 469 GLN e 469 GLN f 469 GLN H 39 GLN C 28 ASN C 39 GLN G 39 GLN L 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.147601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.090079 restraints weight = 19062.482| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.56 r_work: 0.2891 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17424 Z= 0.104 Angle : 0.523 6.863 23712 Z= 0.273 Chirality : 0.045 0.235 2640 Planarity : 0.004 0.046 3012 Dihedral : 6.253 58.846 2347 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.39 % Favored : 96.23 % Rotamer: Outliers : 4.15 % Allowed : 22.43 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.18), residues: 2124 helix: 1.90 (0.28), residues: 375 sheet: 0.52 (0.22), residues: 579 loop : -1.82 (0.15), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 234 TYR 0.008 0.001 TYR f 368 PHE 0.012 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/Z covalent geometry : bond 0.00218 / 0.10 (17379) covalent geometry : angle 0.51678 / 0.27 (23595) SS BOND : bond 0.00237 / 0.14 ( 18) SS BOND : angle 0.55679 / 0.36 ( 36) hydrogen bonds : bond 0.05463 / 3.72 ( 604) hydrogen bonds : angle 4.78811 / 3.33 ( 1731) link_BETA1-4 : bond 0.00492 / 0.33 ( 12) link_BETA1-4 : angle 1.35770 / 0.91 ( 36) link_NAG-ASN : bond 0.00231 / 0.14 ( 15) link_NAG-ASN : angle 1.58983 / 0.99 ( 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 332 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 257 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 ILE cc_start: 0.8373 (mt) cc_final: 0.7976 (mp) REVERT: D 78 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7760 (mm) REVERT: E 137 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: E 166 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8493 (tt) REVERT: e 381 ASP cc_start: 0.8434 (t70) cc_final: 0.8119 (t70) REVERT: F 137 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7215 (mp0) REVERT: f 498 ASN cc_start: 0.8032 (t0) cc_final: 0.7657 (t0) REVERT: B 82 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: L 18 VAL cc_start: 0.5277 (OUTLIER) cc_final: 0.5049 (m) outliers start: 75 outliers final: 34 residues processed: 311 average time/residue: 0.5763 time to fit residues: 199.9268 Evaluate side-chains 277 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 237 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 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 137 GLU Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 166 LEU 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 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 54 ILE 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 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: 0.4980 chunk 60 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 188 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 469 GLN e 469 GLN ** F 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 469 GLN C 39 GLN C 80 GLN G 39 GLN G 80 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.142561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.084132 restraints weight = 18921.145| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.55 r_work: 0.2799 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 17424 Z= 0.235 Angle : 0.677 10.166 23712 Z= 0.351 Chirality : 0.050 0.207 2640 Planarity : 0.005 0.048 3012 Dihedral : 6.203 58.785 2332 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.43 % Favored : 95.24 % Rotamer: Outliers : 5.92 % Allowed : 20.87 % Favored : 73.20 % 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: -0.76 (0.17), residues: 2124 helix: 1.71 (0.28), residues: 375 sheet: 0.46 (0.22), residues: 600 loop : -1.92 (0.15), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 234 TYR 0.011 0.002 TYR L 99 PHE 0.021 0.002 PHE E 128 TRP 0.009 0.002 TRP D 77 HIS 0.007 0.001 HIS F 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.23 (17379) covalent geometry : angle 0.67249 / 0.35 (23595) SS BOND : bond 0.00415 / 0.26 ( 18) SS BOND : angle 0.64217 / 0.43 ( 36) hydrogen bonds : bond 0.07943 / 5.42 ( 604) hydrogen bonds : angle 5.04460 / 3.51 ( 1731) link_BETA1-4 : bond 0.00441 / 0.28 ( 12) link_BETA1-4 : angle 1.55103 / 1.04 ( 36) link_NAG-ASN : bond 0.00090 / 0.06 ( 15) link_NAG-ASN : angle 1.54775 / 0.98 ( 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 350 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 243 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: D 78 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7633 (mm) REVERT: d 487 LYS cc_start: 0.8269 (ttpp) cc_final: 0.7995 (ttmm) REVERT: E 68 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.7311 (tt0) REVERT: E 137 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7441 (mp0) REVERT: E 166 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8451 (tt) REVERT: e 381 ASP cc_start: 0.8543 (t70) cc_final: 0.8120 (t70) REVERT: F 22 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8829 (mm) REVERT: F 68 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.7215 (tp40) REVERT: F 137 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: f 394 ASN cc_start: 0.8850 (OUTLIER) cc_final: 0.8475 (t0) REVERT: f 498 ASN cc_start: 0.8082 (t0) cc_final: 0.7644 (t0) REVERT: A 46 GLU cc_start: 0.8347 (tt0) cc_final: 0.8106 (tt0) REVERT: B 82 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8159 (tt0) REVERT: G 80 GLN cc_start: 0.5177 (OUTLIER) cc_final: 0.4911 (mp10) REVERT: L 18 VAL cc_start: 0.5254 (OUTLIER) cc_final: 0.5020 (m) outliers start: 107 outliers final: 53 residues processed: 325 average time/residue: 0.6049 time to fit residues: 218.8308 Evaluate side-chains 302 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 237 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 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 64 ILE Chi-restraints excluded: chain E residue 68 GLN 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 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 22 ILE 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 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 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 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: 1.9990 chunk 183 optimal weight: 10.0000 chunk 131 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 300 GLN d 469 GLN E 300 GLN e 469 GLN f 469 GLN L 80 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.144314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.085780 restraints weight = 18853.364| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.56 r_work: 0.2829 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17424 Z= 0.151 Angle : 0.589 9.081 23712 Z= 0.307 Chirality : 0.047 0.219 2640 Planarity : 0.005 0.045 3012 Dihedral : 6.043 58.293 2331 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.91 % Favored : 95.81 % Rotamer: Outliers : 4.93 % Allowed : 22.26 % 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: -0.61 (0.18), residues: 2124 helix: 1.77 (0.28), residues: 375 sheet: 0.62 (0.22), residues: 600 loop : -1.83 (0.15), residues: 1149 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 0.016 0.002 PHE D 128 TRP 0.008 0.001 TRP d 436 HIS 0.005 0.001 HIS E 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (17379) covalent geometry : angle 0.58327 / 0.31 (23595) SS BOND : bond 0.00304 / 0.20 ( 18) SS BOND : angle 0.53169 / 0.35 ( 36) hydrogen bonds : bond 0.06783 / 4.63 ( 604) hydrogen bonds : angle 4.88512 / 3.40 ( 1731) link_BETA1-4 : bond 0.00471 / 0.30 ( 12) link_BETA1-4 : angle 1.43388 / 0.96 ( 36) link_NAG-ASN : bond 0.00115 / 0.07 ( 15) link_NAG-ASN : angle 1.50507 / 0.95 ( 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 325 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 236 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 78 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7665 (mm) REVERT: E 137 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: E 166 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8422 (tt) REVERT: e 381 ASP cc_start: 0.8517 (t70) cc_final: 0.8106 (t70) REVERT: F 78 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7849 (mm) REVERT: F 137 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: f 394 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8364 (t0) REVERT: f 498 ASN cc_start: 0.8047 (t0) cc_final: 0.7541 (t0) REVERT: H 82 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8324 (tt0) REVERT: A 46 GLU cc_start: 0.8330 (tt0) cc_final: 0.8082 (tt0) REVERT: B 82 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8134 (tt0) REVERT: L 80 GLN cc_start: 0.5379 (OUTLIER) cc_final: 0.5111 (mp10) outliers start: 89 outliers final: 47 residues processed: 305 average time/residue: 0.5830 time to fit residues: 198.0336 Evaluate side-chains 294 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 238 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 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 166 LEU Chi-restraints excluded: chain E residue 228 ILE 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 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 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 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 82 GLU 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 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 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: 0.9990 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: 2.9990 chunk 128 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 469 GLN E 300 GLN e 469 GLN F 286 ASN f 469 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.142919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.084499 restraints weight = 18705.178| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.54 r_work: 0.2807 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17424 Z= 0.212 Angle : 0.647 9.533 23712 Z= 0.335 Chirality : 0.049 0.213 2640 Planarity : 0.005 0.050 3012 Dihedral : 6.113 58.195 2331 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.24 % Favored : 95.48 % Rotamer: Outliers : 5.70 % Allowed : 21.26 % Favored : 73.03 % 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: -0.65 (0.18), residues: 2124 helix: 1.70 (0.28), residues: 375 sheet: 0.61 (0.22), residues: 600 loop : -1.86 (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/Z covalent geometry : bond 0.00530 / 0.21 (17379) covalent geometry : angle 0.64199 / 0.33 (23595) SS BOND : bond 0.00397 / 0.25 ( 18) SS BOND : angle 0.57858 / 0.39 ( 36) hydrogen bonds : bond 0.07560 / 5.16 ( 604) hydrogen bonds : angle 4.95344 / 3.45 ( 1731) link_BETA1-4 : bond 0.00439 / 0.28 ( 12) link_BETA1-4 : angle 1.50180 / 1.01 ( 36) link_NAG-ASN : bond 0.00112 / 0.08 ( 15) link_NAG-ASN : angle 1.51411 / 0.96 ( 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 339 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 236 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.7497 (tt0) REVERT: D 78 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7646 (mm) REVERT: E 137 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: E 166 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8444 (tt) REVERT: F 39 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.7610 (mmtt) REVERT: F 68 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.7660 (tt0) REVERT: F 78 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7897 (mm) REVERT: F 137 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: F 185 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7743 (ptpt) REVERT: F 189 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8192 (tt0) REVERT: F 234 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.7581 (mtt90) REVERT: f 394 ASN cc_start: 0.8838 (OUTLIER) cc_final: 0.8448 (t0) REVERT: f 498 ASN cc_start: 0.8074 (t0) cc_final: 0.7578 (t0) REVERT: A 46 GLU cc_start: 0.8338 (tt0) cc_final: 0.8070 (tt0) REVERT: B 82 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8185 (tt0) outliers start: 103 outliers final: 62 residues processed: 314 average time/residue: 0.6002 time to fit residues: 209.6792 Evaluate side-chains 309 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 234 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 160 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 249 THR 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 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 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 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 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 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 185 LYS Chi-restraints excluded: chain F residue 189 GLU 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 103 optimal weight: 0.4980 chunk 73 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 469 GLN E 300 GLN 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 = 0.3677 r_free = 0.3677 target = 0.144740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.086546 restraints weight = 18707.528| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.54 r_work: 0.2839 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17424 Z= 0.142 Angle : 0.570 8.338 23712 Z= 0.297 Chirality : 0.046 0.219 2640 Planarity : 0.005 0.045 3012 Dihedral : 5.926 57.944 2331 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.86 % Favored : 95.86 % Rotamer: Outliers : 4.82 % Allowed : 22.54 % 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: -0.49 (0.18), residues: 2124 helix: 1.83 (0.28), residues: 375 sheet: 0.77 (0.22), residues: 594 loop : -1.78 (0.15), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 60 TYR 0.008 0.001 TYR e 368 PHE 0.015 0.002 PHE D 128 TRP 0.008 0.001 TRP d 436 HIS 0.005 0.001 HIS E 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (17379) covalent geometry : angle 0.56460 / 0.30 (23595) SS BOND : bond 0.00294 / 0.19 ( 18) SS BOND : angle 0.53517 / 0.36 ( 36) hydrogen bonds : bond 0.06523 / 4.45 ( 604) hydrogen bonds : angle 4.80410 / 3.35 ( 1731) link_BETA1-4 : bond 0.00469 / 0.30 ( 12) link_BETA1-4 : angle 1.38797 / 0.93 ( 36) link_NAG-ASN : bond 0.00141 / 0.09 ( 15) link_NAG-ASN : angle 1.48922 / 0.94 ( 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 324 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 237 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 78 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7678 (mm) REVERT: E 137 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: E 166 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8428 (tt) REVERT: E 226 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7837 (ttt90) REVERT: F 39 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.7561 (mmtt) REVERT: F 78 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7851 (mm) REVERT: F 137 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: F 189 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: F 234 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.7568 (mtt90) REVERT: f 394 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8535 (t0) REVERT: f 498 ASN cc_start: 0.8013 (t0) cc_final: 0.7462 (t0) REVERT: A 46 GLU cc_start: 0.8281 (tt0) cc_final: 0.8008 (tt0) REVERT: B 82 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: L 80 GLN cc_start: 0.5830 (OUTLIER) cc_final: 0.5528 (mp10) outliers start: 87 outliers final: 54 residues processed: 303 average time/residue: 0.5999 time to fit residues: 201.7185 Evaluate side-chains 300 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 234 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 160 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 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 154 SER Chi-restraints excluded: chain E residue 166 LEU 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 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 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 169 THR 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 202 SER Chi-restraints excluded: chain F residue 228 ILE 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 111 LEU Chi-restraints excluded: chain L residue 16 GLN 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: 3.9990 chunk 43 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 198 optimal weight: 30.0000 chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 300 GLN d 469 GLN E 300 GLN e 469 GLN f 469 GLN L 80 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.143998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.085606 restraints weight = 18834.566| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.55 r_work: 0.2824 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17424 Z= 0.169 Angle : 0.601 8.556 23712 Z= 0.312 Chirality : 0.047 0.210 2640 Planarity : 0.005 0.048 3012 Dihedral : 5.837 58.050 2328 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.91 % Favored : 95.81 % Rotamer: Outliers : 5.04 % Allowed : 22.59 % Favored : 72.37 % 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: -0.47 (0.18), residues: 2124 helix: 1.82 (0.28), residues: 375 sheet: 0.81 (0.22), residues: 594 loop : -1.77 (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 0.017 0.002 PHE D 128 TRP 0.008 0.001 TRP d 436 HIS 0.006 0.001 HIS E 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (17379) covalent geometry : angle 0.59619 / 0.31 (23595) SS BOND : bond 0.00331 / 0.21 ( 18) SS BOND : angle 0.59719 / 0.40 ( 36) hydrogen bonds : bond 0.06933 / 4.73 ( 604) hydrogen bonds : angle 4.82841 / 3.36 ( 1731) link_BETA1-4 : bond 0.00433 / 0.28 ( 12) link_BETA1-4 : angle 1.41707 / 0.95 ( 36) link_NAG-ASN : bond 0.00118 / 0.08 ( 15) link_NAG-ASN : angle 1.46924 / 0.93 ( 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 323 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 232 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 78 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7683 (mm) REVERT: E 137 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: E 166 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8438 (tt) REVERT: E 226 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7922 (ttt90) REVERT: F 39 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.7586 (mmtt) REVERT: F 78 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7862 (mm) REVERT: F 137 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: F 189 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8198 (tt0) REVERT: F 234 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7590 (mtt90) REVERT: f 394 ASN cc_start: 0.8830 (OUTLIER) cc_final: 0.8398 (t0) REVERT: f 498 ASN cc_start: 0.8025 (t0) cc_final: 0.7473 (t0) REVERT: A 46 GLU cc_start: 0.8299 (tt0) cc_final: 0.7995 (tt0) REVERT: B 82 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: L 80 GLN cc_start: 0.5920 (OUTLIER) cc_final: 0.5422 (mp10) outliers start: 91 outliers final: 55 residues processed: 302 average time/residue: 0.5724 time to fit residues: 192.2838 Evaluate side-chains 299 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 232 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 160 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 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 174 SER Chi-restraints excluded: chain E residue 226 ARG Chi-restraints excluded: chain E residue 228 ILE 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 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 169 THR 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 202 SER 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 335 LEU 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 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 80 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 31 optimal weight: 0.0870 chunk 184 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 186 optimal weight: 0.0870 chunk 198 optimal weight: 30.0000 chunk 118 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3694 r_free = 0.3694 target = 0.146304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.088287 restraints weight = 18773.431| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.55 r_work: 0.2865 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1266 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= 0.116 Angle : 0.536 7.467 23712 Z= 0.280 Chirality : 0.045 0.216 2640 Planarity : 0.004 0.042 3012 Dihedral : 5.627 57.881 2328 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.63 % Favored : 96.09 % Rotamer: Outliers : 3.54 % Allowed : 24.14 % Favored : 72.31 % 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: -0.33 (0.18), residues: 2124 helix: 1.93 (0.28), residues: 375 sheet: 0.90 (0.22), residues: 594 loop : -1.67 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 234 TYR 0.008 0.001 TYR f 368 PHE 0.012 0.001 PHE D 128 TRP 0.009 0.001 TRP d 436 HIS 0.003 0.001 HIS E 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (17379) covalent geometry : angle 0.53069 / 0.28 (23595) SS BOND : bond 0.00240 / 0.16 ( 18) SS BOND : angle 0.49395 / 0.32 ( 36) hydrogen bonds : bond 0.05867 / 4.00 ( 604) hydrogen bonds : angle 4.66582 / 3.25 ( 1731) link_BETA1-4 : bond 0.00457 / 0.30 ( 12) link_BETA1-4 : angle 1.30335 / 0.88 ( 36) link_NAG-ASN : bond 0.00180 / 0.11 ( 15) link_NAG-ASN : angle 1.44338 / 0.91 ( 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 300 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 236 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 78 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7698 (mm) REVERT: E 137 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: E 166 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8418 (tt) REVERT: F 78 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7815 (mm) REVERT: F 137 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: F 189 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: f 394 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8509 (t0) REVERT: f 498 ASN cc_start: 0.7984 (t0) cc_final: 0.7426 (t0) REVERT: A 46 GLU cc_start: 0.8230 (tt0) cc_final: 0.7989 (tt0) REVERT: L 80 GLN cc_start: 0.5825 (OUTLIER) cc_final: 0.5345 (mp10) outliers start: 64 outliers final: 45 residues processed: 286 average time/residue: 0.6139 time to fit residues: 194.9881 Evaluate side-chains 285 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 232 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 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 166 LEU Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 228 ILE 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 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 202 SER Chi-restraints excluded: chain F residue 228 ILE 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 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 20 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL 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 80 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: 0.4980 chunk 168 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 300 GLN d 469 GLN E 300 GLN e 390 ASN 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 = 0.3679 r_free = 0.3679 target = 0.144949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.086504 restraints weight = 18686.493| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.56 r_work: 0.2837 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17424 Z= 0.149 Angle : 0.574 8.068 23712 Z= 0.298 Chirality : 0.046 0.207 2640 Planarity : 0.004 0.043 3012 Dihedral : 5.655 58.186 2328 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.91 % Favored : 95.81 % Rotamer: Outliers : 3.77 % Allowed : 24.03 % Favored : 72.20 % 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: -0.34 (0.18), residues: 2124 helix: 1.92 (0.28), residues: 375 sheet: 0.90 (0.22), residues: 594 loop : -1.68 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 234 TYR 0.009 0.001 TYR f 368 PHE 0.015 0.002 PHE D 128 TRP 0.008 0.001 TRP d 436 HIS 0.005 0.001 HIS E 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (17379) covalent geometry : angle 0.56904 / 0.30 (23595) SS BOND : bond 0.00293 / 0.19 ( 18) SS BOND : angle 0.55413 / 0.37 ( 36) hydrogen bonds : bond 0.06497 / 4.43 ( 604) hydrogen bonds : angle 4.71034 / 3.28 ( 1731) link_BETA1-4 : bond 0.00426 / 0.27 ( 12) link_BETA1-4 : angle 1.34326 / 0.91 ( 36) link_NAG-ASN : bond 0.00138 / 0.09 ( 15) link_NAG-ASN : angle 1.42130 / 0.90 ( 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 298 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 230 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 ILE cc_start: 0.8249 (mt) cc_final: 0.7829 (mp) REVERT: D 68 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.7573 (tt0) REVERT: D 78 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7695 (mm) REVERT: E 64 ILE cc_start: 0.8233 (mt) cc_final: 0.7862 (mp) REVERT: E 137 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: E 166 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8433 (tt) REVERT: F 137 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: F 158 LYS cc_start: 0.7409 (pptt) cc_final: 0.7095 (pmtt) REVERT: f 394 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8539 (t0) REVERT: f 498 ASN cc_start: 0.8002 (t0) cc_final: 0.7451 (t0) REVERT: A 46 GLU cc_start: 0.8217 (tt0) cc_final: 0.7991 (tt0) REVERT: L 80 GLN cc_start: 0.5713 (OUTLIER) cc_final: 0.5270 (mp10) outliers start: 68 outliers final: 50 residues processed: 280 average time/residue: 0.5901 time to fit residues: 183.8232 Evaluate side-chains 288 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 231 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 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 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 166 LEU Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 228 ILE 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 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 202 SER Chi-restraints excluded: chain F residue 228 ILE 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 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 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 80 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 105 optimal weight: 0.5980 chunk 177 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 300 GLN d 469 GLN E 300 GLN e 469 GLN ** F 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 469 GLN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.142699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.083996 restraints weight = 18705.910| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.56 r_work: 0.2795 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 17424 Z= 0.244 Angle : 0.684 9.533 23712 Z= 0.354 Chirality : 0.050 0.211 2640 Planarity : 0.005 0.049 3012 Dihedral : 5.950 58.642 2328 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.52 % Favored : 95.20 % Rotamer: Outliers : 4.37 % Allowed : 23.59 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.52 (0.18), residues: 2124 helix: 1.79 (0.28), residues: 372 sheet: 0.75 (0.22), residues: 600 loop : -1.78 (0.15), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 62 TYR 0.011 0.002 TYR L 99 PHE 0.020 0.002 PHE F 128 TRP 0.011 0.002 TRP D 77 HIS 0.008 0.001 HIS F 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.24 (17379) covalent geometry : angle 0.67993 / 0.35 (23595) SS BOND : bond 0.00436 / 0.28 ( 18) SS BOND : angle 0.65373 / 0.44 ( 36) hydrogen bonds : bond 0.07985 / 5.44 ( 604) hydrogen bonds : angle 4.95390 / 3.45 ( 1731) link_BETA1-4 : bond 0.00435 / 0.28 ( 12) link_BETA1-4 : angle 1.50148 / 1.01 ( 36) link_NAG-ASN : bond 0.00149 / 0.11 ( 15) link_NAG-ASN : angle 1.45267 / 0.94 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7854.23 seconds wall clock time: 133 minutes 59.77 seconds (8039.77 seconds total)