Starting phenix.real_space_refine on Thu Jul 31 18:28:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ci1_16665/07_2025/8ci1_16665_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ci1_16665/07_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_16665/07_2025/8ci1_16665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ci1_16665/07_2025/8ci1_16665.map" model { file = "/net/cci-nas-00/data/ceres_data/8ci1_16665/07_2025/8ci1_16665_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ci1_16665/07_2025/8ci1_16665_trim.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 19.33, per 1000 atoms: 1.42 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: 3.38 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 1.93 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: 4.29 Time building geometry restraints manager: 4.02 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' 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: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 45.740 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.740 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (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 TRP 0.004 0.000 TRP B 59 HIS 0.002 0.000 HIS A 62 PHE 0.006 0.001 PHE H 47 TYR 0.008 0.001 TYR A 117 ARG 0.001 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 15) link_NAG-ASN : angle 1.20720 ( 45) link_BETA1-4 : bond 0.01337 ( 5) link_BETA1-4 : angle 4.64996 ( 15) hydrogen bonds : bond 0.15664 ( 395) hydrogen bonds : angle 5.82109 ( 1200) SS BOND : bond 0.00104 ( 15) SS BOND : angle 0.43276 ( 30) covalent geometry : bond 0.00243 (13970) covalent geometry : angle 0.46676 (18975) *********************** 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 : 1.427 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: 1.7781 time to fit residues: 615.4838 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 : 1.406 ------------------------------------------------------------------------------- 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 135 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 0.2980 chunk 93 optimal weight: 0.0770 chunk 145 optimal weight: 4.9990 overall best weight: 2.4744 ------------------------------------------------------------------------------- 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 = 0.2886 r_free = 0.2886 target = 0.063522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.045238 restraints weight = 76151.016| |-----------------------------------------------------------------------------| r_work (start): 0.2401 rms_B_bonded: 4.95 r_work: 0.2225 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2225 ------------------------------------------------------------------------------- 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 = 0.50 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 = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14005 Z= 0.189 Angle : 0.701 8.969 19065 Z= 0.340 Chirality : 0.049 0.339 2035 Planarity : 0.005 0.058 2430 Dihedral : 6.089 32.305 2318 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.70 % Allowed : 11.50 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.19), residues: 1645 helix: 3.66 (0.74), residues: 50 sheet: 0.66 (0.19), residues: 710 loop : -0.98 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 133 HIS 0.005 0.001 HIS A 62 PHE 0.025 0.002 PHE A 134 TYR 0.010 0.001 TYR E 117 ARG 0.008 0.001 ARG G 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 15) link_NAG-ASN : angle 1.96518 ( 45) link_BETA1-4 : bond 0.01667 ( 5) link_BETA1-4 : angle 5.59128 ( 15) hydrogen bonds : bond 0.04013 ( 395) hydrogen bonds : angle 4.54687 ( 1200) SS BOND : bond 0.00371 ( 15) SS BOND : angle 0.71492 ( 30) covalent geometry : bond 0.00445 (13970) covalent geometry : angle 0.67750 (18975) *********************** 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 279 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 269 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9364 (m110) cc_final: 0.8983 (m-40) REVERT: A 75 LYS cc_start: 0.9430 (OUTLIER) cc_final: 0.9171 (mtpp) REVERT: B 46 ASN cc_start: 0.9433 (m110) cc_final: 0.9076 (m-40) REVERT: B 75 LYS cc_start: 0.9448 (OUTLIER) cc_final: 0.8934 (mtpp) REVERT: B 98 ARG cc_start: 0.9362 (mtm110) cc_final: 0.9096 (mtm180) REVERT: D 98 ARG cc_start: 0.9382 (mtm180) cc_final: 0.9085 (mtm180) REVERT: D 172 GLU cc_start: 0.8218 (tp30) cc_final: 0.7947 (tp30) REVERT: E 98 ARG cc_start: 0.9310 (mtm180) cc_final: 0.9082 (mtm180) REVERT: F 13 GLN cc_start: 0.8441 (tp40) cc_final: 0.7973 (tp-100) REVERT: F 16 ASP cc_start: 0.8929 (m-30) cc_final: 0.8577 (m-30) REVERT: F 85 ASN cc_start: 0.9319 (t0) cc_final: 0.8580 (t0) REVERT: F 87 LYS cc_start: 0.9132 (mttt) cc_final: 0.8729 (mttm) REVERT: G 13 GLN cc_start: 0.8341 (tp40) cc_final: 0.7912 (tp-100) REVERT: G 16 ASP cc_start: 0.8941 (m-30) cc_final: 0.8604 (m-30) REVERT: G 85 ASN cc_start: 0.9293 (t0) cc_final: 0.8875 (t0) REVERT: H 13 GLN cc_start: 0.8319 (tp40) cc_final: 0.7919 (tp-100) REVERT: H 16 ASP cc_start: 0.8884 (m-30) cc_final: 0.8477 (m-30) REVERT: I 13 GLN cc_start: 0.8350 (tp40) cc_final: 0.7947 (tp-100) REVERT: I 16 ASP cc_start: 0.8954 (m-30) cc_final: 0.8614 (m-30) REVERT: I 76 LYS cc_start: 0.9524 (mptt) cc_final: 0.9285 (mtmm) REVERT: I 85 ASN cc_start: 0.9314 (t0) cc_final: 0.8668 (t0) REVERT: I 87 LYS cc_start: 0.9022 (mttt) cc_final: 0.8691 (mttm) REVERT: J 13 GLN cc_start: 0.8375 (tp40) cc_final: 0.7899 (tp-100) REVERT: J 16 ASP cc_start: 0.8991 (m-30) cc_final: 0.8633 (m-30) REVERT: J 76 LYS cc_start: 0.9553 (mptt) cc_final: 0.9273 (mtmm) REVERT: J 85 ASN cc_start: 0.9339 (t0) cc_final: 0.8747 (t0) outliers start: 10 outliers final: 0 residues processed: 274 average time/residue: 1.9666 time to fit residues: 570.2742 Evaluate side-chains 257 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 255 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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 66 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 I 116 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.062168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.044259 restraints weight = 74688.107| |-----------------------------------------------------------------------------| r_work (start): 0.2354 rms_B_bonded: 4.81 r_work: 0.2180 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2176 r_free = 0.2176 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2176 r_free = 0.2176 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9106 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 14005 Z= 0.187 Angle : 0.648 9.334 19065 Z= 0.317 Chirality : 0.048 0.354 2035 Planarity : 0.005 0.031 2430 Dihedral : 5.709 30.229 2315 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.67 % Allowed : 11.29 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.19), residues: 1645 helix: 3.13 (0.73), residues: 50 sheet: 0.64 (0.19), residues: 710 loop : -1.13 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 133 HIS 0.003 0.001 HIS A 62 PHE 0.026 0.001 PHE A 134 TYR 0.011 0.001 TYR E 117 ARG 0.008 0.001 ARG H 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 15) link_NAG-ASN : angle 2.13615 ( 45) link_BETA1-4 : bond 0.01692 ( 5) link_BETA1-4 : angle 5.75594 ( 15) hydrogen bonds : bond 0.03974 ( 395) hydrogen bonds : angle 4.47356 ( 1200) SS BOND : bond 0.00225 ( 15) SS BOND : angle 0.57372 ( 30) covalent geometry : bond 0.00438 (13970) covalent geometry : angle 0.62039 (18975) *********************** 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 280 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 256 time to evaluate : 1.487 Fit side-chains revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9388 (m110) cc_final: 0.8999 (m-40) REVERT: A 70 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8716 (mp0) REVERT: A 75 LYS cc_start: 0.9462 (OUTLIER) cc_final: 0.9206 (mtpp) REVERT: A 98 ARG cc_start: 0.9314 (mtm110) cc_final: 0.9093 (mtm110) REVERT: A 172 GLU cc_start: 0.9085 (tt0) cc_final: 0.8524 (tp30) REVERT: A 185 ARG cc_start: 0.8920 (mtm110) cc_final: 0.8643 (mtp-110) REVERT: B 46 ASN cc_start: 0.9413 (m110) cc_final: 0.9023 (m-40) REVERT: B 98 ARG cc_start: 0.9357 (mtm110) cc_final: 0.9084 (mtm180) REVERT: B 172 GLU cc_start: 0.9091 (tt0) cc_final: 0.8588 (tp30) REVERT: C 70 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8617 (mp0) REVERT: C 172 GLU cc_start: 0.9043 (tt0) cc_final: 0.8423 (tp30) REVERT: D 98 ARG cc_start: 0.9372 (mtm180) cc_final: 0.9098 (mtm180) REVERT: D 172 GLU cc_start: 0.8535 (tp30) cc_final: 0.8210 (tp30) REVERT: E 70 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8535 (mp0) REVERT: E 98 ARG cc_start: 0.9349 (mtm180) cc_final: 0.9124 (mtm180) REVERT: E 172 GLU cc_start: 0.9049 (tt0) cc_final: 0.8613 (tp30) REVERT: F 13 GLN cc_start: 0.8479 (tp40) cc_final: 0.8001 (tp-100) REVERT: F 16 ASP cc_start: 0.8942 (m-30) cc_final: 0.8584 (m-30) REVERT: F 73 ASP cc_start: 0.8057 (t70) cc_final: 0.7683 (t0) REVERT: F 85 ASN cc_start: 0.9350 (t0) cc_final: 0.8866 (t0) REVERT: G 13 GLN cc_start: 0.8438 (tp40) cc_final: 0.7929 (tp-100) REVERT: G 16 ASP cc_start: 0.8933 (m-30) cc_final: 0.8544 (m-30) REVERT: G 85 ASN cc_start: 0.9322 (t0) cc_final: 0.8731 (t0) REVERT: G 87 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8379 (mttp) REVERT: H 12 VAL cc_start: 0.9240 (OUTLIER) cc_final: 0.9038 (p) REVERT: H 13 GLN cc_start: 0.8402 (tp40) cc_final: 0.7933 (tp-100) REVERT: H 16 ASP cc_start: 0.8930 (m-30) cc_final: 0.8468 (m-30) REVERT: H 76 LYS cc_start: 0.9482 (mtmm) cc_final: 0.9036 (mtmm) REVERT: I 13 GLN cc_start: 0.8357 (tp40) cc_final: 0.7927 (tp-100) REVERT: I 16 ASP cc_start: 0.9008 (m-30) cc_final: 0.8664 (m-30) REVERT: I 76 LYS cc_start: 0.9528 (mptt) cc_final: 0.9305 (mtmm) REVERT: I 85 ASN cc_start: 0.9344 (t0) cc_final: 0.9051 (t0) REVERT: J 13 GLN cc_start: 0.8450 (tp40) cc_final: 0.7941 (tp-100) REVERT: J 16 ASP cc_start: 0.8986 (m-30) cc_final: 0.8651 (m-30) REVERT: J 76 LYS cc_start: 0.9568 (mptt) cc_final: 0.9270 (mtmm) REVERT: J 85 ASN cc_start: 0.9304 (t0) cc_final: 0.8758 (t0) outliers start: 24 outliers final: 2 residues processed: 266 average time/residue: 1.9542 time to fit residues: 549.7963 Evaluate side-chains 258 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 250 time to evaluate : 1.571 ------------------------------------------------------------------------------- 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 44 GLU 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 H residue 12 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 18 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 84 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- 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 = 0.2886 r_free = 0.2886 target = 0.061119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.043443 restraints weight = 85070.281| |-----------------------------------------------------------------------------| r_work (start): 0.2411 rms_B_bonded: 5.01 r_work: 0.2231 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2240 r_free = 0.2240 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2240 r_free = 0.2240 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14005 Z= 0.120 Angle : 0.621 9.044 19065 Z= 0.301 Chirality : 0.045 0.295 2035 Planarity : 0.005 0.036 2430 Dihedral : 5.539 29.997 2315 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.39 % Allowed : 12.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.19), residues: 1645 helix: 3.25 (0.75), residues: 50 sheet: 0.72 (0.19), residues: 710 loop : -1.17 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 133 HIS 0.002 0.000 HIS A 62 PHE 0.025 0.001 PHE A 134 TYR 0.010 0.001 TYR B 117 ARG 0.009 0.001 ARG B 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 15) link_NAG-ASN : angle 2.07567 ( 45) link_BETA1-4 : bond 0.01836 ( 5) link_BETA1-4 : angle 5.64366 ( 15) hydrogen bonds : bond 0.03211 ( 395) hydrogen bonds : angle 4.24638 ( 1200) SS BOND : bond 0.00220 ( 15) SS BOND : angle 0.69273 ( 30) covalent geometry : bond 0.00277 (13970) covalent geometry : angle 0.59233 (18975) *********************** 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: 20 poor density : 257 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.9343 (tp30) cc_final: 0.9094 (tp30) REVERT: A 46 ASN cc_start: 0.9348 (m110) cc_final: 0.8948 (m-40) REVERT: A 70 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8663 (mp0) REVERT: A 75 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9077 (mtpp) REVERT: A 98 ARG cc_start: 0.9298 (mtm110) cc_final: 0.9053 (mtm110) REVERT: A 172 GLU cc_start: 0.9090 (tt0) cc_final: 0.8490 (tp30) REVERT: B 46 ASN cc_start: 0.9303 (m110) cc_final: 0.8915 (m-40) REVERT: B 98 ARG cc_start: 0.9327 (mtm110) cc_final: 0.9035 (mtm180) REVERT: B 172 GLU cc_start: 0.9098 (tt0) cc_final: 0.8514 (tp30) REVERT: C 70 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8549 (mp0) REVERT: C 172 GLU cc_start: 0.9064 (tt0) cc_final: 0.8498 (tp30) REVERT: D 98 ARG cc_start: 0.9280 (mtm180) cc_final: 0.8985 (mtm180) REVERT: D 172 GLU cc_start: 0.8551 (tp30) cc_final: 0.8169 (tp30) REVERT: E 70 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8547 (mp0) REVERT: E 98 ARG cc_start: 0.9301 (mtm180) cc_final: 0.9039 (mtm180) REVERT: E 172 GLU cc_start: 0.9070 (tt0) cc_final: 0.8607 (tp30) REVERT: F 13 GLN cc_start: 0.8422 (tp40) cc_final: 0.7963 (tp-100) REVERT: F 16 ASP cc_start: 0.8859 (m-30) cc_final: 0.8449 (m-30) REVERT: F 73 ASP cc_start: 0.7847 (t70) cc_final: 0.7501 (t0) REVERT: F 85 ASN cc_start: 0.9286 (t0) cc_final: 0.8756 (t0) REVERT: G 13 GLN cc_start: 0.8342 (tp40) cc_final: 0.7835 (tp-100) REVERT: G 16 ASP cc_start: 0.8879 (m-30) cc_final: 0.8437 (m-30) REVERT: G 85 ASN cc_start: 0.9257 (t0) cc_final: 0.8667 (t0) REVERT: G 87 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8446 (mttp) REVERT: H 12 VAL cc_start: 0.9089 (OUTLIER) cc_final: 0.8852 (p) REVERT: H 13 GLN cc_start: 0.8305 (tp40) cc_final: 0.7835 (tp-100) REVERT: H 16 ASP cc_start: 0.8869 (m-30) cc_final: 0.8431 (m-30) REVERT: H 85 ASN cc_start: 0.9161 (t0) cc_final: 0.8634 (t0) REVERT: I 13 GLN cc_start: 0.8258 (tp40) cc_final: 0.7856 (tp-100) REVERT: I 16 ASP cc_start: 0.8997 (m-30) cc_final: 0.8629 (m-30) REVERT: I 73 ASP cc_start: 0.8004 (t70) cc_final: 0.7480 (t0) REVERT: I 85 ASN cc_start: 0.9365 (t0) cc_final: 0.9030 (t0) REVERT: J 13 GLN cc_start: 0.8380 (tp40) cc_final: 0.7874 (tp-100) REVERT: J 16 ASP cc_start: 0.8963 (m-30) cc_final: 0.8626 (m-30) REVERT: J 73 ASP cc_start: 0.7950 (t70) cc_final: 0.7711 (t0) REVERT: J 85 ASN cc_start: 0.9223 (t0) cc_final: 0.8652 (t0) outliers start: 20 outliers final: 4 residues processed: 264 average time/residue: 1.9621 time to fit residues: 548.5675 Evaluate side-chains 264 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 254 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 70 GLU Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain I 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 50 optimal weight: 0.0270 chunk 47 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 38 optimal weight: 0.0670 chunk 78 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.5980 ------------------------------------------------------------------------------- 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 = 0.2878 r_free = 0.2878 target = 0.060754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.043171 restraints weight = 78887.655| |-----------------------------------------------------------------------------| r_work (start): 0.2405 rms_B_bonded: 4.86 r_work: 0.2228 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2238 r_free = 0.2238 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2238 r_free = 0.2238 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.2407 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= 0.137 Angle : 0.625 9.074 19065 Z= 0.304 Chirality : 0.045 0.276 2035 Planarity : 0.005 0.041 2430 Dihedral : 5.438 28.491 2315 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.25 % Allowed : 12.47 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.19), residues: 1645 helix: 3.13 (0.74), residues: 50 sheet: 0.72 (0.19), residues: 710 loop : -1.21 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 133 HIS 0.002 0.000 HIS A 62 PHE 0.026 0.001 PHE A 134 TYR 0.010 0.001 TYR G 94 ARG 0.010 0.001 ARG F 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 15) link_NAG-ASN : angle 2.07603 ( 45) link_BETA1-4 : bond 0.01722 ( 5) link_BETA1-4 : angle 5.68756 ( 15) hydrogen bonds : bond 0.03316 ( 395) hydrogen bonds : angle 4.23377 ( 1200) SS BOND : bond 0.00412 ( 15) SS BOND : angle 1.50044 ( 30) covalent geometry : bond 0.00320 (13970) covalent geometry : angle 0.59375 (18975) *********************** 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 278 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 260 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9351 (m110) cc_final: 0.8962 (m-40) REVERT: A 70 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8648 (mp0) REVERT: A 75 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.9029 (mtpp) REVERT: A 98 ARG cc_start: 0.9315 (mtm110) cc_final: 0.9060 (mtm110) REVERT: A 172 GLU cc_start: 0.9116 (tt0) cc_final: 0.8504 (tp30) REVERT: B 46 ASN cc_start: 0.9307 (m110) cc_final: 0.8915 (m-40) REVERT: B 98 ARG cc_start: 0.9331 (mtm110) cc_final: 0.9033 (mtm180) REVERT: B 172 GLU cc_start: 0.9102 (tt0) cc_final: 0.8536 (tp30) REVERT: C 70 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8581 (mp0) REVERT: C 172 GLU cc_start: 0.9071 (tt0) cc_final: 0.8514 (tp30) REVERT: D 70 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8469 (mp0) REVERT: D 98 ARG cc_start: 0.9273 (mtm180) cc_final: 0.8981 (mtm180) REVERT: D 172 GLU cc_start: 0.8615 (tp30) cc_final: 0.8217 (tp30) REVERT: E 70 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8652 (mp0) REVERT: E 98 ARG cc_start: 0.9312 (mtm180) cc_final: 0.9041 (mtm180) REVERT: E 172 GLU cc_start: 0.9080 (tt0) cc_final: 0.8617 (tp30) REVERT: F 13 GLN cc_start: 0.8443 (tp40) cc_final: 0.7975 (tp-100) REVERT: F 16 ASP cc_start: 0.8860 (m-30) cc_final: 0.8449 (m-30) REVERT: F 73 ASP cc_start: 0.7939 (t70) cc_final: 0.7507 (t0) REVERT: F 85 ASN cc_start: 0.9298 (t0) cc_final: 0.8751 (t0) REVERT: G 13 GLN cc_start: 0.8322 (tp40) cc_final: 0.7789 (tp-100) REVERT: G 16 ASP cc_start: 0.8860 (m-30) cc_final: 0.8424 (m-30) REVERT: G 73 ASP cc_start: 0.8058 (t70) cc_final: 0.7120 (t0) REVERT: G 76 LYS cc_start: 0.9510 (mtmm) cc_final: 0.9011 (mtmm) REVERT: G 85 ASN cc_start: 0.9264 (t0) cc_final: 0.8808 (t0) REVERT: G 87 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8326 (mttp) REVERT: H 13 GLN cc_start: 0.8304 (tp40) cc_final: 0.7864 (tp-100) REVERT: H 16 ASP cc_start: 0.8852 (m-30) cc_final: 0.8432 (m-30) REVERT: H 85 ASN cc_start: 0.9194 (t0) cc_final: 0.8663 (t0) REVERT: I 13 GLN cc_start: 0.8263 (tp40) cc_final: 0.7873 (tp-100) REVERT: I 16 ASP cc_start: 0.8974 (m-30) cc_final: 0.8596 (m-30) REVERT: I 73 ASP cc_start: 0.8065 (t70) cc_final: 0.7504 (t0) REVERT: I 85 ASN cc_start: 0.9352 (t0) cc_final: 0.8999 (t0) REVERT: J 13 GLN cc_start: 0.8358 (tp40) cc_final: 0.7851 (tp-100) REVERT: J 16 ASP cc_start: 0.8956 (m-30) cc_final: 0.8576 (m-30) REVERT: J 73 ASP cc_start: 0.7984 (t70) cc_final: 0.7659 (t0) REVERT: J 85 ASN cc_start: 0.9227 (t0) cc_final: 0.8644 (t0) outliers start: 18 outliers final: 7 residues processed: 269 average time/residue: 1.8730 time to fit residues: 533.9414 Evaluate side-chains 267 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 254 time to evaluate : 1.393 ------------------------------------------------------------------------------- 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 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 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 30 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.2883 r_free = 0.2883 target = 0.060848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.043434 restraints weight = 81673.409| |-----------------------------------------------------------------------------| r_work (start): 0.2411 rms_B_bonded: 4.87 r_work: 0.2232 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2239 r_free = 0.2239 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2239 r_free = 0.2239 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14005 Z= 0.134 Angle : 0.625 9.082 19065 Z= 0.304 Chirality : 0.045 0.260 2035 Planarity : 0.005 0.042 2430 Dihedral : 5.394 28.057 2315 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.46 % Allowed : 13.59 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.19), residues: 1645 helix: 3.10 (0.73), residues: 50 sheet: 0.74 (0.19), residues: 710 loop : -1.21 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 133 HIS 0.002 0.000 HIS A 62 PHE 0.027 0.001 PHE A 134 TYR 0.009 0.001 TYR E 117 ARG 0.010 0.001 ARG F 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 15) link_NAG-ASN : angle 2.04464 ( 45) link_BETA1-4 : bond 0.01798 ( 5) link_BETA1-4 : angle 5.69433 ( 15) hydrogen bonds : bond 0.03223 ( 395) hydrogen bonds : angle 4.20172 ( 1200) SS BOND : bond 0.00315 ( 15) SS BOND : angle 1.57772 ( 30) covalent geometry : bond 0.00315 (13970) covalent geometry : angle 0.59403 (18975) *********************** 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 278 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 257 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9350 (m110) cc_final: 0.8960 (m-40) REVERT: A 70 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8685 (mp0) REVERT: A 98 ARG cc_start: 0.9329 (mtm110) cc_final: 0.9066 (mtm110) REVERT: A 172 GLU cc_start: 0.9126 (tt0) cc_final: 0.8550 (tp30) REVERT: B 46 ASN cc_start: 0.9313 (m110) cc_final: 0.8908 (m-40) REVERT: B 98 ARG cc_start: 0.9344 (mtm110) cc_final: 0.9047 (mtm180) REVERT: B 172 GLU cc_start: 0.9104 (tt0) cc_final: 0.8542 (tp30) REVERT: C 70 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8641 (mp0) REVERT: C 172 GLU cc_start: 0.9083 (tt0) cc_final: 0.8533 (tp30) REVERT: D 70 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8483 (mp0) REVERT: D 98 ARG cc_start: 0.9279 (mtm180) cc_final: 0.9002 (mtm180) REVERT: D 172 GLU cc_start: 0.8652 (tp30) cc_final: 0.8242 (tp30) REVERT: E 70 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8667 (mp0) REVERT: E 98 ARG cc_start: 0.9323 (mtm180) cc_final: 0.9041 (mtm180) REVERT: E 172 GLU cc_start: 0.9104 (tt0) cc_final: 0.8649 (tp30) REVERT: F 13 GLN cc_start: 0.8435 (tp40) cc_final: 0.7898 (tp-100) REVERT: F 16 ASP cc_start: 0.8835 (m-30) cc_final: 0.8366 (m-30) REVERT: F 73 ASP cc_start: 0.7970 (t70) cc_final: 0.7541 (t0) REVERT: F 85 ASN cc_start: 0.9303 (t0) cc_final: 0.8754 (t0) REVERT: G 13 GLN cc_start: 0.8289 (tp40) cc_final: 0.7760 (tp-100) REVERT: G 16 ASP cc_start: 0.8838 (m-30) cc_final: 0.8374 (m-30) REVERT: G 73 ASP cc_start: 0.8084 (t70) cc_final: 0.7086 (t0) REVERT: G 76 LYS cc_start: 0.9512 (mtmm) cc_final: 0.8991 (mtmm) REVERT: G 87 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8363 (mttp) REVERT: H 13 GLN cc_start: 0.8315 (tp40) cc_final: 0.7880 (tp-100) REVERT: H 16 ASP cc_start: 0.8850 (m-30) cc_final: 0.8446 (m-30) REVERT: H 85 ASN cc_start: 0.9214 (t0) cc_final: 0.8677 (t0) REVERT: I 13 GLN cc_start: 0.8341 (tp40) cc_final: 0.7972 (tp-100) REVERT: I 16 ASP cc_start: 0.8971 (m-30) cc_final: 0.8599 (m-30) REVERT: I 73 ASP cc_start: 0.8092 (t70) cc_final: 0.7531 (t0) REVERT: I 85 ASN cc_start: 0.9360 (t0) cc_final: 0.8994 (t0) REVERT: J 13 GLN cc_start: 0.8381 (tp40) cc_final: 0.7883 (tp-100) REVERT: J 16 ASP cc_start: 0.8927 (m-30) cc_final: 0.8528 (m-30) REVERT: J 73 ASP cc_start: 0.8020 (t70) cc_final: 0.7681 (t0) REVERT: J 85 ASN cc_start: 0.9219 (t0) cc_final: 0.8634 (t0) outliers start: 21 outliers final: 12 residues processed: 269 average time/residue: 1.8733 time to fit residues: 534.6240 Evaluate side-chains 270 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 253 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain D 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 F residue 120 VAL Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 95 CYS Chi-restraints excluded: chain G residue 114 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 I residue 95 CYS Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 105 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 44 optimal weight: 0.0040 chunk 101 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- 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 = 0.2884 r_free = 0.2884 target = 0.060944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.043469 restraints weight = 88225.658| |-----------------------------------------------------------------------------| r_work (start): 0.2409 rms_B_bonded: 5.01 r_work: 0.2227 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2237 r_free = 0.2237 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2237 r_free = 0.2237 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14005 Z= 0.130 Angle : 0.629 9.091 19065 Z= 0.307 Chirality : 0.044 0.250 2035 Planarity : 0.005 0.046 2430 Dihedral : 5.334 27.455 2315 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.39 % Allowed : 13.87 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.19), residues: 1645 helix: 3.02 (0.74), residues: 50 sheet: 0.66 (0.18), residues: 760 loop : -1.08 (0.19), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 133 HIS 0.002 0.000 HIS A 62 PHE 0.027 0.001 PHE D 134 TYR 0.008 0.001 TYR E 117 ARG 0.010 0.001 ARG H 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 15) link_NAG-ASN : angle 2.01514 ( 45) link_BETA1-4 : bond 0.01840 ( 5) link_BETA1-4 : angle 5.68372 ( 15) hydrogen bonds : bond 0.03126 ( 395) hydrogen bonds : angle 4.16432 ( 1200) SS BOND : bond 0.00289 ( 15) SS BOND : angle 0.43023 ( 30) covalent geometry : bond 0.00306 (13970) covalent geometry : angle 0.60136 (18975) *********************** 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 276 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 256 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9348 (m110) cc_final: 0.8958 (m-40) REVERT: A 70 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8702 (mp0) REVERT: A 75 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.9017 (mtpp) REVERT: A 98 ARG cc_start: 0.9333 (mtm110) cc_final: 0.9065 (mtm110) REVERT: A 172 GLU cc_start: 0.9128 (tt0) cc_final: 0.8587 (tp30) REVERT: B 46 ASN cc_start: 0.9307 (m110) cc_final: 0.8902 (m-40) REVERT: B 98 ARG cc_start: 0.9331 (mtm110) cc_final: 0.9027 (mtm180) REVERT: B 172 GLU cc_start: 0.9126 (tt0) cc_final: 0.8567 (tp30) REVERT: C 70 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8673 (mp0) REVERT: C 172 GLU cc_start: 0.9090 (tt0) cc_final: 0.8540 (tp30) REVERT: D 70 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8511 (mp0) REVERT: D 98 ARG cc_start: 0.9274 (mtm180) cc_final: 0.9001 (mtm180) REVERT: D 172 GLU cc_start: 0.8699 (tp30) cc_final: 0.8286 (tp30) REVERT: E 70 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8725 (mp0) REVERT: E 98 ARG cc_start: 0.9311 (mtm180) cc_final: 0.9032 (mtm180) REVERT: E 172 GLU cc_start: 0.9120 (tt0) cc_final: 0.8704 (tp30) REVERT: F 13 GLN cc_start: 0.8433 (tp40) cc_final: 0.7886 (tp-100) REVERT: F 16 ASP cc_start: 0.8827 (m-30) cc_final: 0.8350 (m-30) REVERT: F 73 ASP cc_start: 0.7983 (t70) cc_final: 0.7515 (t0) REVERT: F 85 ASN cc_start: 0.9304 (t0) cc_final: 0.8732 (t0) REVERT: G 13 GLN cc_start: 0.8278 (tp40) cc_final: 0.7731 (tp-100) REVERT: G 16 ASP cc_start: 0.8802 (m-30) cc_final: 0.8338 (m-30) REVERT: G 73 ASP cc_start: 0.8096 (t70) cc_final: 0.7095 (t0) REVERT: G 76 LYS cc_start: 0.9515 (mtmm) cc_final: 0.8983 (mtmm) REVERT: H 13 GLN cc_start: 0.8296 (tp40) cc_final: 0.7846 (tp-100) REVERT: H 16 ASP cc_start: 0.8840 (m-30) cc_final: 0.8437 (m-30) REVERT: H 85 ASN cc_start: 0.9222 (t0) cc_final: 0.8678 (t0) REVERT: I 13 GLN cc_start: 0.8346 (tp40) cc_final: 0.7987 (tp-100) REVERT: I 16 ASP cc_start: 0.8942 (m-30) cc_final: 0.8557 (m-30) REVERT: I 73 ASP cc_start: 0.8100 (t70) cc_final: 0.7533 (t0) REVERT: I 85 ASN cc_start: 0.9359 (t0) cc_final: 0.9012 (t0) REVERT: J 13 GLN cc_start: 0.8372 (tp40) cc_final: 0.7872 (tp-100) REVERT: J 16 ASP cc_start: 0.8915 (m-30) cc_final: 0.8505 (m-30) REVERT: J 43 LYS cc_start: 0.8466 (mppt) cc_final: 0.8234 (mppt) REVERT: J 73 ASP cc_start: 0.8026 (t70) cc_final: 0.7656 (t0) REVERT: J 85 ASN cc_start: 0.9205 (t0) cc_final: 0.8619 (t0) outliers start: 20 outliers final: 10 residues processed: 267 average time/residue: 1.8764 time to fit residues: 531.4363 Evaluate side-chains 267 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 252 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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 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 86 LEU Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 95 CYS 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 31 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.2877 r_free = 0.2877 target = 0.060778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.043104 restraints weight = 90028.559| |-----------------------------------------------------------------------------| r_work (start): 0.2402 rms_B_bonded: 5.09 r_work: 0.2219 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2228 r_free = 0.2228 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2228 r_free = 0.2228 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14005 Z= 0.139 Angle : 0.640 9.051 19065 Z= 0.313 Chirality : 0.044 0.245 2035 Planarity : 0.005 0.056 2430 Dihedral : 5.309 26.636 2315 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.25 % Allowed : 14.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.19), residues: 1645 helix: 3.06 (0.74), residues: 50 sheet: 0.78 (0.19), residues: 710 loop : -1.18 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 133 HIS 0.002 0.000 HIS A 62 PHE 0.031 0.001 PHE A 134 TYR 0.008 0.001 TYR E 117 ARG 0.014 0.001 ARG F 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 15) link_NAG-ASN : angle 2.00417 ( 45) link_BETA1-4 : bond 0.01763 ( 5) link_BETA1-4 : angle 5.69446 ( 15) hydrogen bonds : bond 0.03218 ( 395) hydrogen bonds : angle 4.17872 ( 1200) SS BOND : bond 0.00219 ( 15) SS BOND : angle 0.43554 ( 30) covalent geometry : bond 0.00331 (13970) covalent geometry : angle 0.61317 (18975) *********************** 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 272 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 254 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9346 (m110) cc_final: 0.8955 (m-40) REVERT: A 70 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8707 (mp0) REVERT: A 75 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.9013 (mtpp) REVERT: A 98 ARG cc_start: 0.9332 (mtm110) cc_final: 0.9062 (mtm110) REVERT: A 172 GLU cc_start: 0.9125 (tt0) cc_final: 0.8588 (tp30) REVERT: B 46 ASN cc_start: 0.9310 (m110) cc_final: 0.8906 (m-40) REVERT: B 98 ARG cc_start: 0.9336 (mtm110) cc_final: 0.9029 (mtm180) REVERT: B 172 GLU cc_start: 0.9111 (tt0) cc_final: 0.8553 (tp30) REVERT: C 70 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8678 (mp0) REVERT: C 172 GLU cc_start: 0.9094 (tt0) cc_final: 0.8540 (tp30) REVERT: D 98 ARG cc_start: 0.9265 (mtm180) cc_final: 0.8993 (mtm180) REVERT: D 172 GLU cc_start: 0.8733 (tp30) cc_final: 0.8313 (tp30) REVERT: E 70 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8746 (mp0) REVERT: E 98 ARG cc_start: 0.9309 (mtm180) cc_final: 0.9027 (mtm180) REVERT: E 172 GLU cc_start: 0.9110 (tt0) cc_final: 0.8717 (tp30) REVERT: F 13 GLN cc_start: 0.8435 (tp40) cc_final: 0.7867 (tp-100) REVERT: F 16 ASP cc_start: 0.8818 (m-30) cc_final: 0.8348 (m-30) REVERT: F 73 ASP cc_start: 0.8031 (t70) cc_final: 0.7545 (t0) REVERT: F 85 ASN cc_start: 0.9303 (t0) cc_final: 0.8729 (t0) REVERT: G 13 GLN cc_start: 0.8271 (tp40) cc_final: 0.7740 (tp-100) REVERT: G 16 ASP cc_start: 0.8800 (m-30) cc_final: 0.8330 (m-30) REVERT: G 73 ASP cc_start: 0.8126 (t70) cc_final: 0.7120 (t0) REVERT: G 76 LYS cc_start: 0.9517 (mtmm) cc_final: 0.8985 (mtmm) REVERT: H 13 GLN cc_start: 0.8284 (tp40) cc_final: 0.7843 (tp-100) REVERT: H 16 ASP cc_start: 0.8826 (m-30) cc_final: 0.8436 (m-30) REVERT: H 85 ASN cc_start: 0.9226 (t0) cc_final: 0.8679 (t0) REVERT: I 13 GLN cc_start: 0.8382 (tp40) cc_final: 0.8038 (tp-100) REVERT: I 16 ASP cc_start: 0.8931 (m-30) cc_final: 0.8556 (m-30) REVERT: I 73 ASP cc_start: 0.8104 (t70) cc_final: 0.7505 (t0) REVERT: I 85 ASN cc_start: 0.9370 (t0) cc_final: 0.8998 (t0) REVERT: J 13 GLN cc_start: 0.8395 (tp40) cc_final: 0.7882 (tp-100) REVERT: J 16 ASP cc_start: 0.8892 (m-30) cc_final: 0.8467 (m-30) REVERT: J 73 ASP cc_start: 0.8045 (t70) cc_final: 0.7687 (t0) REVERT: J 85 ASN cc_start: 0.9203 (t0) cc_final: 0.8626 (t0) outliers start: 18 outliers final: 12 residues processed: 264 average time/residue: 1.8883 time to fit residues: 528.0120 Evaluate side-chains 269 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 253 time to evaluate : 1.413 ------------------------------------------------------------------------------- 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 44 GLU Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain E 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 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 86 LEU Chi-restraints excluded: chain J residue 95 CYS 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 122 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 = 0.2841 r_free = 0.2841 target = 0.059208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2392 r_free = 0.2392 target = 0.041751 restraints weight = 77815.237| |-----------------------------------------------------------------------------| r_work (start): 0.2365 rms_B_bonded: 4.76 r_work: 0.2187 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2194 r_free = 0.2194 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 = 0.2194 r_free = 0.2194 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.2637 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 : 0.689 9.460 19065 Z= 0.340 Chirality : 0.046 0.250 2035 Planarity : 0.005 0.057 2430 Dihedral : 5.485 25.491 2315 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.18 % Allowed : 14.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.19), residues: 1645 helix: 2.64 (0.71), residues: 50 sheet: 0.69 (0.19), residues: 710 loop : -1.18 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 133 HIS 0.003 0.001 HIS A 62 PHE 0.030 0.001 PHE E 134 TYR 0.008 0.001 TYR C 92 ARG 0.012 0.001 ARG J 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 15) link_NAG-ASN : angle 2.12006 ( 45) link_BETA1-4 : bond 0.01592 ( 5) link_BETA1-4 : angle 5.94073 ( 15) hydrogen bonds : bond 0.03944 ( 395) hydrogen bonds : angle 4.39892 ( 1200) SS BOND : bond 0.00220 ( 15) SS BOND : angle 0.50834 ( 30) covalent geometry : bond 0.00488 (13970) covalent geometry : angle 0.66231 (18975) *********************** 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 263 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 246 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.9348 (tp30) cc_final: 0.9137 (tp30) REVERT: A 46 ASN cc_start: 0.9344 (m110) cc_final: 0.8948 (m-40) REVERT: A 70 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8747 (mp0) REVERT: A 75 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.9104 (mtpp) REVERT: A 98 ARG cc_start: 0.9343 (mtm110) cc_final: 0.9100 (mtm180) REVERT: A 172 GLU cc_start: 0.9140 (tt0) cc_final: 0.8606 (tp30) REVERT: B 46 ASN cc_start: 0.9328 (m110) cc_final: 0.8927 (m-40) REVERT: B 98 ARG cc_start: 0.9332 (mtm110) cc_final: 0.9012 (mtm180) REVERT: B 172 GLU cc_start: 0.9125 (tt0) cc_final: 0.8575 (tp30) REVERT: C 70 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8667 (mp0) REVERT: C 172 GLU cc_start: 0.9116 (tt0) cc_final: 0.8506 (tp30) REVERT: D 70 GLU cc_start: 0.8428 (mp0) cc_final: 0.7986 (mp0) REVERT: D 98 ARG cc_start: 0.9301 (mtm180) cc_final: 0.9022 (mtm180) REVERT: D 172 GLU cc_start: 0.8758 (tp30) cc_final: 0.8348 (tp30) REVERT: E 70 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8758 (mp0) REVERT: E 98 ARG cc_start: 0.9313 (mtm180) cc_final: 0.9025 (mtm180) REVERT: E 172 GLU cc_start: 0.9160 (tt0) cc_final: 0.8700 (tp30) REVERT: E 203 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.8931 (ptp) REVERT: F 13 GLN cc_start: 0.8405 (tp40) cc_final: 0.7926 (tp-100) REVERT: F 16 ASP cc_start: 0.8756 (m-30) cc_final: 0.8290 (m-30) REVERT: F 73 ASP cc_start: 0.8131 (t70) cc_final: 0.7653 (t0) REVERT: F 85 ASN cc_start: 0.9329 (t0) cc_final: 0.8755 (t0) REVERT: G 13 GLN cc_start: 0.8277 (tp40) cc_final: 0.7718 (tp-100) REVERT: G 16 ASP cc_start: 0.8758 (m-30) cc_final: 0.8281 (m-30) REVERT: G 73 ASP cc_start: 0.8166 (t70) cc_final: 0.7120 (t0) REVERT: G 76 LYS cc_start: 0.9513 (mtmm) cc_final: 0.8961 (mtmm) REVERT: H 13 GLN cc_start: 0.8271 (tp40) cc_final: 0.7806 (tp-100) REVERT: H 16 ASP cc_start: 0.8756 (m-30) cc_final: 0.8349 (m-30) REVERT: H 76 LYS cc_start: 0.9438 (mtmm) cc_final: 0.9227 (mtmm) REVERT: I 13 GLN cc_start: 0.8381 (tp40) cc_final: 0.8028 (tp-100) REVERT: I 16 ASP cc_start: 0.8908 (m-30) cc_final: 0.8558 (m-30) REVERT: I 73 ASP cc_start: 0.8160 (t70) cc_final: 0.7552 (t0) REVERT: I 85 ASN cc_start: 0.9378 (t0) cc_final: 0.9010 (t0) REVERT: J 13 GLN cc_start: 0.8398 (tp40) cc_final: 0.7874 (tp-100) REVERT: J 16 ASP cc_start: 0.8805 (m-30) cc_final: 0.8340 (m-30) REVERT: J 73 ASP cc_start: 0.8091 (t70) cc_final: 0.7685 (t0) REVERT: J 85 ASN cc_start: 0.9196 (t0) cc_final: 0.8733 (t0) outliers start: 17 outliers final: 8 residues processed: 255 average time/residue: 1.9476 time to fit residues: 524.7198 Evaluate side-chains 256 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 243 time to evaluate : 1.408 ------------------------------------------------------------------------------- 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 C residue 184 GLU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain E 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 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 35 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.2849 r_free = 0.2849 target = 0.059525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.042240 restraints weight = 76248.848| |-----------------------------------------------------------------------------| r_work (start): 0.2376 rms_B_bonded: 4.71 r_work: 0.2200 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2207 r_free = 0.2207 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 = 0.2207 r_free = 0.2207 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14005 Z= 0.183 Angle : 0.681 9.584 19065 Z= 0.335 Chirality : 0.046 0.247 2035 Planarity : 0.005 0.061 2430 Dihedral : 5.499 26.166 2315 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.05 % Allowed : 15.19 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.19), residues: 1645 helix: 2.80 (0.73), residues: 50 sheet: 0.71 (0.19), residues: 710 loop : -1.18 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 133 HIS 0.003 0.001 HIS A 62 PHE 0.028 0.001 PHE A 134 TYR 0.010 0.001 TYR D 128 ARG 0.014 0.001 ARG G 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 15) link_NAG-ASN : angle 2.10712 ( 45) link_BETA1-4 : bond 0.01778 ( 5) link_BETA1-4 : angle 5.96721 ( 15) hydrogen bonds : bond 0.03622 ( 395) hydrogen bonds : angle 4.33643 ( 1200) SS BOND : bond 0.00211 ( 15) SS BOND : angle 0.49733 ( 30) covalent geometry : bond 0.00437 (13970) covalent geometry : angle 0.65312 (18975) ********************** 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: 15 poor density : 248 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.9333 (tp30) cc_final: 0.9106 (tp30) REVERT: A 46 ASN cc_start: 0.9351 (m110) cc_final: 0.8959 (m-40) REVERT: A 70 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8746 (mp0) REVERT: A 75 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.9103 (mtpp) REVERT: A 98 ARG cc_start: 0.9345 (mtm110) cc_final: 0.9067 (mtm110) REVERT: A 172 GLU cc_start: 0.9133 (tt0) cc_final: 0.8594 (tp30) REVERT: B 46 ASN cc_start: 0.9325 (m110) cc_final: 0.8922 (m-40) REVERT: B 70 GLU cc_start: 0.8270 (mp0) cc_final: 0.8029 (mp0) REVERT: B 98 ARG cc_start: 0.9324 (mtm110) cc_final: 0.8995 (mtm180) REVERT: B 172 GLU cc_start: 0.9128 (tt0) cc_final: 0.8592 (tp30) REVERT: C 70 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8691 (mp0) REVERT: C 172 GLU cc_start: 0.9112 (tt0) cc_final: 0.8544 (tp30) REVERT: D 98 ARG cc_start: 0.9284 (mtm180) cc_final: 0.9004 (mtm180) REVERT: D 172 GLU cc_start: 0.8792 (tp30) cc_final: 0.8382 (tp30) REVERT: E 98 ARG cc_start: 0.9317 (mtm180) cc_final: 0.9029 (mtm180) REVERT: E 172 GLU cc_start: 0.9167 (tt0) cc_final: 0.8713 (tp30) REVERT: E 203 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8933 (ptp) REVERT: F 13 GLN cc_start: 0.8393 (tp40) cc_final: 0.7812 (tp-100) REVERT: F 16 ASP cc_start: 0.8764 (m-30) cc_final: 0.8245 (m-30) REVERT: F 73 ASP cc_start: 0.8136 (t70) cc_final: 0.7662 (t0) REVERT: F 85 ASN cc_start: 0.9318 (t0) cc_final: 0.8726 (t0) REVERT: G 13 GLN cc_start: 0.8266 (tp40) cc_final: 0.8040 (tp-100) REVERT: G 73 ASP cc_start: 0.8169 (t70) cc_final: 0.7099 (t0) REVERT: G 76 LYS cc_start: 0.9505 (mtmm) cc_final: 0.8937 (mtmm) REVERT: H 13 GLN cc_start: 0.8285 (tp40) cc_final: 0.7838 (tp-100) REVERT: H 16 ASP cc_start: 0.8752 (m-30) cc_final: 0.8338 (m-30) REVERT: H 76 LYS cc_start: 0.9430 (mtmm) cc_final: 0.9090 (mtmm) REVERT: I 13 GLN cc_start: 0.8422 (tp40) cc_final: 0.8116 (tp-100) REVERT: I 16 ASP cc_start: 0.8897 (m-30) cc_final: 0.8567 (m-30) REVERT: I 73 ASP cc_start: 0.8178 (t70) cc_final: 0.7586 (t0) REVERT: I 85 ASN cc_start: 0.9363 (t0) cc_final: 0.8964 (t0) REVERT: J 13 GLN cc_start: 0.8417 (tp40) cc_final: 0.7906 (tp-100) REVERT: J 16 ASP cc_start: 0.8790 (m-30) cc_final: 0.8322 (m-30) REVERT: J 43 LYS cc_start: 0.8573 (mppt) cc_final: 0.8350 (mppt) REVERT: J 73 ASP cc_start: 0.8121 (t70) cc_final: 0.7726 (t0) REVERT: J 85 ASN cc_start: 0.9260 (t0) cc_final: 0.9029 (t0) outliers start: 15 outliers final: 7 residues processed: 257 average time/residue: 2.1478 time to fit residues: 584.1277 Evaluate side-chains 255 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 244 time to evaluate : 2.054 ------------------------------------------------------------------------------- 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 C residue 184 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 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 55 optimal weight: 0.0970 chunk 120 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 0.0270 chunk 132 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 155 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.3836 ------------------------------------------------------------------------------- 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 = 0.2910 r_free = 0.2910 target = 0.062077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.044816 restraints weight = 67500.751| |-----------------------------------------------------------------------------| r_work (start): 0.2455 rms_B_bonded: 4.59 r_work: 0.2283 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2286 r_free = 0.2286 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2286 r_free = 0.2286 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14005 Z= 0.111 Angle : 0.640 8.918 19065 Z= 0.315 Chirality : 0.043 0.228 2035 Planarity : 0.005 0.053 2430 Dihedral : 5.252 26.529 2315 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.49 % Allowed : 15.89 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.20), residues: 1645 helix: 2.11 (0.76), residues: 55 sheet: 0.86 (0.19), residues: 710 loop : -1.21 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 133 HIS 0.001 0.000 HIS G 31 PHE 0.029 0.001 PHE B 134 TYR 0.009 0.001 TYR E 71 ARG 0.013 0.001 ARG J 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00342 ( 15) link_NAG-ASN : angle 1.91331 ( 45) link_BETA1-4 : bond 0.01940 ( 5) link_BETA1-4 : angle 5.58726 ( 15) hydrogen bonds : bond 0.02589 ( 395) hydrogen bonds : angle 4.05977 ( 1200) SS BOND : bond 0.00179 ( 15) SS BOND : angle 0.45420 ( 30) covalent geometry : bond 0.00266 (13970) covalent geometry : angle 0.61520 (18975) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12912.58 seconds wall clock time: 222 minutes 14.45 seconds (13334.45 seconds total)