Starting phenix.real_space_refine on Sat Aug 23 17:46:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ci1_16665/08_2025/8ci1_16665_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ci1_16665/08_2025/8ci1_16665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ci1_16665/08_2025/8ci1_16665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ci1_16665/08_2025/8ci1_16665.map" model { file = "/net/cci-nas-00/data/ceres_data/8ci1_16665/08_2025/8ci1_16665_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ci1_16665/08_2025/8ci1_16665_trim.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 70 5.16 5 C 8625 2.51 5 N 2305 2.21 5 O 2595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13595 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 208, 1729 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} Conformer: "B" Number of residues, atoms: 208, 1729 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} bond proxies already assigned to first conformer: 1775 Chain: "B" Number of atoms: 1736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 208, 1729 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} Conformer: "B" Number of residues, atoms: 208, 1729 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} bond proxies already assigned to first conformer: 1775 Chain: "C" Number of atoms: 1736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 208, 1729 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} Conformer: "B" Number of residues, atoms: 208, 1729 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} bond proxies already assigned to first conformer: 1775 Chain: "D" Number of atoms: 1736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 208, 1729 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} Conformer: "B" Number of residues, atoms: 208, 1729 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} bond proxies already assigned to first conformer: 1775 Chain: "E" Number of atoms: 1736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 208, 1729 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} Conformer: "B" Number of residues, atoms: 208, 1729 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} bond proxies already assigned to first conformer: 1775 Chain: "F" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 915 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "G" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 915 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "H" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 915 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "I" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 915 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "J" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 915 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} 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: 3.87, per 1000 atoms: 0.28 Number of scatterers: 13595 At special positions: 0 Unit cell: (92.88, 94.6, 117.82, 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 70 16.00 O 2595 8.00 N 2305 7.00 C 8625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, 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 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 95 " - pdb=" SG CYS F 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 95 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 95 " - pdb=" SG CYS H 114 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 95 " - pdb=" SG CYS I 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 95 " - pdb=" SG CYS J 114 " 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 401 " - " ASN A 23 " " NAG A 402 " - " ASN A 67 " " NAG B 401 " - " ASN B 23 " " NAG B 402 " - " ASN B 67 " " NAG C 401 " - " ASN C 23 " " NAG C 402 " - " ASN C 67 " " NAG D 401 " - " ASN D 23 " " NAG D 402 " - " ASN D 67 " " NAG E 401 " - " ASN E 23 " " NAG E 402 " - " 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: 0.78 Conformation dependent library (CDL) restraints added in 828.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3080 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 30 sheets defined 5.8% alpha, 43.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 removed outlier: 4.170A pdb=" N LYS A 5 " --> pdb=" O GLU A 1 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 12 " --> pdb=" O LYS A 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 12 removed outlier: 3.631A pdb=" N LYS B 12 " --> pdb=" O LYS B 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 removed outlier: 3.632A pdb=" N LYS C 12 " --> pdb=" O LYS C 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 12 removed outlier: 3.631A pdb=" N LYS D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 removed outlier: 3.631A pdb=" N LYS E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.586A pdb=" N THR F 91 " --> pdb=" O PRO F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.586A pdb=" N THR G 91 " --> pdb=" O PRO G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.587A pdb=" N THR H 91 " --> pdb=" O PRO H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 30 No H-bonds generated for 'chain 'I' and resid 28 through 30' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.586A pdb=" N THR I 91 " --> pdb=" O PRO I 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.586A pdb=" N THR J 91 " --> pdb=" O PRO J 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.172A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.172A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASN A 52 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE A 39 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N TRP A 54 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU A 37 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N GLN A 56 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N SER A 35 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N SER A 58 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N SER A 33 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N THR A 60 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N TYR A 31 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU A 28 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN A 158 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL A 30 " --> pdb=" O GLN A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.577A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLU A 192 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N TYR A 187 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.172A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.172A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASN B 52 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE B 39 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N TRP B 54 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU B 37 " --> pdb=" O TRP B 54 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLN B 56 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N SER B 35 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N SER B 58 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N SER B 33 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N THR B 60 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N TYR B 31 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 30 " --> pdb=" O GLN B 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.576A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLU B 192 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N TYR B 187 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.173A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.173A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASN C 52 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE C 39 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N TRP C 54 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU C 37 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLN C 56 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N SER C 35 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N SER C 58 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N SER C 33 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N THR C 60 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 9.555A pdb=" N TYR C 31 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.577A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLU C 192 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N TYR C 187 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 138 through 139 Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.172A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.172A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASN D 52 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE D 39 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N TRP D 54 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU D 37 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N GLN D 56 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N SER D 35 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N SER D 58 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N SER D 33 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N THR D 60 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N TYR D 31 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU D 28 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL D 30 " --> pdb=" O GLN D 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.577A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLU D 192 " --> pdb=" O TYR D 187 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N TYR D 187 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 138 through 139 Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.174A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.174A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASN E 52 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE E 39 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N TRP E 54 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU E 37 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N GLN E 56 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N SER E 35 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N SER E 58 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N SER E 33 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N THR E 60 " --> pdb=" O TYR E 31 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N TYR E 31 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU E 28 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN E 158 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL E 30 " --> pdb=" O GLN E 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.576A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLU E 192 " --> pdb=" O TYR E 187 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N TYR E 187 " --> pdb=" O GLU E 192 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 138 through 139 Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AC4, first strand: chain 'F' and resid 11 through 13 removed outlier: 3.750A pdb=" N ALA F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'G' and resid 11 through 13 removed outlier: 3.750A pdb=" N ALA G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ARG G 38 " --> pdb=" O PHE G 47 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N PHE G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.750A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ARG H 38 " --> pdb=" O PHE H 47 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AD1, first strand: chain 'I' and resid 11 through 13 removed outlier: 3.750A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ARG I 38 " --> pdb=" O PHE I 47 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N PHE I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'J' and resid 11 through 13 removed outlier: 3.750A pdb=" N ALA J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ARG J 38 " --> pdb=" O PHE J 47 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1200 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: 1.84 Time building geometry restraints manager: 1.17 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: 4360 1.34 - 1.46: 3580 1.46 - 1.58: 5935 1.58 - 1.69: 0 1.69 - 1.81: 95 Bond restraints: 13970 Sorted by residual: bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.85e+00 bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.77e+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 3.72e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.68e+00 ... (remaining 13965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 18266 1.02 - 2.03: 522 2.03 - 3.05: 152 3.05 - 4.06: 25 4.06 - 5.08: 10 Bond angle restraints: 18975 Sorted by residual: angle pdb=" N VAL J 64 " pdb=" CA VAL J 64 " pdb=" C VAL J 64 " ideal model delta sigma weight residual 113.20 108.32 4.88 9.60e-01 1.09e+00 2.58e+01 angle pdb=" N VAL H 64 " pdb=" CA VAL H 64 " pdb=" C VAL H 64 " ideal model delta sigma weight residual 113.20 108.34 4.86 9.60e-01 1.09e+00 2.56e+01 angle pdb=" N VAL F 64 " pdb=" CA VAL F 64 " pdb=" C VAL F 64 " ideal model delta sigma weight residual 113.20 108.35 4.85 9.60e-01 1.09e+00 2.55e+01 angle pdb=" N VAL I 64 " pdb=" CA VAL I 64 " pdb=" C VAL I 64 " ideal model delta sigma weight residual 113.20 108.36 4.84 9.60e-01 1.09e+00 2.54e+01 angle pdb=" N VAL G 64 " pdb=" CA VAL G 64 " pdb=" C VAL G 64 " ideal model delta sigma weight residual 113.20 108.38 4.82 9.60e-01 1.09e+00 2.52e+01 ... (remaining 18970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.77: 8105 14.77 - 29.53: 269 29.53 - 44.30: 86 44.30 - 59.06: 40 59.06 - 73.83: 5 Dihedral angle restraints: 8505 sinusoidal: 3685 harmonic: 4820 Sorted by residual: dihedral pdb=" N GLN J 39 " pdb=" CA GLN J 39 " pdb=" CB GLN J 39 " pdb=" CG GLN J 39 " ideal model delta sinusoidal sigma weight residual -180.00 -128.13 -51.87 3 1.50e+01 4.44e-03 9.06e+00 dihedral pdb=" N GLN G 39 " pdb=" CA GLN G 39 " pdb=" CB GLN G 39 " pdb=" CG GLN G 39 " ideal model delta sinusoidal sigma weight residual -180.00 -128.15 -51.85 3 1.50e+01 4.44e-03 9.06e+00 dihedral pdb=" N GLN F 39 " pdb=" CA GLN F 39 " pdb=" CB GLN F 39 " pdb=" CG GLN F 39 " ideal model delta sinusoidal sigma weight residual 180.00 -128.15 -51.85 3 1.50e+01 4.44e-03 9.06e+00 ... (remaining 8502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1527 0.038 - 0.075: 319 0.075 - 0.113: 161 0.113 - 0.151: 23 0.151 - 0.188: 5 Chirality restraints: 2035 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 110 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.88e-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 8.74e-01 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 -2.21 -0.19 2.00e-01 2.50e+01 8.73e-01 ... (remaining 2032 not shown) Planarity restraints: 2445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA J 97 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO J 98 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO J 98 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO J 98 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 97 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO H 98 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO H 98 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 98 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 97 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO I 98 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO I 98 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO I 98 " -0.017 5.00e-02 4.00e+02 ... (remaining 2442 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 261 2.68 - 3.23: 11924 3.23 - 3.79: 19402 3.79 - 4.34: 28194 4.34 - 4.90: 47290 Nonbonded interactions: 107071 Sorted by model distance: nonbonded pdb=" O TYR J 32 " pdb=" NH2 ARG J 72 " model vdw 2.122 3.120 nonbonded pdb=" O TYR F 32 " pdb=" NH2 ARG F 72 " model vdw 2.122 3.120 nonbonded pdb=" O TYR H 32 " pdb=" NH2 ARG H 72 " model vdw 2.122 3.120 nonbonded pdb=" O TYR G 32 " pdb=" NH2 ARG G 72 " model vdw 2.122 3.120 nonbonded pdb=" O TYR I 32 " pdb=" NH2 ARG I 72 " model vdw 2.122 3.120 ... (remaining 107066 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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=0.50 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: 2.080 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.380 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:8.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 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 : 0.002 0.039 14005 Z= 0.125 Angle : 0.487 7.566 19065 Z= 0.262 Chirality : 0.041 0.188 2035 Planarity : 0.003 0.031 2430 Dihedral : 9.050 73.830 5380 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.70 % Allowed : 3.28 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.20), residues: 1645 helix: 3.04 (0.75), residues: 55 sheet: 0.74 (0.19), residues: 700 loop : -0.81 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 38 TYR 0.008 0.001 TYR A 117 PHE 0.006 0.001 PHE H 47 TRP 0.004 0.000 TRP B 59 HIS 0.002 0.000 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00243 (13970) covalent geometry : angle 0.46676 (18975) SS BOND : bond 0.00104 ( 15) SS BOND : angle 0.43276 ( 30) hydrogen bonds : bond 0.15664 ( 395) hydrogen bonds : angle 5.82109 ( 1200) link_BETA1-4 : bond 0.01337 ( 5) link_BETA1-4 : angle 4.64996 ( 15) link_NAG-ASN : bond 0.00345 ( 15) link_NAG-ASN : angle 1.20720 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 321 time to evaluate : 0.384 Fit side-chains REVERT: A 46 ASN cc_start: 0.9327 (m110) cc_final: 0.8932 (m-40) REVERT: B 46 ASN cc_start: 0.9363 (m110) cc_final: 0.9077 (m-40) REVERT: D 98 ARG cc_start: 0.9121 (mtm180) cc_final: 0.8862 (mtm180) REVERT: F 13 GLN cc_start: 0.8429 (tp-100) cc_final: 0.7901 (mm-40) REVERT: F 16 ASP cc_start: 0.8787 (m-30) cc_final: 0.8386 (m-30) REVERT: F 39 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8526 (tp-100) REVERT: F 76 LYS cc_start: 0.9391 (mptt) cc_final: 0.9191 (mtmm) REVERT: F 85 ASN cc_start: 0.9247 (t0) cc_final: 0.8673 (t0) REVERT: F 87 LYS cc_start: 0.9373 (mttt) cc_final: 0.9113 (mttm) REVERT: G 13 GLN cc_start: 0.8446 (tp-100) cc_final: 0.7847 (mm-40) REVERT: G 16 ASP cc_start: 0.8705 (m-30) cc_final: 0.8262 (m-30) REVERT: G 76 LYS cc_start: 0.9400 (mptt) cc_final: 0.9169 (mtmm) REVERT: G 85 ASN cc_start: 0.9258 (t0) cc_final: 0.8634 (t0) REVERT: G 87 LYS cc_start: 0.9366 (mttt) cc_final: 0.9111 (mttm) REVERT: H 13 GLN cc_start: 0.8439 (tp-100) cc_final: 0.7761 (mm-40) REVERT: H 16 ASP cc_start: 0.8688 (m-30) cc_final: 0.8246 (m-30) REVERT: H 39 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8649 (tp-100) REVERT: I 13 GLN cc_start: 0.8409 (tp-100) cc_final: 0.7938 (mm-40) REVERT: I 16 ASP cc_start: 0.8709 (m-30) cc_final: 0.8420 (m-30) REVERT: I 39 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8667 (tp-100) REVERT: I 76 LYS cc_start: 0.9427 (mptt) cc_final: 0.9190 (mtmm) REVERT: I 85 ASN cc_start: 0.9238 (t0) cc_final: 0.8714 (t0) REVERT: I 87 LYS cc_start: 0.9301 (mttt) cc_final: 0.9012 (mttm) REVERT: J 13 GLN cc_start: 0.8422 (tp-100) cc_final: 0.7793 (mm-40) REVERT: J 16 ASP cc_start: 0.8795 (m-30) cc_final: 0.8383 (m-30) REVERT: J 39 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8657 (tp-100) REVERT: J 76 LYS cc_start: 0.9401 (mptt) cc_final: 0.9186 (mtmm) REVERT: J 85 ASN cc_start: 0.9271 (t0) cc_final: 0.8576 (t0) REVERT: J 87 LYS cc_start: 0.9340 (mttt) cc_final: 0.9066 (mttp) outliers start: 10 outliers final: 1 residues processed: 326 average time/residue: 0.7621 time to fit residues: 263.4138 Evaluate side-chains 265 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 264 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 52 ASN B 26 GLN B 52 ASN C 26 GLN C 52 ASN D 26 GLN D 52 ASN E 26 GLN E 52 ASN F 3 GLN F 13 GLN F 82 GLN F 116 GLN G 13 GLN G 82 GLN G 116 GLN H 3 GLN H 13 GLN H 82 GLN H 85 ASN H 116 GLN I 3 GLN I 13 GLN I 82 GLN I 116 GLN J 3 GLN J 13 GLN J 82 GLN J 116 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.063728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.045391 restraints weight = 78570.873| |-----------------------------------------------------------------------------| r_work (start): 0.2385 rms_B_bonded: 5.01 r_work: 0.2213 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2209 r_free = 0.2209 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2209 r_free = 0.2209 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14005 Z= 0.207 Angle : 0.676 9.130 19065 Z= 0.331 Chirality : 0.048 0.342 2035 Planarity : 0.005 0.059 2430 Dihedral : 6.368 34.671 2318 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.77 % Allowed : 11.57 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.20), residues: 1645 helix: 3.67 (0.73), residues: 50 sheet: 0.66 (0.19), residues: 710 loop : -0.90 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 45 TYR 0.009 0.001 TYR E 117 PHE 0.021 0.002 PHE A 134 TRP 0.015 0.001 TRP C 133 HIS 0.004 0.001 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00484 (13970) covalent geometry : angle 0.65245 (18975) SS BOND : bond 0.00679 ( 15) SS BOND : angle 0.91896 ( 30) hydrogen bonds : bond 0.04525 ( 395) hydrogen bonds : angle 4.69464 ( 1200) link_BETA1-4 : bond 0.01721 ( 5) link_BETA1-4 : angle 5.64004 ( 15) link_NAG-ASN : bond 0.00301 ( 15) link_NAG-ASN : angle 1.78462 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 267 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9368 (m110) cc_final: 0.8977 (m-40) REVERT: A 75 LYS cc_start: 0.9438 (OUTLIER) cc_final: 0.9179 (mtpp) REVERT: B 46 ASN cc_start: 0.9392 (m110) cc_final: 0.9033 (m-40) REVERT: B 75 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.8945 (mtpp) REVERT: B 98 ARG cc_start: 0.9334 (mtm110) cc_final: 0.8938 (mtm180) REVERT: D 172 GLU cc_start: 0.8228 (tp30) cc_final: 0.7965 (tp30) REVERT: E 98 ARG cc_start: 0.9266 (mtm180) cc_final: 0.9031 (mtm180) REVERT: F 13 GLN cc_start: 0.8443 (tp40) cc_final: 0.7972 (tp-100) REVERT: F 16 ASP cc_start: 0.8926 (m-30) cc_final: 0.8569 (m-30) REVERT: F 85 ASN cc_start: 0.9326 (t0) cc_final: 0.8623 (t0) REVERT: F 87 LYS cc_start: 0.9126 (mttt) cc_final: 0.8728 (mttm) REVERT: G 13 GLN cc_start: 0.8382 (tp40) cc_final: 0.7931 (tp-100) REVERT: G 16 ASP cc_start: 0.8958 (m-30) cc_final: 0.8628 (m-30) REVERT: G 85 ASN cc_start: 0.9309 (t0) cc_final: 0.8901 (t0) REVERT: H 13 GLN cc_start: 0.8352 (tp40) cc_final: 0.7911 (tp-100) REVERT: H 16 ASP cc_start: 0.8935 (m-30) cc_final: 0.8532 (m-30) REVERT: H 76 LYS cc_start: 0.9436 (mtmm) cc_final: 0.9005 (mtmm) REVERT: I 13 GLN cc_start: 0.8398 (tp40) cc_final: 0.8005 (tp-100) REVERT: I 16 ASP cc_start: 0.8966 (m-30) cc_final: 0.8651 (m-30) REVERT: I 76 LYS cc_start: 0.9513 (mptt) cc_final: 0.9270 (mtmm) REVERT: I 85 ASN cc_start: 0.9331 (t0) cc_final: 0.8686 (t0) REVERT: I 87 LYS cc_start: 0.9053 (mttt) cc_final: 0.8697 (mttm) REVERT: J 13 GLN cc_start: 0.8377 (tp40) cc_final: 0.7879 (tp-100) REVERT: J 16 ASP cc_start: 0.8988 (m-30) cc_final: 0.8634 (m-30) REVERT: J 76 LYS cc_start: 0.9571 (mptt) cc_final: 0.9294 (mtmm) REVERT: J 85 ASN cc_start: 0.9347 (t0) cc_final: 0.8758 (t0) outliers start: 11 outliers final: 0 residues processed: 273 average time/residue: 1.0283 time to fit residues: 295.9540 Evaluate side-chains 255 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 253 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain B residue 75 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.062293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.044207 restraints weight = 81393.441| |-----------------------------------------------------------------------------| r_work (start): 0.2367 rms_B_bonded: 4.99 r_work: 0.2188 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2182 r_free = 0.2182 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2182 r_free = 0.2182 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9100 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14005 Z= 0.186 Angle : 0.661 9.345 19065 Z= 0.323 Chirality : 0.048 0.347 2035 Planarity : 0.005 0.032 2430 Dihedral : 5.743 31.086 2315 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.32 % Allowed : 11.15 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.19), residues: 1645 helix: 3.19 (0.73), residues: 50 sheet: 0.64 (0.19), residues: 710 loop : -1.11 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 45 TYR 0.011 0.001 TYR E 117 PHE 0.027 0.002 PHE C 134 TRP 0.030 0.001 TRP B 133 HIS 0.004 0.001 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00436 (13970) covalent geometry : angle 0.63396 (18975) SS BOND : bond 0.00271 ( 15) SS BOND : angle 0.60184 ( 30) hydrogen bonds : bond 0.03929 ( 395) hydrogen bonds : angle 4.45903 ( 1200) link_BETA1-4 : bond 0.01773 ( 5) link_BETA1-4 : angle 5.77045 ( 15) link_NAG-ASN : bond 0.00252 ( 15) link_NAG-ASN : angle 2.13854 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 254 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9373 (m110) cc_final: 0.8992 (m-40) REVERT: A 70 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8709 (mp0) REVERT: A 75 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.9206 (mtpp) REVERT: A 98 ARG cc_start: 0.9328 (mtm110) cc_final: 0.9097 (mtm110) REVERT: A 172 GLU cc_start: 0.9065 (tt0) cc_final: 0.8532 (tp30) REVERT: B 46 ASN cc_start: 0.9438 (m110) cc_final: 0.9052 (m-40) REVERT: B 98 ARG cc_start: 0.9361 (mtm110) cc_final: 0.9087 (mtm180) REVERT: B 172 GLU cc_start: 0.9085 (tt0) cc_final: 0.8625 (tp30) REVERT: D 98 ARG cc_start: 0.9300 (mtm180) cc_final: 0.9057 (mtm180) REVERT: D 172 GLU cc_start: 0.8477 (tp30) cc_final: 0.8130 (tp30) REVERT: E 70 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8627 (mp0) REVERT: E 98 ARG cc_start: 0.9336 (mtm180) cc_final: 0.9107 (mtm180) REVERT: E 172 GLU cc_start: 0.9046 (tt0) cc_final: 0.8625 (tp30) REVERT: F 13 GLN cc_start: 0.8481 (tp40) cc_final: 0.8004 (tp-100) REVERT: F 16 ASP cc_start: 0.8928 (m-30) cc_final: 0.8565 (m-30) REVERT: F 73 ASP cc_start: 0.7956 (t70) cc_final: 0.7631 (t0) REVERT: F 85 ASN cc_start: 0.9345 (t0) cc_final: 0.8858 (t0) REVERT: G 13 GLN cc_start: 0.8477 (tp40) cc_final: 0.7975 (tp-100) REVERT: G 16 ASP cc_start: 0.8879 (m-30) cc_final: 0.8452 (m-30) REVERT: G 76 LYS cc_start: 0.9568 (mptt) cc_final: 0.9278 (mtmm) REVERT: G 85 ASN cc_start: 0.9303 (t0) cc_final: 0.8712 (t0) REVERT: G 87 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8456 (mttp) REVERT: H 13 GLN cc_start: 0.8413 (tp40) cc_final: 0.7989 (tp-100) REVERT: H 16 ASP cc_start: 0.8862 (m-30) cc_final: 0.8437 (m-30) REVERT: H 76 LYS cc_start: 0.9479 (mtmm) cc_final: 0.9142 (mtmm) REVERT: I 13 GLN cc_start: 0.8372 (tp40) cc_final: 0.7959 (tp-100) REVERT: I 16 ASP cc_start: 0.8988 (m-30) cc_final: 0.8641 (m-30) REVERT: I 76 LYS cc_start: 0.9517 (mptt) cc_final: 0.9293 (mtmm) REVERT: I 85 ASN cc_start: 0.9321 (t0) cc_final: 0.9023 (t0) REVERT: J 13 GLN cc_start: 0.8420 (tp40) cc_final: 0.7924 (tp-100) REVERT: J 16 ASP cc_start: 0.8968 (m-30) cc_final: 0.8634 (m-30) REVERT: J 85 ASN cc_start: 0.9290 (t0) cc_final: 0.8738 (t0) outliers start: 19 outliers final: 3 residues processed: 262 average time/residue: 1.0615 time to fit residues: 293.0506 Evaluate side-chains 254 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 247 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain J residue 11 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 19 optimal weight: 0.0270 chunk 55 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 overall best weight: 1.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN J 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.063273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.045085 restraints weight = 95654.721| |-----------------------------------------------------------------------------| r_work (start): 0.2380 rms_B_bonded: 5.28 r_work: 0.2197 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2193 r_free = 0.2193 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2193 r_free = 0.2193 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9091 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14005 Z= 0.117 Angle : 0.618 8.993 19065 Z= 0.299 Chirality : 0.045 0.292 2035 Planarity : 0.005 0.038 2430 Dihedral : 5.556 30.637 2315 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.32 % Allowed : 12.20 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.19), residues: 1645 helix: 3.28 (0.74), residues: 50 sheet: 0.69 (0.19), residues: 710 loop : -1.15 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 185 TYR 0.010 0.001 TYR I 94 PHE 0.026 0.001 PHE A 134 TRP 0.030 0.001 TRP E 133 HIS 0.002 0.000 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00269 (13970) covalent geometry : angle 0.58987 (18975) SS BOND : bond 0.00159 ( 15) SS BOND : angle 0.46987 ( 30) hydrogen bonds : bond 0.03214 ( 395) hydrogen bonds : angle 4.26686 ( 1200) link_BETA1-4 : bond 0.01832 ( 5) link_BETA1-4 : angle 5.60855 ( 15) link_NAG-ASN : bond 0.00294 ( 15) link_NAG-ASN : angle 2.06029 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 258 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9393 (m110) cc_final: 0.8993 (m-40) REVERT: A 70 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8770 (mp0) REVERT: A 75 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.9129 (mtpp) REVERT: A 98 ARG cc_start: 0.9332 (mtm110) cc_final: 0.9083 (mtm110) REVERT: A 172 GLU cc_start: 0.9117 (tt0) cc_final: 0.8585 (tp30) REVERT: B 46 ASN cc_start: 0.9406 (m110) cc_final: 0.9027 (m-40) REVERT: B 98 ARG cc_start: 0.9360 (mtm110) cc_final: 0.9076 (mtm180) REVERT: B 172 GLU cc_start: 0.9121 (tt0) cc_final: 0.8627 (tp30) REVERT: C 70 GLU cc_start: 0.8893 (mp0) cc_final: 0.8475 (mp0) REVERT: C 172 GLU cc_start: 0.9025 (tt0) cc_final: 0.8568 (tp30) REVERT: D 70 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8525 (mp0) REVERT: D 98 ARG cc_start: 0.9289 (mtm180) cc_final: 0.9064 (mtm180) REVERT: D 172 GLU cc_start: 0.8608 (tp30) cc_final: 0.8224 (tp30) REVERT: E 70 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8704 (mp0) REVERT: E 98 ARG cc_start: 0.9350 (mtm180) cc_final: 0.9097 (mtm180) REVERT: E 172 GLU cc_start: 0.9047 (tt0) cc_final: 0.8622 (tp30) REVERT: F 3 GLN cc_start: 0.8742 (mt0) cc_final: 0.8538 (mt0) REVERT: F 13 GLN cc_start: 0.8484 (tp40) cc_final: 0.8018 (tp-100) REVERT: F 16 ASP cc_start: 0.8953 (m-30) cc_final: 0.8565 (m-30) REVERT: F 73 ASP cc_start: 0.8084 (t70) cc_final: 0.7738 (t0) REVERT: F 85 ASN cc_start: 0.9349 (t0) cc_final: 0.8851 (t0) REVERT: G 13 GLN cc_start: 0.8430 (tp40) cc_final: 0.7912 (tp-100) REVERT: G 16 ASP cc_start: 0.8922 (m-30) cc_final: 0.8502 (m-30) REVERT: G 73 ASP cc_start: 0.8262 (t70) cc_final: 0.7358 (t0) REVERT: G 76 LYS cc_start: 0.9577 (mptt) cc_final: 0.9302 (mtmm) REVERT: G 85 ASN cc_start: 0.9338 (t0) cc_final: 0.8787 (t0) REVERT: G 87 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8531 (mttp) REVERT: H 13 GLN cc_start: 0.8373 (tp40) cc_final: 0.7937 (tp-100) REVERT: H 16 ASP cc_start: 0.8952 (m-30) cc_final: 0.8536 (m-30) REVERT: H 76 LYS cc_start: 0.9487 (mtmm) cc_final: 0.9116 (mtmm) REVERT: I 13 GLN cc_start: 0.8317 (tp40) cc_final: 0.7885 (tp-100) REVERT: I 16 ASP cc_start: 0.9022 (m-30) cc_final: 0.8676 (m-30) REVERT: I 76 LYS cc_start: 0.9536 (mptt) cc_final: 0.9317 (mtmm) REVERT: I 85 ASN cc_start: 0.9378 (t0) cc_final: 0.9054 (t0) REVERT: J 13 GLN cc_start: 0.8421 (tp40) cc_final: 0.7913 (tp-100) REVERT: J 16 ASP cc_start: 0.9007 (m-30) cc_final: 0.8697 (m-30) REVERT: J 43 LYS cc_start: 0.8801 (mppt) cc_final: 0.8515 (mppt) REVERT: J 73 ASP cc_start: 0.8194 (t70) cc_final: 0.7959 (t0) REVERT: J 85 ASN cc_start: 0.9287 (t0) cc_final: 0.8726 (t0) outliers start: 19 outliers final: 5 residues processed: 266 average time/residue: 0.9443 time to fit residues: 265.2691 Evaluate side-chains 261 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 252 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 chunk 95 optimal weight: 0.3980 chunk 120 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN J 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.062418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.044545 restraints weight = 77708.112| |-----------------------------------------------------------------------------| r_work (start): 0.2364 rms_B_bonded: 4.89 r_work: 0.2188 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2184 r_free = 0.2184 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2184 r_free = 0.2184 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9123 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14005 Z= 0.160 Angle : 0.635 9.250 19065 Z= 0.309 Chirality : 0.046 0.362 2035 Planarity : 0.005 0.045 2430 Dihedral : 5.511 28.798 2315 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.25 % Allowed : 12.54 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.19), residues: 1645 helix: 3.03 (0.74), residues: 50 sheet: 0.71 (0.19), residues: 710 loop : -1.20 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 45 TYR 0.012 0.001 TYR F 94 PHE 0.026 0.001 PHE A 134 TRP 0.030 0.001 TRP E 133 HIS 0.003 0.000 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00377 (13970) covalent geometry : angle 0.60557 (18975) SS BOND : bond 0.00231 ( 15) SS BOND : angle 1.05386 ( 30) hydrogen bonds : bond 0.03556 ( 395) hydrogen bonds : angle 4.30810 ( 1200) link_BETA1-4 : bond 0.01754 ( 5) link_BETA1-4 : angle 5.77802 ( 15) link_NAG-ASN : bond 0.00281 ( 15) link_NAG-ASN : angle 2.09567 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 257 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9392 (m110) cc_final: 0.9000 (m-40) REVERT: A 70 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8767 (mp0) REVERT: A 75 LYS cc_start: 0.9441 (OUTLIER) cc_final: 0.9148 (mtpp) REVERT: A 98 ARG cc_start: 0.9365 (mtm110) cc_final: 0.9112 (mtm110) REVERT: A 172 GLU cc_start: 0.9097 (tt0) cc_final: 0.8579 (tp30) REVERT: B 46 ASN cc_start: 0.9404 (m110) cc_final: 0.8991 (m-40) REVERT: B 98 ARG cc_start: 0.9367 (mtm110) cc_final: 0.9081 (mtm180) REVERT: B 172 GLU cc_start: 0.9092 (tt0) cc_final: 0.8626 (tp30) REVERT: C 70 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8568 (mp0) REVERT: C 172 GLU cc_start: 0.9040 (tt0) cc_final: 0.8533 (tp30) REVERT: D 98 ARG cc_start: 0.9318 (mtm180) cc_final: 0.9088 (mtm180) REVERT: D 172 GLU cc_start: 0.8673 (tp30) cc_final: 0.8316 (tp30) REVERT: E 70 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8728 (mp0) REVERT: E 98 ARG cc_start: 0.9380 (mtm180) cc_final: 0.9124 (mtm180) REVERT: E 172 GLU cc_start: 0.9085 (tt0) cc_final: 0.8660 (tp30) REVERT: F 13 GLN cc_start: 0.8510 (tp40) cc_final: 0.8044 (tp-100) REVERT: F 16 ASP cc_start: 0.8940 (m-30) cc_final: 0.8543 (m-30) REVERT: F 73 ASP cc_start: 0.8226 (t70) cc_final: 0.7765 (t0) REVERT: F 85 ASN cc_start: 0.9373 (t0) cc_final: 0.8863 (t0) REVERT: G 13 GLN cc_start: 0.8417 (tp40) cc_final: 0.7836 (tp-100) REVERT: G 16 ASP cc_start: 0.8885 (m-30) cc_final: 0.8458 (m-30) REVERT: G 73 ASP cc_start: 0.8329 (t70) cc_final: 0.7309 (t0) REVERT: G 76 LYS cc_start: 0.9571 (mptt) cc_final: 0.9277 (mtmm) REVERT: G 87 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8581 (mttp) REVERT: H 13 GLN cc_start: 0.8373 (tp40) cc_final: 0.7937 (tp-100) REVERT: H 16 ASP cc_start: 0.8942 (m-30) cc_final: 0.8556 (m-30) REVERT: H 85 ASN cc_start: 0.9255 (t0) cc_final: 0.8724 (t0) REVERT: I 13 GLN cc_start: 0.8361 (tp40) cc_final: 0.7950 (tp-100) REVERT: I 16 ASP cc_start: 0.9011 (m-30) cc_final: 0.8662 (m-30) REVERT: I 73 ASP cc_start: 0.8295 (t70) cc_final: 0.7742 (t0) REVERT: I 85 ASN cc_start: 0.9383 (t0) cc_final: 0.9047 (t0) REVERT: I 109 ASP cc_start: 0.9277 (p0) cc_final: 0.8994 (p0) REVERT: J 13 GLN cc_start: 0.8431 (tp40) cc_final: 0.7904 (tp-100) REVERT: J 16 ASP cc_start: 0.8980 (m-30) cc_final: 0.8611 (m-30) REVERT: J 43 LYS cc_start: 0.8849 (mppt) cc_final: 0.8551 (mppt) REVERT: J 73 ASP cc_start: 0.8294 (t70) cc_final: 0.8046 (t0) REVERT: J 85 ASN cc_start: 0.9302 (t0) cc_final: 0.8735 (t0) outliers start: 18 outliers final: 9 residues processed: 266 average time/residue: 0.8835 time to fit residues: 248.4978 Evaluate side-chains 266 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 252 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 95 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 132 optimal weight: 0.0980 chunk 143 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 44 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN H 3 GLN J 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.064085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.046256 restraints weight = 77405.783| |-----------------------------------------------------------------------------| r_work (start): 0.2412 rms_B_bonded: 4.92 r_work: 0.2237 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2258 r_free = 0.2258 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2258 r_free = 0.2258 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9071 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14005 Z= 0.105 Angle : 0.619 8.880 19065 Z= 0.301 Chirality : 0.044 0.324 2035 Planarity : 0.005 0.041 2430 Dihedral : 5.356 29.092 2315 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.18 % Allowed : 13.59 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.19), residues: 1645 helix: 2.45 (0.77), residues: 55 sheet: 0.79 (0.19), residues: 710 loop : -1.25 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 45 TYR 0.010 0.001 TYR I 94 PHE 0.027 0.001 PHE C 134 TRP 0.032 0.001 TRP B 133 HIS 0.001 0.000 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00243 (13970) covalent geometry : angle 0.58545 (18975) SS BOND : bond 0.00400 ( 15) SS BOND : angle 2.33626 ( 30) hydrogen bonds : bond 0.02830 ( 395) hydrogen bonds : angle 4.10697 ( 1200) link_BETA1-4 : bond 0.01914 ( 5) link_BETA1-4 : angle 5.55681 ( 15) link_NAG-ASN : bond 0.00325 ( 15) link_NAG-ASN : angle 1.98971 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 263 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.9369 (tp30) cc_final: 0.9168 (tp30) REVERT: A 46 ASN cc_start: 0.9383 (m110) cc_final: 0.8985 (m-40) REVERT: A 70 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8757 (mp0) REVERT: A 75 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9074 (mtpp) REVERT: A 98 ARG cc_start: 0.9352 (mtm110) cc_final: 0.9093 (mtm110) REVERT: A 172 GLU cc_start: 0.9137 (tt0) cc_final: 0.8637 (tp30) REVERT: B 46 ASN cc_start: 0.9390 (m110) cc_final: 0.8994 (m-40) REVERT: B 98 ARG cc_start: 0.9358 (mtm110) cc_final: 0.9071 (mtm180) REVERT: B 172 GLU cc_start: 0.9107 (tt0) cc_final: 0.8652 (tp30) REVERT: C 70 GLU cc_start: 0.8958 (mp0) cc_final: 0.8592 (mp0) REVERT: C 172 GLU cc_start: 0.9055 (tt0) cc_final: 0.8601 (tp30) REVERT: D 98 ARG cc_start: 0.9294 (mtm180) cc_final: 0.9067 (mtm180) REVERT: D 172 GLU cc_start: 0.8715 (tp30) cc_final: 0.8341 (tp30) REVERT: E 70 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8394 (mp0) REVERT: E 98 ARG cc_start: 0.9365 (mtm180) cc_final: 0.9111 (mtm180) REVERT: E 172 GLU cc_start: 0.9075 (tt0) cc_final: 0.8653 (tp30) REVERT: E 206 ARG cc_start: 0.8355 (mtm-85) cc_final: 0.7835 (mtm-85) REVERT: F 13 GLN cc_start: 0.8501 (tp40) cc_final: 0.8030 (tp-100) REVERT: F 16 ASP cc_start: 0.8912 (m-30) cc_final: 0.8487 (m-30) REVERT: F 73 ASP cc_start: 0.8175 (t70) cc_final: 0.7746 (t0) REVERT: F 85 ASN cc_start: 0.9357 (t0) cc_final: 0.8823 (t0) REVERT: G 13 GLN cc_start: 0.8353 (tp40) cc_final: 0.7777 (tp-100) REVERT: G 16 ASP cc_start: 0.8879 (m-30) cc_final: 0.8442 (m-30) REVERT: G 43 LYS cc_start: 0.8479 (mppt) cc_final: 0.8239 (mppt) REVERT: G 73 ASP cc_start: 0.8278 (t70) cc_final: 0.7237 (t0) REVERT: G 76 LYS cc_start: 0.9569 (mptt) cc_final: 0.9268 (mtmm) REVERT: G 85 ASN cc_start: 0.9324 (t0) cc_final: 0.9012 (t0) REVERT: H 13 GLN cc_start: 0.8319 (tp40) cc_final: 0.7865 (tp-100) REVERT: H 16 ASP cc_start: 0.8992 (m-30) cc_final: 0.8596 (m-30) REVERT: H 85 ASN cc_start: 0.9261 (t0) cc_final: 0.8725 (t0) REVERT: I 13 GLN cc_start: 0.8343 (tp40) cc_final: 0.7974 (tp-100) REVERT: I 16 ASP cc_start: 0.8997 (m-30) cc_final: 0.8648 (m-30) REVERT: I 73 ASP cc_start: 0.8265 (t70) cc_final: 0.7706 (t0) REVERT: I 85 ASN cc_start: 0.9384 (t0) cc_final: 0.9039 (t0) REVERT: I 109 ASP cc_start: 0.9266 (p0) cc_final: 0.8975 (p0) REVERT: J 13 GLN cc_start: 0.8422 (tp40) cc_final: 0.7895 (tp-100) REVERT: J 16 ASP cc_start: 0.8980 (m-30) cc_final: 0.8586 (m-30) REVERT: J 43 LYS cc_start: 0.8778 (mppt) cc_final: 0.8449 (mppt) REVERT: J 73 ASP cc_start: 0.8235 (t70) cc_final: 0.7913 (t0) REVERT: J 85 ASN cc_start: 0.9283 (t0) cc_final: 0.8712 (t0) outliers start: 17 outliers final: 9 residues processed: 271 average time/residue: 0.9822 time to fit residues: 281.3272 Evaluate side-chains 264 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 252 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 95 CYS Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 95 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 72 optimal weight: 0.0470 chunk 86 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN F 3 GLN H 3 GLN J 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.059440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2405 r_free = 0.2405 target = 0.041957 restraints weight = 79405.845| |-----------------------------------------------------------------------------| r_work (start): 0.2389 rms_B_bonded: 4.80 r_work: 0.2215 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2198 r_free = 0.2198 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2198 r_free = 0.2198 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9108 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14005 Z= 0.151 Angle : 0.634 9.136 19065 Z= 0.310 Chirality : 0.045 0.312 2035 Planarity : 0.005 0.045 2430 Dihedral : 5.340 27.150 2315 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.46 % Allowed : 13.94 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.19), residues: 1645 helix: 3.18 (0.75), residues: 50 sheet: 0.81 (0.19), residues: 710 loop : -1.17 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 108 TYR 0.008 0.001 TYR E 117 PHE 0.028 0.001 PHE E 134 TRP 0.033 0.001 TRP D 133 HIS 0.002 0.000 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00357 (13970) covalent geometry : angle 0.60660 (18975) SS BOND : bond 0.00259 ( 15) SS BOND : angle 0.41023 ( 30) hydrogen bonds : bond 0.03360 ( 395) hydrogen bonds : angle 4.20399 ( 1200) link_BETA1-4 : bond 0.01710 ( 5) link_BETA1-4 : angle 5.71650 ( 15) link_NAG-ASN : bond 0.00288 ( 15) link_NAG-ASN : angle 2.01149 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 253 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9379 (m110) cc_final: 0.8986 (m-40) REVERT: A 70 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8781 (mp0) REVERT: A 75 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.9120 (mtpp) REVERT: A 98 ARG cc_start: 0.9368 (mtm110) cc_final: 0.9100 (mtm110) REVERT: A 172 GLU cc_start: 0.9117 (tt0) cc_final: 0.8636 (tp30) REVERT: B 46 ASN cc_start: 0.9375 (m110) cc_final: 0.8976 (m-40) REVERT: B 98 ARG cc_start: 0.9369 (mtm110) cc_final: 0.9074 (mtm180) REVERT: B 172 GLU cc_start: 0.9102 (tt0) cc_final: 0.8640 (tp30) REVERT: C 70 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8607 (mp0) REVERT: C 172 GLU cc_start: 0.9087 (tt0) cc_final: 0.8614 (tp30) REVERT: D 70 GLU cc_start: 0.8895 (mp0) cc_final: 0.8608 (mp0) REVERT: D 98 ARG cc_start: 0.9300 (mtm180) cc_final: 0.9073 (mtm180) REVERT: D 172 GLU cc_start: 0.8756 (tp30) cc_final: 0.8380 (tp30) REVERT: E 98 ARG cc_start: 0.9363 (mtm180) cc_final: 0.9093 (mtm180) REVERT: E 172 GLU cc_start: 0.9095 (tt0) cc_final: 0.8672 (tp30) REVERT: F 13 GLN cc_start: 0.8489 (tp40) cc_final: 0.8018 (tp-100) REVERT: F 16 ASP cc_start: 0.8905 (m-30) cc_final: 0.8464 (m-30) REVERT: F 73 ASP cc_start: 0.8257 (t70) cc_final: 0.7796 (t0) REVERT: F 85 ASN cc_start: 0.9363 (t0) cc_final: 0.8825 (t0) REVERT: G 13 GLN cc_start: 0.8356 (tp40) cc_final: 0.7774 (tp-100) REVERT: G 16 ASP cc_start: 0.8850 (m-30) cc_final: 0.8395 (m-30) REVERT: G 73 ASP cc_start: 0.8348 (t70) cc_final: 0.7294 (t0) REVERT: G 76 LYS cc_start: 0.9570 (mptt) cc_final: 0.9268 (mtmm) REVERT: H 13 GLN cc_start: 0.8330 (tp40) cc_final: 0.7845 (tp-100) REVERT: H 16 ASP cc_start: 0.8919 (m-30) cc_final: 0.8519 (m-30) REVERT: H 85 ASN cc_start: 0.9292 (t0) cc_final: 0.8738 (t0) REVERT: I 13 GLN cc_start: 0.8407 (tp40) cc_final: 0.8058 (tp-100) REVERT: I 16 ASP cc_start: 0.8979 (m-30) cc_final: 0.8645 (m-30) REVERT: I 73 ASP cc_start: 0.8327 (t70) cc_final: 0.7772 (t0) REVERT: I 85 ASN cc_start: 0.9386 (t0) cc_final: 0.9052 (t0) REVERT: I 109 ASP cc_start: 0.9286 (p0) cc_final: 0.9004 (p0) REVERT: J 13 GLN cc_start: 0.8446 (tp40) cc_final: 0.7923 (tp-100) REVERT: J 16 ASP cc_start: 0.8959 (m-30) cc_final: 0.8557 (m-30) REVERT: J 43 LYS cc_start: 0.8822 (mppt) cc_final: 0.8455 (mppt) REVERT: J 73 ASP cc_start: 0.8307 (t70) cc_final: 0.7945 (t0) REVERT: J 85 ASN cc_start: 0.9288 (t0) cc_final: 0.8722 (t0) outliers start: 21 outliers final: 11 residues processed: 265 average time/residue: 0.9289 time to fit residues: 260.2472 Evaluate side-chains 266 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 252 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 95 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 2 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN H 3 GLN J 3 GLN ** J 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.057820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2352 r_free = 0.2352 target = 0.040078 restraints weight = 101460.177| |-----------------------------------------------------------------------------| r_work (start): 0.2336 rms_B_bonded: 5.19 r_work: 0.2154 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2133 r_free = 0.2133 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2133 r_free = 0.2133 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9147 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14005 Z= 0.230 Angle : 0.694 9.739 19065 Z= 0.342 Chirality : 0.047 0.320 2035 Planarity : 0.005 0.054 2430 Dihedral : 5.576 26.376 2315 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.18 % Allowed : 14.56 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.19), residues: 1645 helix: 2.62 (0.71), residues: 50 sheet: 0.71 (0.19), residues: 710 loop : -1.21 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 108 TYR 0.010 0.001 TYR C 92 PHE 0.030 0.002 PHE A 134 TRP 0.032 0.001 TRP B 133 HIS 0.004 0.001 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00543 (13970) covalent geometry : angle 0.66651 (18975) SS BOND : bond 0.00276 ( 15) SS BOND : angle 0.51650 ( 30) hydrogen bonds : bond 0.04133 ( 395) hydrogen bonds : angle 4.44885 ( 1200) link_BETA1-4 : bond 0.01609 ( 5) link_BETA1-4 : angle 6.03307 ( 15) link_NAG-ASN : bond 0.00302 ( 15) link_NAG-ASN : angle 2.16708 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 244 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9376 (m110) cc_final: 0.8983 (m-40) REVERT: A 70 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8833 (mp0) REVERT: A 75 LYS cc_start: 0.9471 (OUTLIER) cc_final: 0.9151 (mtpp) REVERT: A 98 ARG cc_start: 0.9385 (mtm110) cc_final: 0.9147 (mtm180) REVERT: A 172 GLU cc_start: 0.9160 (tt0) cc_final: 0.8657 (tp30) REVERT: B 46 ASN cc_start: 0.9384 (m110) cc_final: 0.8981 (m-40) REVERT: B 98 ARG cc_start: 0.9362 (mtm110) cc_final: 0.9059 (mtm180) REVERT: B 172 GLU cc_start: 0.9150 (tt0) cc_final: 0.8664 (tp30) REVERT: C 70 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8672 (mp0) REVERT: C 172 GLU cc_start: 0.9135 (tt0) cc_final: 0.8607 (tp30) REVERT: D 70 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8720 (mp0) REVERT: D 172 GLU cc_start: 0.8836 (tp30) cc_final: 0.8438 (tp30) REVERT: E 98 ARG cc_start: 0.9376 (mtm180) cc_final: 0.9092 (mtm180) REVERT: E 172 GLU cc_start: 0.9159 (tt0) cc_final: 0.8704 (tp30) REVERT: E 203 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.9000 (ptp) REVERT: F 13 GLN cc_start: 0.8508 (tp40) cc_final: 0.8034 (tp-100) REVERT: F 16 ASP cc_start: 0.8876 (m-30) cc_final: 0.8434 (m-30) REVERT: F 73 ASP cc_start: 0.8367 (t70) cc_final: 0.7898 (t0) REVERT: F 85 ASN cc_start: 0.9394 (t0) cc_final: 0.8863 (t0) REVERT: G 13 GLN cc_start: 0.8383 (tp40) cc_final: 0.7788 (tp-100) REVERT: G 16 ASP cc_start: 0.8837 (m-30) cc_final: 0.8372 (m-30) REVERT: G 73 ASP cc_start: 0.8414 (t70) cc_final: 0.7293 (t0) REVERT: G 76 LYS cc_start: 0.9574 (mptt) cc_final: 0.9264 (mtmm) REVERT: H 13 GLN cc_start: 0.8351 (tp40) cc_final: 0.7887 (tp-100) REVERT: H 16 ASP cc_start: 0.8875 (m-30) cc_final: 0.8478 (m-30) REVERT: H 73 ASP cc_start: 0.8517 (t0) cc_final: 0.7936 (t0) REVERT: H 76 LYS cc_start: 0.9580 (mtmm) cc_final: 0.9302 (mtmm) REVERT: I 13 GLN cc_start: 0.8419 (tp40) cc_final: 0.8059 (tp-100) REVERT: I 16 ASP cc_start: 0.8956 (m-30) cc_final: 0.8624 (m-30) REVERT: I 73 ASP cc_start: 0.8366 (t70) cc_final: 0.7778 (t0) REVERT: I 85 ASN cc_start: 0.9390 (t0) cc_final: 0.9015 (t0) REVERT: I 109 ASP cc_start: 0.9316 (p0) cc_final: 0.9042 (p0) REVERT: J 13 GLN cc_start: 0.8454 (tp40) cc_final: 0.7936 (tp-100) REVERT: J 16 ASP cc_start: 0.8897 (m-30) cc_final: 0.8480 (m-30) REVERT: J 43 LYS cc_start: 0.8960 (mppt) cc_final: 0.8590 (mppt) REVERT: J 73 ASP cc_start: 0.8341 (t70) cc_final: 0.7949 (t0) REVERT: J 85 ASN cc_start: 0.9278 (t0) cc_final: 0.8724 (t0) outliers start: 17 outliers final: 7 residues processed: 253 average time/residue: 0.8826 time to fit residues: 235.6498 Evaluate side-chains 254 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 242 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 38 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 134 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN H 3 GLN J 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.058978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.041474 restraints weight = 81691.621| |-----------------------------------------------------------------------------| r_work (start): 0.2376 rms_B_bonded: 4.83 r_work: 0.2203 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2184 r_free = 0.2184 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2184 r_free = 0.2184 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14005 Z= 0.150 Angle : 0.658 9.460 19065 Z= 0.323 Chirality : 0.045 0.300 2035 Planarity : 0.005 0.052 2430 Dihedral : 5.481 27.164 2315 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.84 % Allowed : 14.98 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.19), residues: 1645 helix: 2.82 (0.74), residues: 50 sheet: 0.77 (0.19), residues: 710 loop : -1.21 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 108 TYR 0.008 0.001 TYR D 128 PHE 0.028 0.001 PHE C 134 TRP 0.034 0.001 TRP B 133 HIS 0.002 0.000 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00357 (13970) covalent geometry : angle 0.62989 (18975) SS BOND : bond 0.00214 ( 15) SS BOND : angle 0.46061 ( 30) hydrogen bonds : bond 0.03364 ( 395) hydrogen bonds : angle 4.26205 ( 1200) link_BETA1-4 : bond 0.01870 ( 5) link_BETA1-4 : angle 5.88642 ( 15) link_NAG-ASN : bond 0.00283 ( 15) link_NAG-ASN : angle 2.08758 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 253 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9384 (m110) cc_final: 0.8993 (m-40) REVERT: A 70 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8828 (mp0) REVERT: A 75 LYS cc_start: 0.9437 (OUTLIER) cc_final: 0.9168 (mtpp) REVERT: A 98 ARG cc_start: 0.9373 (mtm110) cc_final: 0.9103 (mtm110) REVERT: A 172 GLU cc_start: 0.9140 (tt0) cc_final: 0.8653 (tp30) REVERT: B 46 ASN cc_start: 0.9394 (m110) cc_final: 0.8998 (m-40) REVERT: B 98 ARG cc_start: 0.9352 (mtm110) cc_final: 0.9040 (mtm180) REVERT: B 172 GLU cc_start: 0.9125 (tt0) cc_final: 0.8667 (tp30) REVERT: C 70 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8677 (mp0) REVERT: C 172 GLU cc_start: 0.9113 (tt0) cc_final: 0.8641 (tp30) REVERT: D 70 GLU cc_start: 0.8939 (mp0) cc_final: 0.8724 (mp0) REVERT: D 172 GLU cc_start: 0.8834 (tp30) cc_final: 0.8465 (tp30) REVERT: E 70 GLU cc_start: 0.8932 (mp0) cc_final: 0.8729 (mp0) REVERT: E 98 ARG cc_start: 0.9369 (mtm180) cc_final: 0.9106 (mtm180) REVERT: E 172 GLU cc_start: 0.9128 (tt0) cc_final: 0.8699 (tp30) REVERT: E 203 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.9023 (ptp) REVERT: F 13 GLN cc_start: 0.8472 (tp40) cc_final: 0.7902 (tp-100) REVERT: F 16 ASP cc_start: 0.8875 (m-30) cc_final: 0.8410 (m-30) REVERT: F 43 LYS cc_start: 0.8535 (mppt) cc_final: 0.8254 (mppt) REVERT: F 73 ASP cc_start: 0.8346 (t70) cc_final: 0.7841 (t0) REVERT: F 85 ASN cc_start: 0.9384 (t0) cc_final: 0.8829 (t0) REVERT: G 13 GLN cc_start: 0.8345 (tp40) cc_final: 0.7745 (tp-100) REVERT: G 16 ASP cc_start: 0.8828 (m-30) cc_final: 0.8369 (m-30) REVERT: G 73 ASP cc_start: 0.8397 (t70) cc_final: 0.7908 (t0) REVERT: H 13 GLN cc_start: 0.8309 (tp40) cc_final: 0.7864 (tp-100) REVERT: H 16 ASP cc_start: 0.8862 (m-30) cc_final: 0.8493 (m-30) REVERT: H 73 ASP cc_start: 0.8493 (t0) cc_final: 0.7791 (t0) REVERT: H 76 LYS cc_start: 0.9556 (mtmm) cc_final: 0.9250 (mtmm) REVERT: H 85 ASN cc_start: 0.9310 (t0) cc_final: 0.8745 (t0) REVERT: I 13 GLN cc_start: 0.8442 (tp40) cc_final: 0.8113 (tp-100) REVERT: I 16 ASP cc_start: 0.8948 (m-30) cc_final: 0.8620 (m-30) REVERT: I 73 ASP cc_start: 0.8364 (t70) cc_final: 0.7780 (t0) REVERT: I 85 ASN cc_start: 0.9392 (t0) cc_final: 0.9008 (t0) REVERT: I 109 ASP cc_start: 0.9284 (p0) cc_final: 0.9000 (p0) REVERT: J 13 GLN cc_start: 0.8458 (tp40) cc_final: 0.7929 (tp-100) REVERT: J 16 ASP cc_start: 0.8897 (m-30) cc_final: 0.8450 (m-30) REVERT: J 43 LYS cc_start: 0.8886 (mppt) cc_final: 0.8488 (mppt) REVERT: J 73 ASP cc_start: 0.8359 (t70) cc_final: 0.7967 (t0) outliers start: 12 outliers final: 6 residues processed: 260 average time/residue: 0.9476 time to fit residues: 260.2177 Evaluate side-chains 259 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 249 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 95 CYS Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 19 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 156 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 108 optimal weight: 0.0370 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN H 3 GLN J 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.058826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.041603 restraints weight = 67390.845| |-----------------------------------------------------------------------------| r_work (start): 0.2378 rms_B_bonded: 4.49 r_work: 0.2214 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2197 r_free = 0.2197 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 = 0.2197 r_free = 0.2197 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14005 Z= 0.162 Angle : 0.668 9.368 19065 Z= 0.328 Chirality : 0.046 0.348 2035 Planarity : 0.005 0.058 2430 Dihedral : 5.445 26.415 2315 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.91 % Allowed : 15.12 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.19), residues: 1645 helix: 2.62 (0.73), residues: 50 sheet: 0.76 (0.19), residues: 710 loop : -1.19 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 108 TYR 0.007 0.001 TYR D 117 PHE 0.028 0.001 PHE D 134 TRP 0.035 0.001 TRP E 133 HIS 0.003 0.000 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00384 (13970) covalent geometry : angle 0.64022 (18975) SS BOND : bond 0.00216 ( 15) SS BOND : angle 0.45467 ( 30) hydrogen bonds : bond 0.03499 ( 395) hydrogen bonds : angle 4.26583 ( 1200) link_BETA1-4 : bond 0.01761 ( 5) link_BETA1-4 : angle 5.88115 ( 15) link_NAG-ASN : bond 0.00272 ( 15) link_NAG-ASN : angle 2.07051 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 250 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9385 (m110) cc_final: 0.8990 (m-40) REVERT: A 70 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8813 (mp0) REVERT: A 75 LYS cc_start: 0.9445 (OUTLIER) cc_final: 0.9188 (mtpp) REVERT: A 98 ARG cc_start: 0.9373 (mtm110) cc_final: 0.9142 (mtm180) REVERT: A 172 GLU cc_start: 0.9116 (tt0) cc_final: 0.8653 (tp30) REVERT: B 46 ASN cc_start: 0.9402 (m110) cc_final: 0.9006 (m-40) REVERT: B 98 ARG cc_start: 0.9353 (mtm110) cc_final: 0.9042 (mtm180) REVERT: B 172 GLU cc_start: 0.9104 (tt0) cc_final: 0.8656 (tp30) REVERT: C 70 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8656 (mp0) REVERT: C 172 GLU cc_start: 0.9087 (tt0) cc_final: 0.8638 (tp30) REVERT: D 70 GLU cc_start: 0.8939 (mp0) cc_final: 0.8733 (mp0) REVERT: D 172 GLU cc_start: 0.8848 (tp30) cc_final: 0.8487 (tp30) REVERT: E 98 ARG cc_start: 0.9368 (mtm180) cc_final: 0.9107 (mtm180) REVERT: E 172 GLU cc_start: 0.9114 (tt0) cc_final: 0.8693 (tp30) REVERT: E 203 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.8975 (ptp) REVERT: F 13 GLN cc_start: 0.8477 (tp40) cc_final: 0.7883 (tp-100) REVERT: F 16 ASP cc_start: 0.8863 (m-30) cc_final: 0.8399 (m-30) REVERT: F 73 ASP cc_start: 0.8373 (t70) cc_final: 0.7868 (t0) REVERT: F 85 ASN cc_start: 0.9381 (t0) cc_final: 0.8821 (t0) REVERT: G 13 GLN cc_start: 0.8337 (tp40) cc_final: 0.7713 (tp-100) REVERT: G 16 ASP cc_start: 0.8799 (m-30) cc_final: 0.8338 (m-30) REVERT: G 73 ASP cc_start: 0.8412 (t70) cc_final: 0.7926 (t0) REVERT: H 13 GLN cc_start: 0.8315 (tp40) cc_final: 0.7852 (tp-100) REVERT: H 16 ASP cc_start: 0.8889 (m-30) cc_final: 0.8509 (m-30) REVERT: H 73 ASP cc_start: 0.8511 (t0) cc_final: 0.7776 (t0) REVERT: H 76 LYS cc_start: 0.9556 (mtmm) cc_final: 0.9247 (mtmm) REVERT: H 85 ASN cc_start: 0.9284 (t0) cc_final: 0.8712 (t0) REVERT: I 13 GLN cc_start: 0.8468 (tp40) cc_final: 0.8143 (tp-100) REVERT: I 16 ASP cc_start: 0.8941 (m-30) cc_final: 0.8617 (m-30) REVERT: I 73 ASP cc_start: 0.8377 (t70) cc_final: 0.7768 (t0) REVERT: I 85 ASN cc_start: 0.9384 (t0) cc_final: 0.8993 (t0) REVERT: I 109 ASP cc_start: 0.9270 (p0) cc_final: 0.8976 (p0) REVERT: J 13 GLN cc_start: 0.8465 (tp40) cc_final: 0.7941 (tp-100) REVERT: J 16 ASP cc_start: 0.8875 (m-30) cc_final: 0.8417 (m-30) REVERT: J 43 LYS cc_start: 0.8941 (mppt) cc_final: 0.8522 (mppt) REVERT: J 73 ASP cc_start: 0.8392 (t70) cc_final: 0.8006 (t0) outliers start: 13 outliers final: 8 residues processed: 259 average time/residue: 0.9849 time to fit residues: 269.2855 Evaluate side-chains 258 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 246 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 95 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 145 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN H 3 GLN J 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.058796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2403 r_free = 0.2403 target = 0.042151 restraints weight = 49234.201| |-----------------------------------------------------------------------------| r_work (start): 0.2392 rms_B_bonded: 3.95 r_work: 0.2238 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2243 r_free = 0.2243 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2243 r_free = 0.2243 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9104 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14005 Z= 0.160 Angle : 0.669 9.360 19065 Z= 0.329 Chirality : 0.046 0.355 2035 Planarity : 0.005 0.057 2430 Dihedral : 5.430 26.101 2315 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.05 % Allowed : 14.98 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.19), residues: 1645 helix: 2.57 (0.73), residues: 50 sheet: 0.77 (0.19), residues: 710 loop : -1.18 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 108 TYR 0.010 0.001 TYR D 128 PHE 0.029 0.001 PHE C 134 TRP 0.035 0.001 TRP B 133 HIS 0.003 0.000 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00381 (13970) covalent geometry : angle 0.64144 (18975) SS BOND : bond 0.00212 ( 15) SS BOND : angle 0.44834 ( 30) hydrogen bonds : bond 0.03450 ( 395) hydrogen bonds : angle 4.26181 ( 1200) link_BETA1-4 : bond 0.01771 ( 5) link_BETA1-4 : angle 5.87500 ( 15) link_NAG-ASN : bond 0.00267 ( 15) link_NAG-ASN : angle 2.05978 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5587.34 seconds wall clock time: 95 minutes 48.98 seconds (5748.98 seconds total)