Starting phenix.real_space_refine on Tue Jun 24 12:37:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dis_27441/06_2025/8dis_27441.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dis_27441/06_2025/8dis_27441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dis_27441/06_2025/8dis_27441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dis_27441/06_2025/8dis_27441.map" model { file = "/net/cci-nas-00/data/ceres_data/8dis_27441/06_2025/8dis_27441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dis_27441/06_2025/8dis_27441.cif" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17044 Number of models: 1 Model: "" Number of chains: 30 Chain: "D" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 18, 'TRANS': 306} Chain: "d" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1306 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 161} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 18, 'TRANS': 306} Chain: "e" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1306 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 161} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 18, 'TRANS': 306} Chain: "f" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1306 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 161} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "d" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "e" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "f" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 9.60, per 1000 atoms: 0.56 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: 4.09 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 2.48 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: 5.83 Time building geometry restraints manager: 5.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 3 1.13 - 1.30: 2809 1.30 - 1.47: 7193 1.47 - 1.65: 7260 1.65 - 1.82: 114 Bond restraints: 17379 Sorted by residual: bond pdb=" CG PRO E 89 " pdb=" CD PRO E 89 " ideal model delta sigma weight residual 1.503 1.040 0.463 3.40e-02 8.65e+02 1.86e+02 bond pdb=" CG PRO D 89 " pdb=" CD PRO D 89 " ideal model delta sigma weight residual 1.503 1.043 0.460 3.40e-02 8.65e+02 1.83e+02 bond pdb=" CB PRO F 89 " pdb=" CG PRO F 89 " ideal model delta sigma weight residual 1.492 0.955 0.537 5.00e-02 4.00e+02 1.15e+02 bond pdb=" CG PRO F 89 " pdb=" CD PRO F 89 " ideal model delta sigma weight residual 1.503 1.183 0.320 3.40e-02 8.65e+02 8.86e+01 bond pdb=" N PRO E 89 " pdb=" CD PRO E 89 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.58e+01 ... (remaining 17374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.10: 23588 13.10 - 26.20: 5 26.20 - 39.29: 1 39.29 - 52.39: 0 52.39 - 65.49: 1 Bond angle restraints: 23595 Sorted by residual: angle pdb=" CB PRO F 89 " pdb=" CG PRO F 89 " pdb=" CD PRO F 89 " ideal model delta sigma weight residual 106.10 171.59 -65.49 3.20e+00 9.77e-02 4.19e+02 angle pdb=" N PRO F 89 " pdb=" CD PRO F 89 " pdb=" CG PRO F 89 " ideal model delta sigma weight residual 103.20 78.74 24.46 1.50e+00 4.44e-01 2.66e+02 angle pdb=" N PRO E 89 " pdb=" CD PRO E 89 " pdb=" CG PRO E 89 " ideal model delta sigma weight residual 103.20 79.25 23.95 1.50e+00 4.44e-01 2.55e+02 angle pdb=" N PRO D 89 " pdb=" CD PRO D 89 " pdb=" CG PRO D 89 " ideal model delta sigma weight residual 103.20 79.33 23.87 1.50e+00 4.44e-01 2.53e+02 angle pdb=" CA PRO F 89 " pdb=" CB PRO F 89 " pdb=" CG PRO F 89 " ideal model delta sigma weight residual 104.50 76.57 27.93 1.90e+00 2.77e-01 2.16e+02 ... (remaining 23590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.02: 9508 22.02 - 44.04: 889 44.04 - 66.07: 187 66.07 - 88.09: 44 88.09 - 110.11: 13 Dihedral angle restraints: 10641 sinusoidal: 4488 harmonic: 6153 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 89 " pdb=" CB CYS C 89 " ideal model delta sinusoidal sigma weight residual 93.00 51.44 41.56 1 1.00e+01 1.00e-02 2.42e+01 dihedral pdb=" N PRO F 89 " pdb=" CG PRO F 89 " pdb=" CD PRO F 89 " pdb=" CB PRO F 89 " ideal model delta sinusoidal sigma weight residual 30.00 91.43 -61.43 1 1.50e+01 4.44e-03 2.23e+01 dihedral pdb=" CB CYS E 72 " pdb=" SG CYS E 72 " pdb=" SG CYS E 84 " pdb=" CB CYS E 84 " ideal model delta sinusoidal sigma weight residual -86.00 -118.73 32.73 1 1.00e+01 1.00e-02 1.52e+01 ... (remaining 10638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2141 0.058 - 0.115: 428 0.115 - 0.173: 63 0.173 - 0.230: 4 0.230 - 0.288: 4 Chirality restraints: 2640 Sorted by residual: chirality pdb=" C1 NAG D 602 " pdb=" ND2 ASN D 304 " pdb=" C2 NAG D 602 " pdb=" O5 NAG D 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2637 not shown) Planarity restraints: 3027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG L 95 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO L 96 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 298 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO D 299 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 299 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 299 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 88 " 0.032 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO F 89 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO F 89 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 89 " 0.026 5.00e-02 4.00e+02 ... (remaining 3024 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2382 2.76 - 3.29: 14086 3.29 - 3.83: 26474 3.83 - 4.36: 32641 4.36 - 4.90: 58666 Nonbonded interactions: 134249 Sorted by model distance: nonbonded pdb=" N GLU G 84 " pdb=" OE1 GLU G 84 " model vdw 2.224 3.120 nonbonded pdb=" O THR F 146 " pdb=" OG1 THR F 146 " model vdw 2.269 3.040 nonbonded pdb=" O THR E 146 " pdb=" OG1 THR E 146 " model vdw 2.270 3.040 nonbonded pdb=" O THR D 146 " pdb=" OG1 THR D 146 " model vdw 2.271 3.040 nonbonded pdb=" O GLY d 356 " pdb=" O HOH d 701 " model vdw 2.282 3.040 ... (remaining 134244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 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: 134.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 42.400 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.120 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:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 190.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.537 17424 Z= 0.275 Angle : 0.910 65.492 23712 Z= 0.476 Chirality : 0.048 0.288 2640 Planarity : 0.005 0.051 3012 Dihedral : 17.843 110.109 6675 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (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 TRP 0.014 0.001 TRP G 92 HIS 0.005 0.001 HIS F 25 PHE 0.016 0.002 PHE D 128 TYR 0.008 0.001 TYR f 501 ARG 0.002 0.000 ARG F 226 Details of bonding type rmsd link_NAG-ASN : bond 0.00138 ( 15) link_NAG-ASN : angle 1.71354 ( 45) link_BETA1-4 : bond 0.00393 ( 12) link_BETA1-4 : angle 1.68248 ( 36) hydrogen bonds : bond 0.14324 ( 604) hydrogen bonds : angle 6.36341 ( 1731) SS BOND : bond 0.00277 ( 18) SS BOND : angle 1.36040 ( 36) covalent geometry : bond 0.00819 (17379) covalent geometry : angle 0.90569 (23595) *********************** 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 : 1.710 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: 1.1476 time to fit residues: 413.2823 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 : 1.852 ------------------------------------------------------------------------------- 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 174 optimal weight: 7.9990 chunk 156 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 262 ASN ** F 300 GLN ** 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 = 0.3655 r_free = 0.3655 target = 0.142646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.084323 restraints weight = 18820.991| |-----------------------------------------------------------------------------| r_work (start): 0.2963 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: 4.21 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.0680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17424 Z= 0.207 Angle : 0.689 12.120 23712 Z= 0.356 Chirality : 0.050 0.225 2640 Planarity : 0.005 0.048 3012 Dihedral : 10.552 70.563 2978 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.95 % Favored : 95.62 % Rotamer: Outliers : 6.31 % Allowed : 20.38 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.17), residues: 2124 helix: 1.60 (0.28), residues: 375 sheet: 0.03 (0.22), residues: 600 loop : -2.14 (0.15), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 436 HIS 0.007 0.001 HIS F 25 PHE 0.018 0.002 PHE D 128 TYR 0.010 0.002 TYR B 95 ARG 0.004 0.000 ARG D 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 15) link_NAG-ASN : angle 1.58379 ( 45) link_BETA1-4 : bond 0.00522 ( 12) link_BETA1-4 : angle 2.04335 ( 36) hydrogen bonds : bond 0.07807 ( 604) hydrogen bonds : angle 5.28847 ( 1731) SS BOND : bond 0.00386 ( 18) SS BOND : angle 0.82871 ( 36) covalent geometry : bond 0.00514 (17379) covalent geometry : angle 0.68135 (23595) *********************** 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 357 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 243 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: D 78 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7679 (mm) REVERT: D 137 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: d 373 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7378 (mt-10) REVERT: E 137 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: E 145 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8293 (m) REVERT: e 381 ASP cc_start: 0.8564 (t70) cc_final: 0.8159 (t70) REVERT: F 68 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.7707 (tt0) REVERT: F 137 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: f 394 ASN cc_start: 0.8832 (OUTLIER) cc_final: 0.8424 (t0) REVERT: B 82 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8147 (tt0) REVERT: G 79 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.6194 (tt) REVERT: L 18 VAL cc_start: 0.5222 (OUTLIER) cc_final: 0.4983 (m) outliers start: 114 outliers final: 55 residues processed: 333 average time/residue: 1.4875 time to fit residues: 556.3808 Evaluate side-chains 304 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 237 time to evaluate : 1.769 ------------------------------------------------------------------------------- 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 99 THR 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 169 THR Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 249 THR 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 373 GLU 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 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 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 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 98 LYS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 71 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 154 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 300 GLN d 469 GLN e 469 GLN ** F 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 469 GLN C 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.142434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.084066 restraints weight = 18713.230| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.54 r_work: 0.2804 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17424 Z= 0.213 Angle : 0.672 6.742 23712 Z= 0.347 Chirality : 0.050 0.227 2640 Planarity : 0.005 0.051 3012 Dihedral : 8.438 59.999 2906 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.19 % Favored : 95.43 % Rotamer: Outliers : 6.87 % Allowed : 19.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.17), residues: 2124 helix: 1.58 (0.28), residues: 375 sheet: 0.28 (0.22), residues: 600 loop : -2.05 (0.15), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 436 HIS 0.007 0.001 HIS F 25 PHE 0.018 0.002 PHE f 353 TYR 0.010 0.002 TYR f 501 ARG 0.003 0.000 ARG F 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00098 ( 15) link_NAG-ASN : angle 1.54595 ( 45) link_BETA1-4 : bond 0.00565 ( 12) link_BETA1-4 : angle 1.91905 ( 36) hydrogen bonds : bond 0.07774 ( 604) hydrogen bonds : angle 5.13829 ( 1731) SS BOND : bond 0.00437 ( 18) SS BOND : angle 0.74323 ( 36) covalent geometry : bond 0.00530 (17379) covalent geometry : angle 0.66560 (23595) *********************** 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 366 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 242 time to evaluate : 3.394 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: 0.7462 (tt0) REVERT: D 78 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7645 (mm) REVERT: D 137 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: E 137 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: E 166 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8438 (tt) REVERT: E 226 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7847 (ttt90) REVERT: F 68 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.7691 (tt0) REVERT: F 137 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: f 382 GLN cc_start: 0.8705 (mp10) cc_final: 0.7925 (mp10) REVERT: f 394 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8440 (t0) REVERT: f 498 ASN cc_start: 0.8030 (t0) cc_final: 0.7628 (t0) REVERT: B 82 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: G 79 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6243 (tt) REVERT: L 18 VAL cc_start: 0.5300 (OUTLIER) cc_final: 0.5041 (m) outliers start: 124 outliers final: 65 residues processed: 338 average time/residue: 1.7225 time to fit residues: 647.7478 Evaluate side-chains 312 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 235 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 36 VAL 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 99 THR Chi-restraints excluded: chain D residue 137 GLU 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 169 THR 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 288 SER Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 128 PHE 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 226 ARG Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain e residue 394 ASN Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 36 VAL 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 202 SER Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 293 ASN 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 2 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain L residue 16 GLN 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 107 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 163 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 124 optimal weight: 0.3980 chunk 88 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 300 GLN d 469 GLN E 300 GLN e 469 GLN f 469 GLN H 39 GLN L 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.145034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.086826 restraints weight = 18686.573| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.55 r_work: 0.2845 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17424 Z= 0.127 Angle : 0.570 6.618 23712 Z= 0.297 Chirality : 0.046 0.234 2640 Planarity : 0.005 0.045 3012 Dihedral : 7.520 57.816 2902 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.63 % Favored : 96.05 % Rotamer: Outliers : 5.54 % Allowed : 21.32 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.17), residues: 2124 helix: 1.77 (0.28), residues: 375 sheet: 0.57 (0.22), residues: 594 loop : -1.90 (0.15), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 436 HIS 0.004 0.001 HIS E 25 PHE 0.014 0.002 PHE e 353 TYR 0.009 0.001 TYR e 368 ARG 0.002 0.000 ARG D 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00158 ( 15) link_NAG-ASN : angle 1.47701 ( 45) link_BETA1-4 : bond 0.00551 ( 12) link_BETA1-4 : angle 1.75311 ( 36) hydrogen bonds : bond 0.06311 ( 604) hydrogen bonds : angle 4.88936 ( 1731) SS BOND : bond 0.00296 ( 18) SS BOND : angle 0.52983 ( 36) covalent geometry : bond 0.00284 (17379) covalent geometry : angle 0.56338 (23595) *********************** 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 338 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 238 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 ILE cc_start: 0.8364 (mt) cc_final: 0.7951 (mp) REVERT: D 78 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7676 (mm) REVERT: D 137 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: d 487 LYS cc_start: 0.8262 (ttpp) cc_final: 0.7988 (ttmm) REVERT: E 166 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8453 (tt) REVERT: F 78 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7846 (mm) REVERT: F 113 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8755 (mp) REVERT: F 137 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: f 394 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8518 (t0) REVERT: f 498 ASN cc_start: 0.8039 (t0) cc_final: 0.7576 (t0) REVERT: B 82 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: L 18 VAL cc_start: 0.5305 (OUTLIER) cc_final: 0.5065 (m) outliers start: 100 outliers final: 50 residues processed: 313 average time/residue: 1.2483 time to fit residues: 436.4242 Evaluate side-chains 289 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 230 time to evaluate : 1.803 ------------------------------------------------------------------------------- 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 137 GLU Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 306 SER 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 160 SER 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 29 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 154 SER 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 292 CYS Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 366 TYR Chi-restraints excluded: chain f residue 394 ASN Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain 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 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 111 LEU 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 77 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 100 optimal weight: 0.0570 chunk 103 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 300 GLN d 469 GLN E 300 GLN e 469 GLN f 469 GLN G 80 GLN L 80 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.145469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.087332 restraints weight = 18963.146| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.55 r_work: 0.2853 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17424 Z= 0.126 Angle : 0.553 6.413 23712 Z= 0.288 Chirality : 0.046 0.228 2640 Planarity : 0.004 0.045 3012 Dihedral : 7.065 57.418 2893 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.72 % Favored : 96.00 % Rotamer: Outliers : 5.76 % Allowed : 21.48 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.18), residues: 2124 helix: 1.87 (0.28), residues: 375 sheet: 0.67 (0.22), residues: 600 loop : -1.77 (0.15), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 436 HIS 0.004 0.001 HIS E 25 PHE 0.014 0.001 PHE D 128 TYR 0.009 0.001 TYR f 368 ARG 0.003 0.000 ARG L 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00173 ( 15) link_NAG-ASN : angle 1.43104 ( 45) link_BETA1-4 : bond 0.00513 ( 12) link_BETA1-4 : angle 1.50214 ( 36) hydrogen bonds : bond 0.06163 ( 604) hydrogen bonds : angle 4.75899 ( 1731) SS BOND : bond 0.00257 ( 18) SS BOND : angle 0.49548 ( 36) covalent geometry : bond 0.00292 (17379) covalent geometry : angle 0.54704 (23595) *********************** 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 341 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 237 time to evaluate : 2.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.7439 (tt0) REVERT: D 78 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7700 (mm) REVERT: D 137 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: d 487 LYS cc_start: 0.8237 (ttpp) cc_final: 0.7985 (ttmm) REVERT: E 137 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: E 166 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8456 (tt) REVERT: F 113 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8740 (mp) REVERT: F 137 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: f 394 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8519 (t0) REVERT: f 498 ASN cc_start: 0.8035 (t0) cc_final: 0.7518 (t0) REVERT: A 81 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8754 (ttp) REVERT: B 82 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: G 80 GLN cc_start: 0.5344 (OUTLIER) cc_final: 0.5044 (mp10) REVERT: L 18 VAL cc_start: 0.5281 (OUTLIER) cc_final: 0.5053 (m) REVERT: L 80 GLN cc_start: 0.5781 (OUTLIER) cc_final: 0.5512 (mp10) outliers start: 104 outliers final: 57 residues processed: 316 average time/residue: 1.2787 time to fit residues: 450.6624 Evaluate side-chains 304 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 234 time to evaluate : 2.375 ------------------------------------------------------------------------------- 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 137 GLU Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 306 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 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 160 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 251 LEU 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 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 113 ILE Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 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 256 THR Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 366 TYR Chi-restraints excluded: chain f residue 394 ASN Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain 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 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 152 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 173 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 300 GLN d 469 GLN E 300 GLN e 390 ASN e 469 GLN f 390 ASN f 469 GLN L 80 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.144154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.085594 restraints weight = 18850.404| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.57 r_work: 0.2823 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17424 Z= 0.169 Angle : 0.597 6.278 23712 Z= 0.310 Chirality : 0.047 0.222 2640 Planarity : 0.005 0.045 3012 Dihedral : 7.074 59.189 2890 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.10 % Favored : 95.62 % Rotamer: Outliers : 6.15 % Allowed : 21.43 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.18), residues: 2124 helix: 1.82 (0.28), residues: 375 sheet: 0.71 (0.22), residues: 600 loop : -1.80 (0.15), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 436 HIS 0.006 0.001 HIS F 25 PHE 0.017 0.002 PHE F 128 TYR 0.009 0.001 TYR L 99 ARG 0.003 0.000 ARG D 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00134 ( 15) link_NAG-ASN : angle 1.42428 ( 45) link_BETA1-4 : bond 0.00477 ( 12) link_BETA1-4 : angle 1.51048 ( 36) hydrogen bonds : bond 0.06867 ( 604) hydrogen bonds : angle 4.82696 ( 1731) SS BOND : bond 0.00336 ( 18) SS BOND : angle 0.55969 ( 36) covalent geometry : bond 0.00416 (17379) covalent geometry : angle 0.59237 (23595) *********************** 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 344 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 233 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 78 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7690 (mm) REVERT: D 137 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: E 137 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: E 166 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8451 (tt) REVERT: F 39 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.7547 (mmtt) REVERT: F 64 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8184 (mp) REVERT: F 78 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7864 (mm) REVERT: F 113 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8814 (mp) REVERT: F 137 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: f 394 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8368 (t0) REVERT: f 498 ASN cc_start: 0.7970 (t0) cc_final: 0.7434 (t0) REVERT: A 46 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: B 82 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8157 (tt0) REVERT: L 80 GLN cc_start: 0.6111 (OUTLIER) cc_final: 0.5840 (mp10) outliers start: 111 outliers final: 63 residues processed: 318 average time/residue: 1.2622 time to fit residues: 447.5886 Evaluate side-chains 308 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 232 time to evaluate : 1.716 ------------------------------------------------------------------------------- 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 137 GLU Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 251 LEU 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 383 LYS Chi-restraints excluded: chain e residue 394 ASN Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 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 288 SER Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 366 TYR Chi-restraints excluded: chain f residue 394 ASN Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 80 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 91 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 chunk 206 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 191 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 300 GLN d 469 GLN E 300 GLN F 286 ASN 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 = 0.3671 r_free = 0.3671 target = 0.144268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.085799 restraints weight = 18727.451| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.58 r_work: 0.2827 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17424 Z= 0.161 Angle : 0.591 6.219 23712 Z= 0.307 Chirality : 0.047 0.220 2640 Planarity : 0.005 0.046 3012 Dihedral : 7.059 59.234 2890 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.67 % Favored : 96.05 % Rotamer: Outliers : 5.54 % Allowed : 21.93 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.18), residues: 2124 helix: 1.84 (0.28), residues: 375 sheet: 0.72 (0.22), residues: 600 loop : -1.77 (0.15), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 436 HIS 0.006 0.001 HIS D 25 PHE 0.016 0.002 PHE F 128 TYR 0.009 0.001 TYR e 368 ARG 0.004 0.000 ARG D 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00154 ( 15) link_NAG-ASN : angle 1.41197 ( 45) link_BETA1-4 : bond 0.00495 ( 12) link_BETA1-4 : angle 1.48531 ( 36) hydrogen bonds : bond 0.06800 ( 604) hydrogen bonds : angle 4.81981 ( 1731) SS BOND : bond 0.00318 ( 18) SS BOND : angle 0.56429 ( 36) covalent geometry : bond 0.00393 (17379) covalent geometry : angle 0.58558 (23595) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 231 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 78 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7683 (mm) REVERT: D 137 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: E 137 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: E 166 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8468 (tt) REVERT: F 64 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8162 (mp) REVERT: F 68 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: F 78 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7852 (mm) REVERT: F 113 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8811 (mp) REVERT: F 137 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: f 394 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8385 (t0) REVERT: f 498 ASN cc_start: 0.7984 (t0) cc_final: 0.7441 (t0) REVERT: A 46 GLU cc_start: 0.8254 (tt0) cc_final: 0.7874 (tt0) REVERT: B 82 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: L 80 GLN cc_start: 0.6132 (OUTLIER) cc_final: 0.5839 (mp10) outliers start: 100 outliers final: 62 residues processed: 309 average time/residue: 1.2418 time to fit residues: 429.3351 Evaluate side-chains 305 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 231 time to evaluate : 2.045 ------------------------------------------------------------------------------- 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 137 GLU Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 251 LEU 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 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 64 ILE Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 288 SER Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 366 TYR Chi-restraints excluded: chain f residue 394 ASN Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain G residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 76 optimal weight: 0.8980 chunk 186 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 80 optimal weight: 0.4980 chunk 110 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 469 GLN E 300 GLN f 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 = 0.3679 r_free = 0.3679 target = 0.144934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.086679 restraints weight = 18788.061| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.55 r_work: 0.2842 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17424 Z= 0.138 Angle : 0.565 6.186 23712 Z= 0.294 Chirality : 0.046 0.219 2640 Planarity : 0.004 0.044 3012 Dihedral : 6.985 58.340 2890 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.77 % Favored : 95.95 % Rotamer: Outliers : 5.09 % Allowed : 22.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.18), residues: 2124 helix: 1.89 (0.28), residues: 375 sheet: 0.84 (0.22), residues: 594 loop : -1.74 (0.15), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 436 HIS 0.005 0.001 HIS E 25 PHE 0.014 0.002 PHE D 128 TYR 0.009 0.001 TYR f 368 ARG 0.004 0.000 ARG D 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00161 ( 15) link_NAG-ASN : angle 1.40525 ( 45) link_BETA1-4 : bond 0.00492 ( 12) link_BETA1-4 : angle 1.43268 ( 36) hydrogen bonds : bond 0.06423 ( 604) hydrogen bonds : angle 4.75990 ( 1731) SS BOND : bond 0.00282 ( 18) SS BOND : angle 0.54096 ( 36) covalent geometry : bond 0.00326 (17379) covalent geometry : angle 0.55995 (23595) *********************** 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 326 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 234 time to evaluate : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: D 78 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7692 (mm) REVERT: D 137 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7147 (mp0) REVERT: d 487 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7635 (ttpp) REVERT: E 166 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8449 (tt) REVERT: F 64 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8137 (mp) REVERT: F 78 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7859 (mm) REVERT: F 113 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8783 (mp) REVERT: F 119 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7933 (mtp85) REVERT: F 137 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: f 394 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8543 (t0) REVERT: f 498 ASN cc_start: 0.7957 (t0) cc_final: 0.7385 (t0) REVERT: A 46 GLU cc_start: 0.8209 (tt0) cc_final: 0.7784 (tt0) REVERT: B 82 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: L 80 GLN cc_start: 0.6291 (OUTLIER) cc_final: 0.6048 (mp10) outliers start: 92 outliers final: 63 residues processed: 303 average time/residue: 1.3614 time to fit residues: 462.1395 Evaluate side-chains 307 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 232 time to evaluate : 1.912 ------------------------------------------------------------------------------- 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 137 GLU Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 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 251 LEU 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 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 64 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 119 ARG 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 288 SER Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 366 TYR Chi-restraints excluded: chain f residue 394 ASN Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 80 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 201 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 171 optimal weight: 0.2980 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 469 GLN E 300 GLN e 415 ASN 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 = 0.3685 r_free = 0.3685 target = 0.145471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.087019 restraints weight = 18915.980| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.57 r_work: 0.2848 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17424 Z= 0.129 Angle : 0.555 6.158 23712 Z= 0.289 Chirality : 0.046 0.218 2640 Planarity : 0.004 0.043 3012 Dihedral : 6.931 57.700 2890 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.72 % Favored : 96.00 % Rotamer: Outliers : 4.54 % Allowed : 22.92 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.18), residues: 2124 helix: 1.92 (0.28), residues: 375 sheet: 0.88 (0.22), residues: 594 loop : -1.72 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 436 HIS 0.004 0.001 HIS E 25 PHE 0.014 0.001 PHE D 128 TYR 0.009 0.001 TYR f 368 ARG 0.004 0.000 ARG D 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00167 ( 15) link_NAG-ASN : angle 1.39198 ( 45) link_BETA1-4 : bond 0.00490 ( 12) link_BETA1-4 : angle 1.39297 ( 36) hydrogen bonds : bond 0.06212 ( 604) hydrogen bonds : angle 4.71325 ( 1731) SS BOND : bond 0.00262 ( 18) SS BOND : angle 0.51327 ( 36) covalent geometry : bond 0.00302 (17379) covalent geometry : angle 0.55009 (23595) *********************** 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 315 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 233 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: D 78 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7688 (mm) REVERT: D 137 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: E 166 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8446 (tt) REVERT: F 64 ILE cc_start: 0.8331 (mt) cc_final: 0.8082 (mp) REVERT: F 78 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7847 (mm) REVERT: F 113 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8737 (mp) REVERT: F 119 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7922 (mtp85) REVERT: F 137 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: f 394 ASN cc_start: 0.8779 (OUTLIER) cc_final: 0.8525 (t0) REVERT: f 498 ASN cc_start: 0.7953 (t0) cc_final: 0.7372 (t0) REVERT: A 46 GLU cc_start: 0.8161 (tt0) cc_final: 0.7746 (tt0) REVERT: B 82 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8142 (tt0) REVERT: L 80 GLN cc_start: 0.6244 (OUTLIER) cc_final: 0.5945 (mp10) outliers start: 82 outliers final: 60 residues processed: 297 average time/residue: 1.4520 time to fit residues: 480.4218 Evaluate side-chains 304 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 233 time to evaluate : 1.910 ------------------------------------------------------------------------------- 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 137 GLU 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 306 SER Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 251 LEU 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 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 113 ILE Chi-restraints excluded: chain F residue 119 ARG Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 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 288 SER Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 366 TYR Chi-restraints excluded: chain f residue 394 ASN Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 80 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 107 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 469 GLN E 300 GLN e 390 ASN e 415 ASN 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 = 0.3683 r_free = 0.3683 target = 0.145231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.086920 restraints weight = 18872.360| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.55 r_work: 0.2848 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 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 0.059 17424 Z= 0.139 Angle : 0.564 6.131 23712 Z= 0.293 Chirality : 0.046 0.215 2640 Planarity : 0.004 0.044 3012 Dihedral : 6.920 57.892 2890 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.86 % Favored : 95.86 % Rotamer: Outliers : 4.76 % Allowed : 22.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.18), residues: 2124 helix: 1.91 (0.28), residues: 375 sheet: 0.89 (0.22), residues: 594 loop : -1.71 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 436 HIS 0.005 0.001 HIS F 25 PHE 0.015 0.002 PHE D 128 TYR 0.009 0.001 TYR f 368 ARG 0.003 0.000 ARG D 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 15) link_NAG-ASN : angle 1.38138 ( 45) link_BETA1-4 : bond 0.00486 ( 12) link_BETA1-4 : angle 1.38967 ( 36) hydrogen bonds : bond 0.06348 ( 604) hydrogen bonds : angle 4.71542 ( 1731) SS BOND : bond 0.00285 ( 18) SS BOND : angle 0.51785 ( 36) covalent geometry : bond 0.00332 (17379) covalent geometry : angle 0.55908 (23595) ********************** 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 319 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 233 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 78 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7687 (mm) REVERT: D 137 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: E 166 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8448 (tt) REVERT: E 226 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7806 (ttt90) REVERT: F 64 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7991 (mp) REVERT: F 78 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7847 (mm) REVERT: F 113 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8778 (mp) REVERT: F 119 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7948 (mtp85) REVERT: F 137 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: f 394 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.8535 (t0) REVERT: f 498 ASN cc_start: 0.7966 (t0) cc_final: 0.7390 (t0) REVERT: A 46 GLU cc_start: 0.8160 (tt0) cc_final: 0.7777 (tt0) REVERT: B 82 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8148 (tt0) outliers start: 86 outliers final: 65 residues processed: 300 average time/residue: 1.2569 time to fit residues: 419.5672 Evaluate side-chains 308 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 232 time to evaluate : 1.722 ------------------------------------------------------------------------------- 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 137 GLU Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 226 ARG Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 251 LEU 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 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 64 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 119 ARG Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 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 288 SER Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 366 TYR Chi-restraints excluded: chain f residue 394 ASN Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 198 optimal weight: 30.0000 chunk 48 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 93 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 300 GLN d 469 GLN E 300 GLN e 415 ASN e 469 GLN 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 = 0.3670 r_free = 0.3670 target = 0.144086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.085705 restraints weight = 18795.072| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.54 r_work: 0.2825 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17424 Z= 0.171 Angle : 0.603 6.069 23712 Z= 0.313 Chirality : 0.047 0.207 2640 Planarity : 0.005 0.046 3012 Dihedral : 6.987 59.611 2890 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.00 % Favored : 95.72 % Rotamer: Outliers : 4.82 % Allowed : 22.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.18), residues: 2124 helix: 1.84 (0.28), residues: 375 sheet: 0.86 (0.22), residues: 594 loop : -1.73 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 77 HIS 0.006 0.001 HIS F 25 PHE 0.017 0.002 PHE F 128 TYR 0.009 0.001 TYR f 368 ARG 0.004 0.000 ARG D 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 15) link_NAG-ASN : angle 1.38464 ( 45) link_BETA1-4 : bond 0.00475 ( 12) link_BETA1-4 : angle 1.42986 ( 36) hydrogen bonds : bond 0.06952 ( 604) hydrogen bonds : angle 4.81208 ( 1731) SS BOND : bond 0.00336 ( 18) SS BOND : angle 0.54360 ( 36) covalent geometry : bond 0.00420 (17379) covalent geometry : angle 0.59845 (23595) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17271.05 seconds wall clock time: 304 minutes 20.06 seconds (18260.06 seconds total)