Starting phenix.real_space_refine on Thu Jul 31 16:33:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cau_16534/07_2025/8cau_16534_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cau_16534/07_2025/8cau_16534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cau_16534/07_2025/8cau_16534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cau_16534/07_2025/8cau_16534.map" model { file = "/net/cci-nas-00/data/ceres_data/8cau_16534/07_2025/8cau_16534_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cau_16534/07_2025/8cau_16534_trim.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 8695 2.51 5 N 2240 2.21 5 O 2550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13545 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Conformer: "B" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} bond proxies already assigned to first conformer: 1760 Chain: "B" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Conformer: "B" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} bond proxies already assigned to first conformer: 1760 Chain: "C" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Conformer: "B" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} bond proxies already assigned to first conformer: 1760 Chain: "D" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Conformer: "B" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} bond proxies already assigned to first conformer: 1760 Chain: "E" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Conformer: "B" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} bond proxies already assigned to first conformer: 1760 Chain: "F" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "G" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "H" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "I" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "J" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} 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: 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: "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: "S" 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: "T" 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: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.16, per 1000 atoms: 0.90 Number of scatterers: 13545 At special positions: 0 Unit cell: (92.02, 92.88, 118.68, 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 60 16.00 O 2550 8.00 N 2240 7.00 C 8695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " 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 P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 501 " - " ASN A 23 " " NAG A 502 " - " ASN A 67 " " NAG B 501 " - " ASN B 23 " " NAG B 502 " - " ASN B 67 " " NAG C 501 " - " ASN C 23 " " NAG C 502 " - " ASN C 67 " " NAG D 501 " - " ASN D 23 " " NAG D 502 " - " ASN D 67 " " NAG E 501 " - " ASN E 23 " " NAG E 502 " - " ASN E 67 " " NAG P 1 " - " ASN A 110 " " NAG Q 1 " - " ASN B 110 " " NAG R 1 " - " ASN C 110 " " NAG S 1 " - " ASN D 110 " " NAG T 1 " - " ASN E 110 " Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 2.4 seconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3030 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 39 sheets defined 4.5% alpha, 48.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.796A pdb=" N LYS A 5 " --> pdb=" O GLU A 1 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 7 " --> pdb=" O GLN A 3 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 8 " --> pdb=" O ARG A 4 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 10 removed outlier: 3.550A pdb=" N TYR B 7 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 8 " --> pdb=" O ARG B 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 removed outlier: 4.170A pdb=" N VAL C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.512A pdb=" N TYR D 7 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS D 8 " --> pdb=" O ARG D 4 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'F' and resid 29 through 33 removed outlier: 4.015A pdb=" N TYR F 33 " --> pdb=" O PHE F 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 33 removed outlier: 4.041A pdb=" N TYR G 33 " --> pdb=" O PHE G 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 33 removed outlier: 4.023A pdb=" N TYR H 33 " --> pdb=" O PHE H 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 33 removed outlier: 4.023A pdb=" N TYR I 33 " --> pdb=" O PHE I 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 33 removed outlier: 3.997A pdb=" N TYR J 33 " --> pdb=" O PHE J 30 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 117 Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 117 removed outlier: 7.291A pdb=" N VAL A 48 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ASP A 41 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR A 60 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR A 29 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 30 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.605A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR A 202 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.605A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 120 through 125 removed outlier: 3.534A pdb=" N LEU B 49 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL B 48 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN B 52 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE B 39 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N TRP B 54 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU B 37 " --> pdb=" O TRP B 54 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLN B 56 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N SER B 35 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N SER B 58 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N SER B 33 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 30 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 79 Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.586A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR B 202 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.586A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 114 through 117 removed outlier: 3.543A pdb=" N TRP C 59 " --> pdb=" O CYS C 115 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 49 " --> pdb=" O SER C 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 114 through 117 removed outlier: 3.543A pdb=" N TRP C 59 " --> pdb=" O CYS C 115 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 48 " --> pdb=" O ASP C 43 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN C 52 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE C 39 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N TRP C 54 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU C 37 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLN C 56 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER C 35 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N SER C 58 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N SER C 33 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N THR C 60 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 10.051A pdb=" N TYR C 31 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 79 Processing sheet with id=AB4, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.581A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR C 202 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.581A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 114 through 117 Processing sheet with id=AB7, first strand: chain 'D' and resid 114 through 117 removed outlier: 3.959A pdb=" N VAL D 48 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASN D 52 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE D 39 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N TRP D 54 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU D 37 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLN D 56 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N SER D 35 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N SER D 58 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N SER D 33 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N THR D 60 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 10.027A pdb=" N TYR D 31 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 30 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 76 through 79 Processing sheet with id=AB9, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.586A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR D 202 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.586A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 114 through 117 Processing sheet with id=AC3, first strand: chain 'E' and resid 114 through 117 removed outlier: 3.920A pdb=" N VAL E 48 " --> pdb=" O ASP E 43 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASN E 52 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE E 39 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N TRP E 54 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU E 37 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLN E 56 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N SER E 35 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N SER E 58 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N SER E 33 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N THR E 60 " --> pdb=" O TYR E 31 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N TYR E 31 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL E 30 " --> pdb=" O ASP E 156 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 76 through 79 Processing sheet with id=AC5, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.563A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR E 202 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.563A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 4 through 8 removed outlier: 3.605A pdb=" N LEU F 21 " --> pdb=" O LEU F 82 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.387A pdb=" N GLY F 11 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL F 119 " --> pdb=" O ALA F 93 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TRP F 37 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.387A pdb=" N GLY F 11 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL F 119 " --> pdb=" O ALA F 93 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR F 112 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 4 through 8 removed outlier: 3.610A pdb=" N LEU G 21 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.388A pdb=" N GLY G 11 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 119 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP G 37 " --> pdb=" O VAL G 49 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.388A pdb=" N GLY G 11 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 119 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR G 112 " --> pdb=" O ALA G 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 8 removed outlier: 3.623A pdb=" N LEU H 21 " --> pdb=" O LEU H 82 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.383A pdb=" N GLY H 11 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL H 119 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP H 37 " --> pdb=" O VAL H 49 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.383A pdb=" N GLY H 11 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL H 119 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TYR H 112 " --> pdb=" O ALA H 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 4 through 8 removed outlier: 3.612A pdb=" N LEU I 21 " --> pdb=" O LEU I 82 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.357A pdb=" N GLY I 11 " --> pdb=" O THR I 120 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL I 119 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP I 37 " --> pdb=" O VAL I 49 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.357A pdb=" N GLY I 11 " --> pdb=" O THR I 120 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL I 119 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR I 112 " --> pdb=" O ALA I 99 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 8 removed outlier: 3.622A pdb=" N LEU J 21 " --> pdb=" O LEU J 82 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.357A pdb=" N GLY J 11 " --> pdb=" O THR J 120 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL J 119 " --> pdb=" O ALA J 93 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP J 37 " --> pdb=" O VAL J 49 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.357A pdb=" N GLY J 11 " --> pdb=" O THR J 120 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL J 119 " --> pdb=" O ALA J 93 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR J 112 " --> pdb=" O ALA J 99 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1083 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.64 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4245 1.34 - 1.46: 3300 1.46 - 1.57: 6310 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 13945 Sorted by residual: bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.20e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.98e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.92e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.83e+00 ... (remaining 13940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 17870 0.98 - 1.97: 829 1.97 - 2.95: 203 2.95 - 3.93: 52 3.93 - 4.91: 6 Bond angle restraints: 18960 Sorted by residual: angle pdb=" N GLY C 166 " pdb=" CA GLY C 166 " pdb=" C GLY C 166 " ideal model delta sigma weight residual 115.80 110.89 4.91 1.74e+00 3.30e-01 7.98e+00 angle pdb=" CA GLY C 166 " pdb=" C GLY C 166 " pdb=" N TYR C 167 " ideal model delta sigma weight residual 118.95 115.96 2.99 1.06e+00 8.90e-01 7.96e+00 angle pdb=" N GLY B 166 " pdb=" CA GLY B 166 " pdb=" C GLY B 166 " ideal model delta sigma weight residual 115.80 110.91 4.89 1.74e+00 3.30e-01 7.88e+00 angle pdb=" CA GLY B 166 " pdb=" C GLY B 166 " pdb=" N TYR B 167 " ideal model delta sigma weight residual 118.95 116.00 2.95 1.06e+00 8.90e-01 7.74e+00 angle pdb=" CA GLY B 166 " pdb=" C GLY B 166 " pdb=" O GLY B 166 " ideal model delta sigma weight residual 119.04 121.02 -1.98 9.10e-01 1.21e+00 4.72e+00 ... (remaining 18955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7315 17.94 - 35.88: 794 35.88 - 53.82: 193 53.82 - 71.76: 56 71.76 - 89.70: 12 Dihedral angle restraints: 8370 sinusoidal: 3605 harmonic: 4765 Sorted by residual: dihedral pdb=" CA LYS E 45 " pdb=" C LYS E 45 " pdb=" N ASN E 46 " pdb=" CA ASN E 46 " ideal model delta harmonic sigma weight residual 180.00 163.52 16.48 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CB CYS C 127 " pdb=" SG CYS C 127 " pdb=" SG CYS C 141 " pdb=" CB CYS C 141 " ideal model delta sinusoidal sigma weight residual -86.00 -112.75 26.75 1 1.00e+01 1.00e-02 1.03e+01 dihedral pdb=" CB CYS B 127 " pdb=" SG CYS B 127 " pdb=" SG CYS B 141 " pdb=" CB CYS B 141 " ideal model delta sinusoidal sigma weight residual -86.00 -112.41 26.41 1 1.00e+01 1.00e-02 1.00e+01 ... (remaining 8367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1437 0.040 - 0.079: 379 0.079 - 0.119: 183 0.119 - 0.158: 16 0.158 - 0.198: 5 Chirality restraints: 2020 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.25e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN E 110 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 110 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.17e-01 ... (remaining 2017 not shown) Planarity restraints: 2415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 79 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.24e+00 pdb=" N PRO B 80 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 80 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 80 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 79 " -0.039 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO A 80 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 80 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 80 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 79 " 0.038 5.00e-02 4.00e+02 5.88e-02 5.52e+00 pdb=" N PRO C 80 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.032 5.00e-02 4.00e+02 ... (remaining 2412 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 177 2.61 - 3.18: 11191 3.18 - 3.75: 17651 3.75 - 4.33: 26285 4.33 - 4.90: 45695 Nonbonded interactions: 100999 Sorted by model distance: nonbonded pdb=" N GLU F 90 " pdb=" OE1 GLU F 90 " model vdw 2.033 3.120 nonbonded pdb=" OG SER D 183 " pdb=" OD1 ASP D 196 " model vdw 2.046 3.040 nonbonded pdb=" OG SER B 183 " pdb=" OD1 ASP B 196 " model vdw 2.062 3.040 nonbonded pdb=" OG SER A 183 " pdb=" OD1 ASP A 196 " model vdw 2.063 3.040 nonbonded pdb=" OG SER C 183 " pdb=" OD1 ASP C 196 " model vdw 2.076 3.040 ... (remaining 100994 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 206 or resid 501 throug \ h 503)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 206 or resid 501 throug \ h 503)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 206 or resid 501 throug \ h 503)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 206 or resid 501 throug \ h 503)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 206 or resid 501 throug \ h 503)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 35.890 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.100 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 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 : 0.003 0.041 13970 Z= 0.140 Angle : 0.535 7.646 19030 Z= 0.271 Chirality : 0.043 0.198 2020 Planarity : 0.005 0.062 2400 Dihedral : 16.187 89.698 5325 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.14 % Allowed : 20.07 % Favored : 79.79 % 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: -3.17 (0.19), residues: 1620 helix: -3.56 (0.62), residues: 45 sheet: -1.10 (0.20), residues: 660 loop : -2.92 (0.17), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 133 HIS 0.002 0.001 HIS D 140 PHE 0.006 0.001 PHE I 69 TYR 0.011 0.001 TYR A 117 ARG 0.005 0.000 ARG C 4 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 15) link_NAG-ASN : angle 1.20670 ( 45) link_BETA1-4 : bond 0.01531 ( 5) link_BETA1-4 : angle 4.49599 ( 15) hydrogen bonds : bond 0.12989 ( 349) hydrogen bonds : angle 5.95530 ( 1083) SS BOND : bond 0.00093 ( 5) SS BOND : angle 0.36092 ( 10) covalent geometry : bond 0.00291 (13945) covalent geometry : angle 0.51718 (18960) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 298 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 60 TYR cc_start: 0.8597 (m-80) cc_final: 0.8329 (m-10) REVERT: F 74 ASP cc_start: 0.7938 (t0) cc_final: 0.7689 (t0) REVERT: F 91 ASP cc_start: 0.9111 (m-30) cc_final: 0.8721 (m-30) REVERT: G 7 GLU cc_start: 0.8264 (mp0) cc_final: 0.7929 (mp0) REVERT: G 74 ASP cc_start: 0.7984 (t0) cc_final: 0.7737 (t0) REVERT: H 74 ASP cc_start: 0.8049 (t0) cc_final: 0.7731 (t0) REVERT: H 91 ASP cc_start: 0.9003 (m-30) cc_final: 0.8601 (m-30) REVERT: I 74 ASP cc_start: 0.7846 (t0) cc_final: 0.7617 (t0) REVERT: J 74 ASP cc_start: 0.8032 (t0) cc_final: 0.7749 (t0) outliers start: 2 outliers final: 1 residues processed: 298 average time/residue: 0.3406 time to fit residues: 136.1720 Evaluate side-chains 269 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 125 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.063353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.045007 restraints weight = 100750.119| |-----------------------------------------------------------------------------| r_work (start): 0.2542 rms_B_bonded: 5.72 r_work: 0.2343 rms_B_bonded: 5.41 restraints_weight: 2.0000 r_work (final): 0.2343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2355 r_free = 0.2355 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2355 r_free = 0.2355 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13970 Z= 0.144 Angle : 0.714 8.959 19030 Z= 0.351 Chirality : 0.049 0.231 2020 Planarity : 0.006 0.058 2400 Dihedral : 10.532 71.923 2299 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 1.55 % Allowed : 18.17 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.19), residues: 1620 helix: -2.59 (0.70), residues: 45 sheet: -0.68 (0.20), residues: 665 loop : -2.94 (0.17), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 133 HIS 0.003 0.001 HIS A 140 PHE 0.021 0.001 PHE D 134 TYR 0.025 0.001 TYR G 60 ARG 0.009 0.001 ARG F 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00118 ( 15) link_NAG-ASN : angle 1.60518 ( 45) link_BETA1-4 : bond 0.01814 ( 5) link_BETA1-4 : angle 5.19202 ( 15) hydrogen bonds : bond 0.03028 ( 349) hydrogen bonds : angle 5.00070 ( 1083) SS BOND : bond 0.00222 ( 5) SS BOND : angle 0.51722 ( 10) covalent geometry : bond 0.00329 (13945) covalent geometry : angle 0.69529 (18960) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 278 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.9526 (mt-10) cc_final: 0.9265 (mp0) REVERT: B 170 ASN cc_start: 0.9082 (t0) cc_final: 0.8839 (t0) REVERT: C 205 ARG cc_start: 0.9049 (ttm110) cc_final: 0.8539 (ttm110) REVERT: D 138 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8482 (t) REVERT: D 205 ARG cc_start: 0.9029 (ttm110) cc_final: 0.8627 (ttm110) REVERT: E 70 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8981 (mt-10) REVERT: E 184 GLU cc_start: 0.9208 (tt0) cc_final: 0.8992 (tt0) REVERT: E 205 ARG cc_start: 0.9010 (ttm110) cc_final: 0.8662 (ttm110) REVERT: F 2 GLN cc_start: 0.8369 (mp10) cc_final: 0.7885 (pm20) REVERT: F 66 LYS cc_start: 0.9072 (tppt) cc_final: 0.8673 (tppp) REVERT: F 74 ASP cc_start: 0.7677 (t0) cc_final: 0.7164 (t0) REVERT: F 108 ASP cc_start: 0.8949 (m-30) cc_final: 0.8713 (m-30) REVERT: G 40 GLN cc_start: 0.9274 (tt0) cc_final: 0.8768 (tp-100) REVERT: G 44 LYS cc_start: 0.9162 (mppt) cc_final: 0.8738 (mppt) REVERT: G 61 TYR cc_start: 0.9011 (m-80) cc_final: 0.8527 (m-80) REVERT: G 74 ASP cc_start: 0.7555 (t0) cc_final: 0.7102 (t0) REVERT: H 74 ASP cc_start: 0.7753 (t0) cc_final: 0.7194 (t0) REVERT: H 83 GLN cc_start: 0.8886 (tp40) cc_final: 0.8474 (tp-100) REVERT: H 84 MET cc_start: 0.9098 (mtm) cc_final: 0.8562 (mtm) REVERT: I 74 ASP cc_start: 0.7452 (t0) cc_final: 0.7023 (t0) REVERT: I 90 GLU cc_start: 0.8944 (mp0) cc_final: 0.8712 (pm20) REVERT: J 66 LYS cc_start: 0.9076 (tppt) cc_final: 0.8669 (tppt) REVERT: J 74 ASP cc_start: 0.7714 (t0) cc_final: 0.7034 (t0) REVERT: J 83 GLN cc_start: 0.8858 (tp40) cc_final: 0.8551 (tp-100) outliers start: 22 outliers final: 11 residues processed: 289 average time/residue: 0.3247 time to fit residues: 127.2034 Evaluate side-chains 279 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 267 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 94 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 37 optimal weight: 0.2980 chunk 130 optimal weight: 0.6980 chunk 144 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.061487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.042986 restraints weight = 83815.303| |-----------------------------------------------------------------------------| r_work (start): 0.2467 rms_B_bonded: 5.36 r_work: 0.2274 rms_B_bonded: 5.09 restraints_weight: 2.0000 r_work (final): 0.2274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2314 r_free = 0.2314 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2314 r_free = 0.2314 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13970 Z= 0.213 Angle : 0.722 9.429 19030 Z= 0.353 Chirality : 0.048 0.239 2020 Planarity : 0.005 0.052 2400 Dihedral : 10.041 62.687 2295 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 1.76 % Allowed : 18.59 % Favored : 79.65 % 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: -2.61 (0.19), residues: 1620 helix: -1.86 (0.78), residues: 45 sheet: -0.50 (0.20), residues: 660 loop : -2.82 (0.17), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 133 HIS 0.003 0.001 HIS A 140 PHE 0.011 0.001 PHE I 69 TYR 0.019 0.001 TYR G 60 ARG 0.006 0.001 ARG A 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 15) link_NAG-ASN : angle 1.91344 ( 45) link_BETA1-4 : bond 0.01809 ( 5) link_BETA1-4 : angle 5.33393 ( 15) hydrogen bonds : bond 0.03068 ( 349) hydrogen bonds : angle 4.90819 ( 1083) SS BOND : bond 0.00393 ( 5) SS BOND : angle 0.63451 ( 10) covalent geometry : bond 0.00500 (13945) covalent geometry : angle 0.70178 (18960) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 270 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: A 172 GLU cc_start: 0.9485 (mt-10) cc_final: 0.9235 (mp0) REVERT: A 205 ARG cc_start: 0.9094 (ttm110) cc_final: 0.8681 (ttm110) REVERT: B 170 ASN cc_start: 0.9163 (t0) cc_final: 0.8717 (t0) REVERT: C 192 GLU cc_start: 0.9220 (pt0) cc_final: 0.8965 (pt0) REVERT: D 205 ARG cc_start: 0.9099 (ttm110) cc_final: 0.8662 (ttm110) REVERT: E 161 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8800 (mm-30) REVERT: E 205 ARG cc_start: 0.9062 (ttm110) cc_final: 0.8774 (ttm110) REVERT: F 2 GLN cc_start: 0.8569 (mp10) cc_final: 0.8170 (mp10) REVERT: F 66 LYS cc_start: 0.9187 (tppt) cc_final: 0.8789 (tppp) REVERT: F 74 ASP cc_start: 0.7940 (t0) cc_final: 0.7374 (t0) REVERT: F 108 ASP cc_start: 0.8987 (m-30) cc_final: 0.8673 (m-30) REVERT: G 40 GLN cc_start: 0.9206 (tt0) cc_final: 0.8587 (tp-100) REVERT: G 44 LYS cc_start: 0.9137 (mppt) cc_final: 0.8786 (mppt) REVERT: G 61 TYR cc_start: 0.9071 (m-80) cc_final: 0.8650 (m-80) REVERT: G 74 ASP cc_start: 0.7741 (t0) cc_final: 0.7186 (t0) REVERT: G 88 LYS cc_start: 0.9088 (mmtm) cc_final: 0.8822 (mmtm) REVERT: H 74 ASP cc_start: 0.7900 (t0) cc_final: 0.7283 (t0) REVERT: I 69 PHE cc_start: 0.8565 (m-10) cc_final: 0.8243 (m-10) REVERT: I 74 ASP cc_start: 0.7767 (t0) cc_final: 0.7263 (t0) REVERT: I 115 GLN cc_start: 0.8692 (tt0) cc_final: 0.8194 (tt0) REVERT: J 61 TYR cc_start: 0.8950 (m-80) cc_final: 0.8555 (m-80) REVERT: J 66 LYS cc_start: 0.9189 (tppt) cc_final: 0.8789 (tppt) REVERT: J 74 ASP cc_start: 0.7934 (t0) cc_final: 0.7231 (t0) REVERT: J 83 GLN cc_start: 0.8882 (tp40) cc_final: 0.8541 (tp-100) outliers start: 25 outliers final: 17 residues processed: 286 average time/residue: 0.3275 time to fit residues: 126.4577 Evaluate side-chains 274 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 257 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 73 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 24 optimal weight: 0.0670 chunk 153 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.063545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.044729 restraints weight = 91709.655| |-----------------------------------------------------------------------------| r_work (start): 0.2544 rms_B_bonded: 5.61 r_work: 0.2347 rms_B_bonded: 5.34 restraints_weight: 2.0000 r_work (final): 0.2347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2360 r_free = 0.2360 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2360 r_free = 0.2360 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13970 Z= 0.114 Angle : 0.686 9.471 19030 Z= 0.332 Chirality : 0.047 0.239 2020 Planarity : 0.005 0.051 2400 Dihedral : 8.880 59.692 2295 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.55 % Allowed : 19.23 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.19), residues: 1620 helix: -1.47 (0.81), residues: 45 sheet: -0.41 (0.21), residues: 625 loop : -2.53 (0.17), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 133 HIS 0.003 0.001 HIS E 140 PHE 0.023 0.001 PHE A 134 TYR 0.013 0.001 TYR G 60 ARG 0.006 0.000 ARG J 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 15) link_NAG-ASN : angle 1.97463 ( 45) link_BETA1-4 : bond 0.02120 ( 5) link_BETA1-4 : angle 5.31286 ( 15) hydrogen bonds : bond 0.02522 ( 349) hydrogen bonds : angle 4.76749 ( 1083) SS BOND : bond 0.00115 ( 5) SS BOND : angle 0.38511 ( 10) covalent geometry : bond 0.00252 (13945) covalent geometry : angle 0.66401 (18960) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 271 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.9395 (mt-10) cc_final: 0.8932 (mp0) REVERT: A 172 GLU cc_start: 0.9486 (mt-10) cc_final: 0.9234 (mp0) REVERT: A 205 ARG cc_start: 0.9084 (ttm110) cc_final: 0.8652 (ttm110) REVERT: B 70 GLU cc_start: 0.9459 (mt-10) cc_final: 0.9041 (mp0) REVERT: B 170 ASN cc_start: 0.9138 (t0) cc_final: 0.8820 (t0) REVERT: C 133 TRP cc_start: 0.8742 (m-90) cc_final: 0.8503 (m-90) REVERT: C 205 ARG cc_start: 0.9140 (ttm110) cc_final: 0.8636 (ttm110) REVERT: D 138 VAL cc_start: 0.9085 (OUTLIER) cc_final: 0.8806 (t) REVERT: D 205 ARG cc_start: 0.9137 (ttm110) cc_final: 0.8721 (ttm110) REVERT: E 161 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8830 (mm-30) REVERT: F 2 GLN cc_start: 0.8620 (mp10) cc_final: 0.8278 (mp10) REVERT: F 66 LYS cc_start: 0.9008 (tppt) cc_final: 0.8574 (tppt) REVERT: F 74 ASP cc_start: 0.7923 (t0) cc_final: 0.7378 (t0) REVERT: G 40 GLN cc_start: 0.9194 (tt0) cc_final: 0.8607 (tp40) REVERT: G 44 LYS cc_start: 0.9216 (mppt) cc_final: 0.8904 (mppt) REVERT: G 46 ARG cc_start: 0.9282 (mtm110) cc_final: 0.9043 (mtm110) REVERT: G 61 TYR cc_start: 0.9081 (m-80) cc_final: 0.8700 (m-80) REVERT: G 74 ASP cc_start: 0.7861 (t0) cc_final: 0.7312 (t0) REVERT: H 60 TYR cc_start: 0.8610 (m-80) cc_final: 0.8306 (m-10) REVERT: H 74 ASP cc_start: 0.7906 (t0) cc_final: 0.7286 (t0) REVERT: H 83 GLN cc_start: 0.8915 (tp40) cc_final: 0.8456 (tp-100) REVERT: H 84 MET cc_start: 0.8992 (mtm) cc_final: 0.8652 (mtm) REVERT: I 74 ASP cc_start: 0.7780 (t0) cc_final: 0.7316 (t0) REVERT: I 115 GLN cc_start: 0.8563 (tt0) cc_final: 0.7727 (tt0) REVERT: J 61 TYR cc_start: 0.8935 (m-80) cc_final: 0.8588 (m-80) REVERT: J 74 ASP cc_start: 0.7903 (t0) cc_final: 0.7198 (t0) REVERT: J 83 GLN cc_start: 0.8938 (tp40) cc_final: 0.8578 (tp-100) REVERT: J 84 MET cc_start: 0.9040 (mtm) cc_final: 0.8696 (mtp) outliers start: 22 outliers final: 12 residues processed: 289 average time/residue: 0.3295 time to fit residues: 129.8645 Evaluate side-chains 277 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 264 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.062499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.044449 restraints weight = 59224.302| |-----------------------------------------------------------------------------| r_work (start): 0.2537 rms_B_bonded: 4.65 r_work: 0.2358 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2372 r_free = 0.2372 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2372 r_free = 0.2372 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13970 Z= 0.165 Angle : 0.692 9.545 19030 Z= 0.334 Chirality : 0.047 0.242 2020 Planarity : 0.004 0.051 2400 Dihedral : 8.475 59.416 2295 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.41 % Allowed : 19.51 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.19), residues: 1620 helix: -1.08 (0.80), residues: 45 sheet: -0.32 (0.21), residues: 625 loop : -2.46 (0.17), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 133 HIS 0.003 0.001 HIS E 140 PHE 0.022 0.001 PHE D 134 TYR 0.017 0.001 TYR I 60 ARG 0.003 0.000 ARG C 4 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 15) link_NAG-ASN : angle 2.01093 ( 45) link_BETA1-4 : bond 0.01860 ( 5) link_BETA1-4 : angle 5.33629 ( 15) hydrogen bonds : bond 0.02614 ( 349) hydrogen bonds : angle 4.70389 ( 1083) SS BOND : bond 0.00253 ( 5) SS BOND : angle 0.52814 ( 10) covalent geometry : bond 0.00388 (13945) covalent geometry : angle 0.67000 (18960) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 262 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.9348 (mt-10) cc_final: 0.8890 (mp0) REVERT: A 172 GLU cc_start: 0.9451 (mt-10) cc_final: 0.9178 (mp0) REVERT: A 205 ARG cc_start: 0.9102 (ttm110) cc_final: 0.8685 (ttm110) REVERT: B 170 ASN cc_start: 0.9123 (t0) cc_final: 0.8799 (t0) REVERT: C 134 PHE cc_start: 0.8291 (t80) cc_final: 0.7979 (t80) REVERT: C 138 VAL cc_start: 0.9192 (OUTLIER) cc_final: 0.8963 (t) REVERT: C 192 GLU cc_start: 0.9206 (pt0) cc_final: 0.8928 (pt0) REVERT: C 205 ARG cc_start: 0.9156 (ttm110) cc_final: 0.8615 (ttm110) REVERT: D 138 VAL cc_start: 0.9171 (OUTLIER) cc_final: 0.8904 (t) REVERT: D 205 ARG cc_start: 0.9165 (ttm110) cc_final: 0.8801 (ttm110) REVERT: E 133 TRP cc_start: 0.8733 (m-90) cc_final: 0.8320 (m-90) REVERT: E 161 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8798 (mm-30) REVERT: E 205 ARG cc_start: 0.9121 (ttm110) cc_final: 0.8697 (ttm110) REVERT: F 66 LYS cc_start: 0.9051 (tppt) cc_final: 0.8614 (tppt) REVERT: F 74 ASP cc_start: 0.8025 (t0) cc_final: 0.7451 (t0) REVERT: F 108 ASP cc_start: 0.9071 (m-30) cc_final: 0.8692 (m-30) REVERT: G 40 GLN cc_start: 0.9205 (tt0) cc_final: 0.8555 (tp40) REVERT: G 44 LYS cc_start: 0.9238 (mppt) cc_final: 0.8796 (mmtm) REVERT: G 46 ARG cc_start: 0.9234 (mtm110) cc_final: 0.8965 (mtm110) REVERT: G 74 ASP cc_start: 0.7983 (t0) cc_final: 0.7394 (t0) REVERT: H 74 ASP cc_start: 0.8017 (t0) cc_final: 0.7400 (t0) REVERT: H 83 GLN cc_start: 0.8934 (tp40) cc_final: 0.8527 (tp-100) REVERT: I 60 TYR cc_start: 0.8520 (m-10) cc_final: 0.8171 (m-10) REVERT: I 74 ASP cc_start: 0.7943 (t0) cc_final: 0.7422 (t0) REVERT: J 74 ASP cc_start: 0.8023 (t0) cc_final: 0.7285 (t0) outliers start: 20 outliers final: 12 residues processed: 278 average time/residue: 0.3509 time to fit residues: 132.7003 Evaluate side-chains 273 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 259 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 139 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.062679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.044227 restraints weight = 76895.720| |-----------------------------------------------------------------------------| r_work (start): 0.2533 rms_B_bonded: 5.19 r_work: 0.2342 rms_B_bonded: 5.01 restraints_weight: 2.0000 r_work (final): 0.2342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2356 r_free = 0.2356 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2356 r_free = 0.2356 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13970 Z= 0.152 Angle : 0.696 9.527 19030 Z= 0.334 Chirality : 0.047 0.240 2020 Planarity : 0.004 0.049 2400 Dihedral : 8.067 59.517 2295 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 1.41 % Allowed : 20.28 % Favored : 78.31 % 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: -2.10 (0.19), residues: 1620 helix: -0.62 (0.79), residues: 45 sheet: -0.22 (0.21), residues: 625 loop : -2.38 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 133 HIS 0.003 0.001 HIS E 140 PHE 0.023 0.001 PHE A 134 TYR 0.011 0.001 TYR I 60 ARG 0.004 0.000 ARG H 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00065 ( 15) link_NAG-ASN : angle 2.02240 ( 45) link_BETA1-4 : bond 0.01979 ( 5) link_BETA1-4 : angle 5.38208 ( 15) hydrogen bonds : bond 0.02555 ( 349) hydrogen bonds : angle 4.62625 ( 1083) SS BOND : bond 0.00233 ( 5) SS BOND : angle 0.51036 ( 10) covalent geometry : bond 0.00354 (13945) covalent geometry : angle 0.67289 (18960) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 265 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.9389 (mt-10) cc_final: 0.8924 (mp0) REVERT: A 172 GLU cc_start: 0.9487 (mt-10) cc_final: 0.9207 (mp0) REVERT: A 205 ARG cc_start: 0.9124 (ttm110) cc_final: 0.8729 (ttm110) REVERT: B 70 GLU cc_start: 0.9467 (mt-10) cc_final: 0.9121 (mp0) REVERT: B 170 ASN cc_start: 0.9130 (t0) cc_final: 0.8807 (t0) REVERT: C 70 GLU cc_start: 0.9411 (mt-10) cc_final: 0.8944 (mp0) REVERT: C 134 PHE cc_start: 0.8243 (t80) cc_final: 0.7908 (t80) REVERT: C 138 VAL cc_start: 0.9235 (OUTLIER) cc_final: 0.9000 (t) REVERT: C 205 ARG cc_start: 0.9192 (ttm110) cc_final: 0.8666 (ttm110) REVERT: D 70 GLU cc_start: 0.9393 (mt-10) cc_final: 0.8849 (mp0) REVERT: D 138 VAL cc_start: 0.9222 (OUTLIER) cc_final: 0.8964 (t) REVERT: D 205 ARG cc_start: 0.9160 (ttm110) cc_final: 0.8728 (ttm110) REVERT: E 133 TRP cc_start: 0.8593 (m-90) cc_final: 0.8205 (m-90) REVERT: E 138 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8862 (t) REVERT: E 161 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8871 (mm-30) REVERT: E 205 ARG cc_start: 0.9129 (ttm110) cc_final: 0.8696 (ttm110) REVERT: F 66 LYS cc_start: 0.9070 (tppt) cc_final: 0.8648 (tppt) REVERT: F 74 ASP cc_start: 0.8067 (t0) cc_final: 0.7493 (t0) REVERT: F 108 ASP cc_start: 0.9113 (m-30) cc_final: 0.8745 (m-30) REVERT: G 40 GLN cc_start: 0.9180 (tt0) cc_final: 0.8495 (tp40) REVERT: G 44 LYS cc_start: 0.9273 (mppt) cc_final: 0.8835 (mmtm) REVERT: G 74 ASP cc_start: 0.8048 (t0) cc_final: 0.7455 (t0) REVERT: H 74 ASP cc_start: 0.8043 (t0) cc_final: 0.7424 (t0) REVERT: H 83 GLN cc_start: 0.8948 (tp40) cc_final: 0.8528 (tp-100) REVERT: I 74 ASP cc_start: 0.8004 (t0) cc_final: 0.7470 (t0) REVERT: J 66 LYS cc_start: 0.9001 (ttmm) cc_final: 0.8632 (ttmt) REVERT: J 74 ASP cc_start: 0.8023 (t0) cc_final: 0.7329 (t0) outliers start: 20 outliers final: 12 residues processed: 281 average time/residue: 0.3240 time to fit residues: 122.8110 Evaluate side-chains 276 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 261 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 2 optimal weight: 0.0770 chunk 66 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 0.0020 chunk 70 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.8150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN G 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.063761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.045444 restraints weight = 95423.932| |-----------------------------------------------------------------------------| r_work (start): 0.2542 rms_B_bonded: 5.56 r_work: 0.2340 rms_B_bonded: 5.29 restraints_weight: 2.0000 r_work (final): 0.2340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2353 r_free = 0.2353 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2353 r_free = 0.2353 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13970 Z= 0.115 Angle : 0.682 9.534 19030 Z= 0.328 Chirality : 0.047 0.241 2020 Planarity : 0.004 0.048 2400 Dihedral : 7.641 58.014 2295 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.99 % Allowed : 20.85 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.19), residues: 1620 helix: 0.02 (0.79), residues: 45 sheet: -0.04 (0.21), residues: 625 loop : -2.33 (0.17), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 133 HIS 0.004 0.001 HIS A 140 PHE 0.027 0.001 PHE D 134 TYR 0.019 0.001 TYR I 60 ARG 0.005 0.000 ARG H 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00147 ( 15) link_NAG-ASN : angle 1.93790 ( 45) link_BETA1-4 : bond 0.02071 ( 5) link_BETA1-4 : angle 5.30872 ( 15) hydrogen bonds : bond 0.02330 ( 349) hydrogen bonds : angle 4.48934 ( 1083) SS BOND : bond 0.00104 ( 5) SS BOND : angle 0.39318 ( 10) covalent geometry : bond 0.00264 (13945) covalent geometry : angle 0.66008 (18960) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 260 time to evaluate : 1.551 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.9422 (mt-10) cc_final: 0.9008 (mp0) REVERT: A 205 ARG cc_start: 0.9117 (ttm110) cc_final: 0.8730 (ttm110) REVERT: B 170 ASN cc_start: 0.9085 (t0) cc_final: 0.8746 (t0) REVERT: C 70 GLU cc_start: 0.9448 (mt-10) cc_final: 0.9026 (mp0) REVERT: C 134 PHE cc_start: 0.8229 (t80) cc_final: 0.8011 (t80) REVERT: C 138 VAL cc_start: 0.9220 (OUTLIER) cc_final: 0.8989 (t) REVERT: C 205 ARG cc_start: 0.9211 (ttm110) cc_final: 0.8662 (ttm110) REVERT: D 70 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9008 (mp0) REVERT: D 138 VAL cc_start: 0.9220 (OUTLIER) cc_final: 0.8965 (t) REVERT: D 172 GLU cc_start: 0.9518 (mt-10) cc_final: 0.9301 (mp0) REVERT: D 205 ARG cc_start: 0.9209 (ttm110) cc_final: 0.8830 (ttm110) REVERT: E 70 GLU cc_start: 0.9500 (mt-10) cc_final: 0.9090 (mp0) REVERT: E 133 TRP cc_start: 0.8557 (m-90) cc_final: 0.8271 (m-90) REVERT: E 138 VAL cc_start: 0.9171 (OUTLIER) cc_final: 0.8917 (t) REVERT: E 161 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8908 (mm-30) REVERT: E 205 ARG cc_start: 0.9168 (ttm110) cc_final: 0.8772 (ttm110) REVERT: F 66 LYS cc_start: 0.8965 (tppt) cc_final: 0.8536 (tppt) REVERT: F 74 ASP cc_start: 0.8050 (t0) cc_final: 0.7492 (t0) REVERT: F 108 ASP cc_start: 0.9085 (m-30) cc_final: 0.8707 (m-30) REVERT: G 40 GLN cc_start: 0.9178 (tt0) cc_final: 0.8501 (tp40) REVERT: G 44 LYS cc_start: 0.9275 (mppt) cc_final: 0.9056 (mmmm) REVERT: G 46 ARG cc_start: 0.9235 (mtm110) cc_final: 0.8998 (mtm110) REVERT: G 74 ASP cc_start: 0.8035 (t0) cc_final: 0.7436 (t0) REVERT: H 46 ARG cc_start: 0.9152 (mtm110) cc_final: 0.8921 (mtm110) REVERT: H 74 ASP cc_start: 0.8055 (t0) cc_final: 0.7456 (t0) REVERT: H 83 GLN cc_start: 0.8918 (tp40) cc_final: 0.8461 (tp-100) REVERT: H 84 MET cc_start: 0.9053 (mtm) cc_final: 0.8766 (mtm) REVERT: I 74 ASP cc_start: 0.8023 (t0) cc_final: 0.7525 (t0) REVERT: J 19 LEU cc_start: 0.9015 (mt) cc_final: 0.8028 (mt) REVERT: J 66 LYS cc_start: 0.8908 (ttmm) cc_final: 0.8473 (ttmt) REVERT: J 74 ASP cc_start: 0.7959 (t0) cc_final: 0.7270 (t0) REVERT: J 83 GLN cc_start: 0.8853 (tp40) cc_final: 0.8449 (tp-100) outliers start: 14 outliers final: 9 residues processed: 273 average time/residue: 0.3468 time to fit residues: 127.5892 Evaluate side-chains 264 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 252 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 148 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 126 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.060857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.042177 restraints weight = 96959.507| |-----------------------------------------------------------------------------| r_work (start): 0.2448 rms_B_bonded: 5.63 r_work: 0.2247 rms_B_bonded: 5.27 restraints_weight: 2.0000 r_work (final): 0.2247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2284 r_free = 0.2284 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2284 r_free = 0.2284 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 13970 Z= 0.280 Angle : 0.757 11.508 19030 Z= 0.364 Chirality : 0.048 0.245 2020 Planarity : 0.004 0.047 2400 Dihedral : 8.207 59.792 2295 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 1.41 % Allowed : 20.21 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.93 (0.19), residues: 1620 helix: 0.09 (0.76), residues: 45 sheet: -0.23 (0.19), residues: 705 loop : -2.36 (0.18), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 133 HIS 0.002 0.001 HIS J 32 PHE 0.025 0.002 PHE I 69 TYR 0.017 0.001 TYR I 60 ARG 0.005 0.001 ARG J 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 15) link_NAG-ASN : angle 2.11867 ( 45) link_BETA1-4 : bond 0.01713 ( 5) link_BETA1-4 : angle 5.51498 ( 15) hydrogen bonds : bond 0.03034 ( 349) hydrogen bonds : angle 4.80550 ( 1083) SS BOND : bond 0.00483 ( 5) SS BOND : angle 0.75359 ( 10) covalent geometry : bond 0.00657 (13945) covalent geometry : angle 0.73476 (18960) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 246 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.9439 (t0) cc_final: 0.9228 (t0) REVERT: A 205 ARG cc_start: 0.9136 (ttm110) cc_final: 0.8728 (ttm110) REVERT: B 70 GLU cc_start: 0.9493 (mt-10) cc_final: 0.9081 (mp0) REVERT: B 170 ASN cc_start: 0.9120 (t0) cc_final: 0.8631 (t0) REVERT: C 70 GLU cc_start: 0.9423 (mt-10) cc_final: 0.8987 (mp0) REVERT: C 138 VAL cc_start: 0.9299 (OUTLIER) cc_final: 0.9080 (t) REVERT: C 205 ARG cc_start: 0.9225 (ttm110) cc_final: 0.8674 (ttm110) REVERT: D 70 GLU cc_start: 0.9414 (mt-10) cc_final: 0.8992 (mp0) REVERT: D 138 VAL cc_start: 0.9293 (OUTLIER) cc_final: 0.9060 (t) REVERT: D 172 GLU cc_start: 0.9536 (mt-10) cc_final: 0.9306 (mp0) REVERT: D 205 ARG cc_start: 0.9210 (ttm110) cc_final: 0.8846 (ttm110) REVERT: E 70 GLU cc_start: 0.9464 (mt-10) cc_final: 0.9060 (mp0) REVERT: E 133 TRP cc_start: 0.8589 (m-90) cc_final: 0.8227 (m-90) REVERT: E 138 VAL cc_start: 0.9222 (OUTLIER) cc_final: 0.8964 (t) REVERT: E 161 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8984 (mm-30) REVERT: E 205 ARG cc_start: 0.9162 (ttm110) cc_final: 0.8744 (ttm110) REVERT: F 74 ASP cc_start: 0.8230 (t0) cc_final: 0.7623 (t0) REVERT: F 108 ASP cc_start: 0.9110 (m-30) cc_final: 0.8645 (m-30) REVERT: G 44 LYS cc_start: 0.9287 (mppt) cc_final: 0.9067 (mmtm) REVERT: G 74 ASP cc_start: 0.8220 (t0) cc_final: 0.7566 (t0) REVERT: G 88 LYS cc_start: 0.8741 (mmtm) cc_final: 0.8536 (mmtm) REVERT: H 74 ASP cc_start: 0.8185 (t0) cc_final: 0.7543 (t0) REVERT: H 83 GLN cc_start: 0.8940 (tp40) cc_final: 0.8503 (tp-100) REVERT: I 74 ASP cc_start: 0.8180 (t0) cc_final: 0.7616 (t0) REVERT: J 74 ASP cc_start: 0.8183 (t0) cc_final: 0.7499 (t0) outliers start: 20 outliers final: 14 residues processed: 262 average time/residue: 0.3377 time to fit residues: 118.6861 Evaluate side-chains 260 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 243 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 5 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 123 optimal weight: 0.0010 chunk 66 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.062551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.044366 restraints weight = 94133.327| |-----------------------------------------------------------------------------| r_work (start): 0.2513 rms_B_bonded: 5.51 r_work: 0.2314 rms_B_bonded: 5.19 restraints_weight: 2.0000 r_work (final): 0.2314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2324 r_free = 0.2324 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2324 r_free = 0.2324 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13970 Z= 0.130 Angle : 0.709 10.061 19030 Z= 0.340 Chirality : 0.047 0.239 2020 Planarity : 0.004 0.046 2400 Dihedral : 7.776 59.959 2295 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.99 % Allowed : 20.70 % Favored : 78.31 % 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: -1.71 (0.20), residues: 1620 helix: 0.69 (0.80), residues: 45 sheet: 0.12 (0.20), residues: 670 loop : -2.35 (0.18), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 133 HIS 0.003 0.001 HIS D 140 PHE 0.027 0.001 PHE D 134 TYR 0.014 0.001 TYR I 60 ARG 0.006 0.000 ARG H 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00153 ( 15) link_NAG-ASN : angle 1.97610 ( 45) link_BETA1-4 : bond 0.02044 ( 5) link_BETA1-4 : angle 5.45272 ( 15) hydrogen bonds : bond 0.02495 ( 349) hydrogen bonds : angle 4.63514 ( 1083) SS BOND : bond 0.00153 ( 5) SS BOND : angle 0.51021 ( 10) covalent geometry : bond 0.00305 (13945) covalent geometry : angle 0.68646 (18960) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 252 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.9425 (t0) cc_final: 0.9225 (t0) REVERT: A 205 ARG cc_start: 0.9127 (ttm110) cc_final: 0.8730 (ttm110) REVERT: B 70 GLU cc_start: 0.9491 (mt-10) cc_final: 0.9133 (mp0) REVERT: B 133 TRP cc_start: 0.8560 (m-90) cc_final: 0.8099 (m-90) REVERT: B 205 ARG cc_start: 0.9156 (ttm110) cc_final: 0.8728 (ttm110) REVERT: C 70 GLU cc_start: 0.9416 (mt-10) cc_final: 0.9028 (mp0) REVERT: C 134 PHE cc_start: 0.8212 (t80) cc_final: 0.7959 (t80) REVERT: C 138 VAL cc_start: 0.9281 (OUTLIER) cc_final: 0.9059 (t) REVERT: C 205 ARG cc_start: 0.9249 (ttm110) cc_final: 0.8736 (ttm110) REVERT: D 70 GLU cc_start: 0.9435 (mt-10) cc_final: 0.9021 (mp0) REVERT: D 138 VAL cc_start: 0.9281 (OUTLIER) cc_final: 0.9047 (t) REVERT: D 205 ARG cc_start: 0.9199 (ttm110) cc_final: 0.8837 (ttm110) REVERT: E 70 GLU cc_start: 0.9478 (mt-10) cc_final: 0.9121 (mp0) REVERT: E 133 TRP cc_start: 0.8537 (m-90) cc_final: 0.8262 (m-90) REVERT: E 138 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.8964 (t) REVERT: E 161 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8952 (mm-30) REVERT: E 205 ARG cc_start: 0.9196 (ttm110) cc_final: 0.8809 (ttm110) REVERT: F 66 LYS cc_start: 0.9240 (tppt) cc_final: 0.8773 (tppt) REVERT: F 74 ASP cc_start: 0.8066 (t0) cc_final: 0.7507 (t0) REVERT: F 108 ASP cc_start: 0.9080 (m-30) cc_final: 0.8623 (m-30) REVERT: G 40 GLN cc_start: 0.9173 (tt0) cc_final: 0.8502 (tp40) REVERT: G 74 ASP cc_start: 0.8114 (t0) cc_final: 0.7481 (t0) REVERT: G 88 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8546 (mmtm) REVERT: H 74 ASP cc_start: 0.8082 (t0) cc_final: 0.7459 (t0) REVERT: H 83 GLN cc_start: 0.8936 (tp40) cc_final: 0.8478 (tp-100) REVERT: H 84 MET cc_start: 0.8951 (mtm) cc_final: 0.8607 (mtm) REVERT: I 69 PHE cc_start: 0.7075 (m-80) cc_final: 0.6845 (m-10) REVERT: I 74 ASP cc_start: 0.8087 (t0) cc_final: 0.7547 (t0) REVERT: J 19 LEU cc_start: 0.8966 (mt) cc_final: 0.8291 (mm) REVERT: J 74 ASP cc_start: 0.8074 (t0) cc_final: 0.7397 (t0) REVERT: J 83 GLN cc_start: 0.8922 (tp40) cc_final: 0.8558 (tp-100) REVERT: J 84 MET cc_start: 0.9015 (mtp) cc_final: 0.8638 (mtp) outliers start: 14 outliers final: 11 residues processed: 264 average time/residue: 0.3472 time to fit residues: 124.1025 Evaluate side-chains 262 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 248 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 60 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 0.0270 chunk 55 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 130 optimal weight: 0.0470 chunk 44 optimal weight: 0.4980 chunk 120 optimal weight: 2.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.064317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.045972 restraints weight = 93596.474| |-----------------------------------------------------------------------------| r_work (start): 0.2556 rms_B_bonded: 5.55 r_work: 0.2358 rms_B_bonded: 5.24 restraints_weight: 2.0000 r_work (final): 0.2358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2373 r_free = 0.2373 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2373 r_free = 0.2373 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13970 Z= 0.113 Angle : 0.702 12.663 19030 Z= 0.335 Chirality : 0.046 0.243 2020 Planarity : 0.004 0.048 2400 Dihedral : 7.320 57.309 2295 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.99 % Allowed : 20.70 % Favored : 78.31 % 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: -1.59 (0.19), residues: 1620 helix: 1.35 (0.81), residues: 45 sheet: 0.32 (0.20), residues: 680 loop : -2.45 (0.17), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 133 HIS 0.004 0.001 HIS E 140 PHE 0.026 0.001 PHE A 134 TYR 0.010 0.001 TYR I 60 ARG 0.007 0.000 ARG H 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00182 ( 15) link_NAG-ASN : angle 1.81371 ( 45) link_BETA1-4 : bond 0.02081 ( 5) link_BETA1-4 : angle 5.29909 ( 15) hydrogen bonds : bond 0.02329 ( 349) hydrogen bonds : angle 4.51231 ( 1083) SS BOND : bond 0.00068 ( 5) SS BOND : angle 0.37400 ( 10) covalent geometry : bond 0.00264 (13945) covalent geometry : angle 0.68205 (18960) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 256 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9057 (mp0) REVERT: A 205 ARG cc_start: 0.9134 (ttm110) cc_final: 0.8766 (ttm110) REVERT: B 70 GLU cc_start: 0.9506 (mt-10) cc_final: 0.9157 (mp0) REVERT: B 133 TRP cc_start: 0.8509 (m-90) cc_final: 0.8140 (m-90) REVERT: B 205 ARG cc_start: 0.9178 (ttm110) cc_final: 0.8779 (ttm110) REVERT: C 70 GLU cc_start: 0.9447 (mt-10) cc_final: 0.9112 (mp0) REVERT: C 134 PHE cc_start: 0.8199 (t80) cc_final: 0.7992 (t80) REVERT: C 138 VAL cc_start: 0.9248 (OUTLIER) cc_final: 0.9030 (t) REVERT: C 205 ARG cc_start: 0.9236 (ttm110) cc_final: 0.8690 (ttm110) REVERT: D 70 GLU cc_start: 0.9455 (mt-10) cc_final: 0.9055 (mp0) REVERT: D 138 VAL cc_start: 0.9274 (OUTLIER) cc_final: 0.9037 (t) REVERT: D 205 ARG cc_start: 0.9213 (ttm110) cc_final: 0.8814 (ttm110) REVERT: E 70 GLU cc_start: 0.9485 (mt-10) cc_final: 0.9133 (mp0) REVERT: E 133 TRP cc_start: 0.8483 (m-90) cc_final: 0.8234 (m-90) REVERT: E 138 VAL cc_start: 0.9209 (OUTLIER) cc_final: 0.8975 (t) REVERT: E 161 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8956 (mm-30) REVERT: E 205 ARG cc_start: 0.9180 (ttm110) cc_final: 0.8817 (ttm110) REVERT: F 66 LYS cc_start: 0.8986 (tppt) cc_final: 0.8532 (tppt) REVERT: F 74 ASP cc_start: 0.8115 (t0) cc_final: 0.7572 (t0) REVERT: F 108 ASP cc_start: 0.9095 (m-30) cc_final: 0.8687 (m-30) REVERT: G 40 GLN cc_start: 0.9181 (tt0) cc_final: 0.8484 (tp40) REVERT: G 69 PHE cc_start: 0.7858 (m-10) cc_final: 0.7512 (m-10) REVERT: G 74 ASP cc_start: 0.8092 (t0) cc_final: 0.7498 (t0) REVERT: G 88 LYS cc_start: 0.8802 (mmtm) cc_final: 0.8591 (mmtm) REVERT: H 66 LYS cc_start: 0.9047 (tppt) cc_final: 0.8515 (tppt) REVERT: H 74 ASP cc_start: 0.8103 (t0) cc_final: 0.7455 (t0) REVERT: H 83 GLN cc_start: 0.8907 (tp40) cc_final: 0.8444 (tp-100) REVERT: I 74 ASP cc_start: 0.8053 (t0) cc_final: 0.7582 (t0) REVERT: J 19 LEU cc_start: 0.8976 (mt) cc_final: 0.8288 (mm) REVERT: J 74 ASP cc_start: 0.8053 (t0) cc_final: 0.7385 (t0) REVERT: J 83 GLN cc_start: 0.8922 (tp40) cc_final: 0.8545 (tp-100) outliers start: 14 outliers final: 9 residues processed: 268 average time/residue: 0.3366 time to fit residues: 121.2283 Evaluate side-chains 259 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 247 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.0010 chunk 122 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 140 optimal weight: 0.0070 chunk 96 optimal weight: 0.8980 chunk 158 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 overall best weight: 0.4806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.065215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.047215 restraints weight = 72872.028| |-----------------------------------------------------------------------------| r_work (start): 0.2592 rms_B_bonded: 5.07 r_work: 0.2405 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2419 r_free = 0.2419 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2419 r_free = 0.2419 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13970 Z= 0.112 Angle : 0.698 12.832 19030 Z= 0.332 Chirality : 0.046 0.245 2020 Planarity : 0.004 0.049 2400 Dihedral : 7.122 56.202 2295 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.13 % Allowed : 20.85 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.49 (0.19), residues: 1620 helix: 1.78 (0.80), residues: 45 sheet: 0.45 (0.19), residues: 675 loop : -2.44 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 133 HIS 0.004 0.001 HIS A 140 PHE 0.032 0.001 PHE D 134 TYR 0.023 0.001 TYR I 81 ARG 0.006 0.000 ARG J 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 15) link_NAG-ASN : angle 1.73412 ( 45) link_BETA1-4 : bond 0.02048 ( 5) link_BETA1-4 : angle 5.20112 ( 15) hydrogen bonds : bond 0.02328 ( 349) hydrogen bonds : angle 4.44199 ( 1083) SS BOND : bond 0.00059 ( 5) SS BOND : angle 0.36768 ( 10) covalent geometry : bond 0.00263 (13945) covalent geometry : angle 0.67813 (18960) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6894.62 seconds wall clock time: 118 minutes 54.71 seconds (7134.71 seconds total)