Starting phenix.real_space_refine on Thu May 15 23:16:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ci1_16665/05_2025/8ci1_16665_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ci1_16665/05_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_16665/05_2025/8ci1_16665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ci1_16665/05_2025/8ci1_16665.map" model { file = "/net/cci-nas-00/data/ceres_data/8ci1_16665/05_2025/8ci1_16665_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ci1_16665/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 11.81, per 1000 atoms: 0.87 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: 3.12 Conformation dependent library (CDL) restraints added in 2.6 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: 2.02 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: 4.05 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 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: 2.340 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 36.610 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.760 ------------------------------------------------------------------------------- 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 : 1.583 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: 1.7031 time to fit residues: 590.9414 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 : 1.410 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.045238 restraints weight = 76151.010| |-----------------------------------------------------------------------------| r_work (start): 0.2401 rms_B_bonded: 4.95 r_work: 0.2225 rms_B_bonded: 4.56 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: 0.9079 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 : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9369 (m110) cc_final: 0.8987 (m-40) REVERT: A 75 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.9172 (mtpp) REVERT: B 46 ASN cc_start: 0.9436 (m110) cc_final: 0.9078 (m-40) REVERT: B 75 LYS cc_start: 0.9448 (OUTLIER) cc_final: 0.8934 (mtpp) REVERT: B 98 ARG cc_start: 0.9360 (mtm110) cc_final: 0.9094 (mtm180) REVERT: D 98 ARG cc_start: 0.9380 (mtm180) cc_final: 0.9083 (mtm180) REVERT: D 172 GLU cc_start: 0.8225 (tp30) cc_final: 0.7954 (tp30) REVERT: E 98 ARG cc_start: 0.9308 (mtm180) cc_final: 0.9080 (mtm180) REVERT: F 13 GLN cc_start: 0.8445 (tp40) cc_final: 0.7977 (tp-100) REVERT: F 16 ASP cc_start: 0.8932 (m-30) cc_final: 0.8581 (m-30) REVERT: F 85 ASN cc_start: 0.9323 (t0) cc_final: 0.8584 (t0) REVERT: F 87 LYS cc_start: 0.9134 (mttt) cc_final: 0.8731 (mttm) REVERT: G 13 GLN cc_start: 0.8343 (tp40) cc_final: 0.7914 (tp-100) REVERT: G 16 ASP cc_start: 0.8943 (m-30) cc_final: 0.8607 (m-30) REVERT: G 85 ASN cc_start: 0.9295 (t0) cc_final: 0.8878 (t0) REVERT: H 13 GLN cc_start: 0.8323 (tp40) cc_final: 0.7922 (tp-100) REVERT: H 16 ASP cc_start: 0.8891 (m-30) cc_final: 0.8484 (m-30) REVERT: I 13 GLN cc_start: 0.8352 (tp40) cc_final: 0.7949 (tp-100) REVERT: I 16 ASP cc_start: 0.8957 (m-30) cc_final: 0.8618 (m-30) REVERT: I 76 LYS cc_start: 0.9525 (mptt) cc_final: 0.9286 (mtmm) REVERT: I 85 ASN cc_start: 0.9317 (t0) cc_final: 0.8672 (t0) REVERT: I 87 LYS cc_start: 0.9024 (mttt) cc_final: 0.8692 (mttm) REVERT: J 13 GLN cc_start: 0.8380 (tp40) cc_final: 0.7902 (tp-100) REVERT: J 16 ASP cc_start: 0.8994 (m-30) cc_final: 0.8637 (m-30) REVERT: J 76 LYS cc_start: 0.9554 (mptt) cc_final: 0.9274 (mtmm) REVERT: J 85 ASN cc_start: 0.9342 (t0) cc_final: 0.8751 (t0) outliers start: 10 outliers final: 0 residues processed: 274 average time/residue: 1.9245 time to fit residues: 558.6324 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 : 1.519 ------------------------------------------------------------------------------- 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: 2.9990 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: 10.0000 chunk 32 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.062696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.044747 restraints weight = 74506.610| |-----------------------------------------------------------------------------| r_work (start): 0.2383 rms_B_bonded: 4.81 r_work: 0.2211 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2193 r_free = 0.2193 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2193 r_free = 0.2193 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9109 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 14005 Z= 0.166 Angle : 0.637 9.089 19065 Z= 0.310 Chirality : 0.047 0.353 2035 Planarity : 0.005 0.030 2430 Dihedral : 5.677 30.838 2315 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.67 % Allowed : 11.22 % Favored : 87.11 % 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: 3.26 (0.73), residues: 50 sheet: 0.66 (0.19), residues: 710 loop : -1.11 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 133 HIS 0.003 0.000 HIS A 62 PHE 0.026 0.001 PHE A 134 TYR 0.011 0.001 TYR E 117 ARG 0.009 0.001 ARG H 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 15) link_NAG-ASN : angle 2.08417 ( 45) link_BETA1-4 : bond 0.01703 ( 5) link_BETA1-4 : angle 5.63929 ( 15) hydrogen bonds : bond 0.03755 ( 395) hydrogen bonds : angle 4.43895 ( 1200) SS BOND : bond 0.00205 ( 15) SS BOND : angle 0.54589 ( 30) covalent geometry : bond 0.00387 (13970) covalent geometry : angle 0.60946 (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 : 1.579 Fit side-chains REVERT: A 46 ASN cc_start: 0.9398 (m110) cc_final: 0.9009 (m-40) REVERT: A 75 LYS cc_start: 0.9455 (OUTLIER) cc_final: 0.9196 (mtpp) REVERT: A 98 ARG cc_start: 0.9292 (mtm110) cc_final: 0.9068 (mtm110) REVERT: A 172 GLU cc_start: 0.9062 (tt0) cc_final: 0.8511 (tp30) REVERT: A 185 ARG cc_start: 0.8926 (mtm110) cc_final: 0.8662 (mtp-110) REVERT: B 46 ASN cc_start: 0.9423 (m110) cc_final: 0.9033 (m-40) REVERT: B 98 ARG cc_start: 0.9359 (mtm110) cc_final: 0.9088 (mtm180) REVERT: B 172 GLU cc_start: 0.9081 (tt0) cc_final: 0.8573 (tp30) REVERT: C 70 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8594 (mp0) REVERT: C 172 GLU cc_start: 0.9004 (tt0) cc_final: 0.8393 (tp30) REVERT: D 172 GLU cc_start: 0.8492 (tp30) cc_final: 0.8150 (tp30) REVERT: E 70 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8528 (mp0) REVERT: E 98 ARG cc_start: 0.9337 (mtm180) cc_final: 0.9109 (mtm180) REVERT: E 172 GLU cc_start: 0.9036 (tt0) cc_final: 0.8613 (tp30) REVERT: F 13 GLN cc_start: 0.8485 (tp40) cc_final: 0.7998 (tp-100) REVERT: F 16 ASP cc_start: 0.8951 (m-30) cc_final: 0.8599 (m-30) REVERT: F 76 LYS cc_start: 0.9546 (mptt) cc_final: 0.9306 (mtmm) REVERT: F 85 ASN cc_start: 0.9348 (t0) cc_final: 0.8872 (t0) REVERT: G 13 GLN cc_start: 0.8436 (tp40) cc_final: 0.7936 (tp-100) REVERT: G 16 ASP cc_start: 0.8941 (m-30) cc_final: 0.8570 (m-30) REVERT: G 76 LYS cc_start: 0.9562 (mptt) cc_final: 0.9282 (mtmm) REVERT: G 85 ASN cc_start: 0.9330 (t0) cc_final: 0.8805 (t0) REVERT: G 87 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8551 (mttp) REVERT: H 12 VAL cc_start: 0.9240 (OUTLIER) cc_final: 0.9037 (p) REVERT: H 13 GLN cc_start: 0.8408 (tp40) cc_final: 0.7929 (tp-100) REVERT: H 16 ASP cc_start: 0.8946 (m-30) cc_final: 0.8502 (m-30) REVERT: H 76 LYS cc_start: 0.9478 (mtmm) cc_final: 0.9021 (mtmm) REVERT: I 13 GLN cc_start: 0.8346 (tp40) cc_final: 0.7893 (tp-100) REVERT: I 16 ASP cc_start: 0.9016 (m-30) cc_final: 0.8669 (m-30) REVERT: I 76 LYS cc_start: 0.9535 (mptt) cc_final: 0.9312 (mtmm) REVERT: I 85 ASN cc_start: 0.9363 (t0) cc_final: 0.9093 (t0) REVERT: J 13 GLN cc_start: 0.8452 (tp40) cc_final: 0.7945 (tp-100) REVERT: J 16 ASP cc_start: 0.9003 (m-30) cc_final: 0.8680 (m-30) REVERT: J 76 LYS cc_start: 0.9572 (mptt) cc_final: 0.9294 (mtmm) REVERT: J 85 ASN cc_start: 0.9315 (t0) cc_final: 0.8760 (t0) outliers start: 24 outliers final: 2 residues processed: 266 average time/residue: 1.8917 time to fit residues: 532.7451 Evaluate side-chains 257 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 250 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 50 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 84 optimal weight: 0.2980 chunk 33 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 118 optimal weight: 0.0770 chunk 98 optimal weight: 0.8980 chunk 14 optimal weight: 0.0980 chunk 149 optimal weight: 9.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 = 0.2885 r_free = 0.2885 target = 0.061283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.043682 restraints weight = 84696.141| |-----------------------------------------------------------------------------| r_work (start): 0.2434 rms_B_bonded: 4.96 r_work: 0.2261 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2246 r_free = 0.2246 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2246 r_free = 0.2246 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14005 Z= 0.101 Angle : 0.603 8.662 19065 Z= 0.292 Chirality : 0.044 0.293 2035 Planarity : 0.004 0.035 2430 Dihedral : 5.418 30.564 2315 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.98 % Allowed : 12.61 % Favored : 86.41 % 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: -0.27 (0.19), residues: 1645 helix: 2.56 (0.76), residues: 55 sheet: 0.77 (0.19), residues: 710 loop : -1.22 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 133 HIS 0.001 0.000 HIS A 62 PHE 0.026 0.001 PHE C 134 TYR 0.010 0.001 TYR B 117 ARG 0.010 0.001 ARG B 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 15) link_NAG-ASN : angle 1.98396 ( 45) link_BETA1-4 : bond 0.01884 ( 5) link_BETA1-4 : angle 5.43883 ( 15) hydrogen bonds : bond 0.02811 ( 395) hydrogen bonds : angle 4.13897 ( 1200) SS BOND : bond 0.00133 ( 15) SS BOND : angle 0.50792 ( 30) covalent geometry : bond 0.00228 (13970) covalent geometry : angle 0.57650 (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: 14 poor density : 263 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9396 (m110) cc_final: 0.9004 (m-40) REVERT: A 75 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.9068 (mtpp) REVERT: A 98 ARG cc_start: 0.9321 (mtm110) cc_final: 0.9091 (mtm110) REVERT: A 172 GLU cc_start: 0.9067 (tt0) cc_final: 0.8540 (tp30) REVERT: B 46 ASN cc_start: 0.9389 (m110) cc_final: 0.9012 (m-40) REVERT: B 98 ARG cc_start: 0.9358 (mtm110) cc_final: 0.9078 (mtm180) REVERT: B 172 GLU cc_start: 0.9091 (tt0) cc_final: 0.8578 (tp30) REVERT: C 70 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8620 (mp0) REVERT: C 172 GLU cc_start: 0.9028 (tt0) cc_final: 0.8525 (tp30) REVERT: D 98 ARG cc_start: 0.9285 (mtm180) cc_final: 0.9045 (mtm180) REVERT: D 172 GLU cc_start: 0.8587 (tp30) cc_final: 0.8198 (tp30) REVERT: E 70 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8545 (mp0) REVERT: E 98 ARG cc_start: 0.9353 (mtm180) cc_final: 0.9112 (mtm180) REVERT: E 172 GLU cc_start: 0.9008 (tt0) cc_final: 0.8615 (tp30) REVERT: F 13 GLN cc_start: 0.8496 (tp40) cc_final: 0.8016 (tp-100) REVERT: F 16 ASP cc_start: 0.8952 (m-30) cc_final: 0.8587 (m-30) REVERT: F 73 ASP cc_start: 0.8081 (t70) cc_final: 0.7709 (t0) REVERT: F 85 ASN cc_start: 0.9350 (t0) cc_final: 0.8865 (t0) REVERT: G 13 GLN cc_start: 0.8411 (tp40) cc_final: 0.7884 (tp-100) REVERT: G 16 ASP cc_start: 0.8938 (m-30) cc_final: 0.8560 (m-30) REVERT: G 73 ASP cc_start: 0.8220 (t70) cc_final: 0.7341 (t0) REVERT: G 76 LYS cc_start: 0.9574 (mptt) cc_final: 0.9306 (mtmm) REVERT: G 85 ASN cc_start: 0.9324 (t0) cc_final: 0.8728 (t0) REVERT: G 87 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8344 (mttp) REVERT: H 13 GLN cc_start: 0.8369 (tp40) cc_final: 0.7938 (tp-100) REVERT: H 16 ASP cc_start: 0.8966 (m-30) cc_final: 0.8553 (m-30) REVERT: H 39 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8216 (tp-100) REVERT: H 43 LYS cc_start: 0.8432 (mppt) cc_final: 0.8094 (mppt) REVERT: H 76 LYS cc_start: 0.9481 (mtmm) cc_final: 0.8979 (mtmm) REVERT: H 85 ASN cc_start: 0.9256 (t0) cc_final: 0.8724 (t0) REVERT: I 13 GLN cc_start: 0.8273 (tp40) cc_final: 0.7866 (tp-100) REVERT: I 16 ASP cc_start: 0.9024 (m-30) cc_final: 0.8684 (m-30) REVERT: I 39 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8184 (tp-100) REVERT: I 43 LYS cc_start: 0.8563 (mppt) cc_final: 0.8173 (mppt) REVERT: I 76 LYS cc_start: 0.9538 (mptt) cc_final: 0.9317 (mtmm) REVERT: I 85 ASN cc_start: 0.9367 (t0) cc_final: 0.9034 (t0) REVERT: J 13 GLN cc_start: 0.8437 (tp40) cc_final: 0.7949 (tp-100) REVERT: J 16 ASP cc_start: 0.9001 (m-30) cc_final: 0.8699 (m-30) REVERT: J 39 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8197 (tp-100) REVERT: J 43 LYS cc_start: 0.8693 (mppt) cc_final: 0.8485 (mppt) REVERT: J 73 ASP cc_start: 0.8177 (t70) cc_final: 0.7958 (t0) REVERT: J 85 ASN cc_start: 0.9298 (t0) cc_final: 0.8735 (t0) outliers start: 14 outliers final: 2 residues processed: 268 average time/residue: 1.8282 time to fit residues: 519.4706 Evaluate side-chains 262 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 256 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 50 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 149 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 78 optimal weight: 0.0470 chunk 31 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 overall best weight: 2.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN F 3 GLN H 3 GLN J 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.059366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2401 r_free = 0.2401 target = 0.041839 restraints weight = 78994.269| |-----------------------------------------------------------------------------| r_work (start): 0.2386 rms_B_bonded: 4.80 r_work: 0.2216 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2197 r_free = 0.2197 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2197 r_free = 0.2197 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14005 Z= 0.168 Angle : 0.627 9.214 19065 Z= 0.306 Chirality : 0.046 0.375 2035 Planarity : 0.005 0.044 2430 Dihedral : 5.416 28.121 2315 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.32 % Allowed : 12.20 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.24 (0.19), residues: 1645 helix: 3.34 (0.75), residues: 50 sheet: 0.74 (0.19), residues: 710 loop : -1.19 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 133 HIS 0.003 0.000 HIS A 62 PHE 0.026 0.001 PHE D 134 TYR 0.009 0.001 TYR E 117 ARG 0.009 0.001 ARG F 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 15) link_NAG-ASN : angle 2.07429 ( 45) link_BETA1-4 : bond 0.01722 ( 5) link_BETA1-4 : angle 5.73241 ( 15) hydrogen bonds : bond 0.03562 ( 395) hydrogen bonds : angle 4.28353 ( 1200) SS BOND : bond 0.00380 ( 15) SS BOND : angle 0.97126 ( 30) covalent geometry : bond 0.00396 (13970) covalent geometry : angle 0.59803 (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 276 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 257 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9384 (m110) cc_final: 0.8984 (m-40) REVERT: A 70 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8703 (mp0) REVERT: A 75 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9126 (mtpp) REVERT: A 98 ARG cc_start: 0.9337 (mtm110) cc_final: 0.9085 (mtm110) REVERT: A 172 GLU cc_start: 0.9110 (tt0) cc_final: 0.8552 (tp30) REVERT: B 46 ASN cc_start: 0.9387 (m110) cc_final: 0.8990 (m-40) REVERT: B 98 ARG cc_start: 0.9362 (mtm110) cc_final: 0.9077 (mtm180) REVERT: B 172 GLU cc_start: 0.9115 (tt0) cc_final: 0.8600 (tp30) REVERT: C 70 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8653 (mp0) REVERT: C 172 GLU cc_start: 0.9062 (tt0) cc_final: 0.8554 (tp30) REVERT: D 70 GLU cc_start: 0.8284 (mp0) cc_final: 0.7976 (mp0) REVERT: D 98 ARG cc_start: 0.9307 (mtm180) cc_final: 0.9094 (mtm180) REVERT: D 172 GLU cc_start: 0.8651 (tp30) cc_final: 0.8282 (tp30) REVERT: E 70 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8685 (mp0) REVERT: E 98 ARG cc_start: 0.9351 (mtm180) cc_final: 0.9088 (mtm180) REVERT: E 172 GLU cc_start: 0.9055 (tt0) cc_final: 0.8632 (tp30) REVERT: F 13 GLN cc_start: 0.8511 (tp40) cc_final: 0.8028 (tp-100) REVERT: F 16 ASP cc_start: 0.8945 (m-30) cc_final: 0.8551 (m-30) REVERT: F 73 ASP cc_start: 0.8192 (t70) cc_final: 0.7751 (t0) REVERT: F 85 ASN cc_start: 0.9361 (t0) cc_final: 0.8840 (t0) REVERT: G 13 GLN cc_start: 0.8387 (tp40) cc_final: 0.7829 (tp-100) REVERT: G 16 ASP cc_start: 0.8906 (m-30) cc_final: 0.8475 (m-30) REVERT: G 73 ASP cc_start: 0.8283 (t70) cc_final: 0.7272 (t0) REVERT: G 76 LYS cc_start: 0.9559 (mptt) cc_final: 0.9268 (mtmm) REVERT: G 85 ASN cc_start: 0.9343 (t0) cc_final: 0.8743 (t0) REVERT: G 87 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8386 (mttp) REVERT: H 13 GLN cc_start: 0.8375 (tp40) cc_final: 0.7929 (tp-100) REVERT: H 16 ASP cc_start: 0.8934 (m-30) cc_final: 0.8523 (m-30) REVERT: H 85 ASN cc_start: 0.9295 (t0) cc_final: 0.8768 (t0) REVERT: I 13 GLN cc_start: 0.8303 (tp40) cc_final: 0.7880 (tp-100) REVERT: I 16 ASP cc_start: 0.9026 (m-30) cc_final: 0.8693 (m-30) REVERT: I 43 LYS cc_start: 0.8681 (mppt) cc_final: 0.8469 (mppt) REVERT: I 73 ASP cc_start: 0.8280 (t70) cc_final: 0.7721 (t0) REVERT: I 85 ASN cc_start: 0.9379 (t0) cc_final: 0.9037 (t0) REVERT: I 109 ASP cc_start: 0.9246 (p0) cc_final: 0.8965 (p0) REVERT: J 13 GLN cc_start: 0.8409 (tp40) cc_final: 0.7883 (tp-100) REVERT: J 16 ASP cc_start: 0.9002 (m-30) cc_final: 0.8669 (m-30) REVERT: J 43 LYS cc_start: 0.8877 (mppt) cc_final: 0.8579 (mppt) REVERT: J 73 ASP cc_start: 0.8251 (t70) cc_final: 0.7929 (t0) REVERT: J 85 ASN cc_start: 0.9300 (t0) cc_final: 0.8734 (t0) outliers start: 19 outliers final: 7 residues processed: 268 average time/residue: 1.7817 time to fit residues: 507.1130 Evaluate side-chains 263 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 251 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 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: 0.1980 chunk 71 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.060787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.043258 restraints weight = 81572.560| |-----------------------------------------------------------------------------| r_work (start): 0.2424 rms_B_bonded: 4.89 r_work: 0.2251 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2235 r_free = 0.2235 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 = 0.2235 r_free = 0.2235 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14005 Z= 0.106 Angle : 0.612 8.815 19065 Z= 0.298 Chirality : 0.044 0.333 2035 Planarity : 0.005 0.041 2430 Dihedral : 5.301 28.587 2315 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.25 % Allowed : 13.38 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.19), residues: 1645 helix: 2.52 (0.76), residues: 55 sheet: 0.81 (0.19), residues: 710 loop : -1.26 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 133 HIS 0.001 0.000 HIS A 62 PHE 0.027 0.001 PHE E 134 TYR 0.010 0.001 TYR F 94 ARG 0.010 0.001 ARG F 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 15) link_NAG-ASN : angle 1.98022 ( 45) link_BETA1-4 : bond 0.01868 ( 5) link_BETA1-4 : angle 5.54102 ( 15) hydrogen bonds : bond 0.02860 ( 395) hydrogen bonds : angle 4.09533 ( 1200) SS BOND : bond 0.00389 ( 15) SS BOND : angle 2.38133 ( 30) covalent geometry : bond 0.00246 (13970) covalent geometry : angle 0.57723 (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 279 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 261 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9384 (m110) cc_final: 0.8981 (m-40) REVERT: A 75 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9070 (mtpp) REVERT: A 98 ARG cc_start: 0.9356 (mtm110) cc_final: 0.9111 (mtm110) REVERT: A 172 GLU cc_start: 0.9121 (tt0) cc_final: 0.8614 (tp30) REVERT: B 46 ASN cc_start: 0.9382 (m110) cc_final: 0.9000 (m-40) REVERT: B 98 ARG cc_start: 0.9372 (mtm110) cc_final: 0.9088 (mtm180) REVERT: B 172 GLU cc_start: 0.9125 (tt0) cc_final: 0.8636 (tp30) REVERT: C 70 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8690 (mp0) REVERT: C 172 GLU cc_start: 0.9050 (tt0) cc_final: 0.8566 (tp30) REVERT: D 70 GLU cc_start: 0.8368 (mp0) cc_final: 0.8013 (mp0) REVERT: D 98 ARG cc_start: 0.9307 (mtm180) cc_final: 0.9100 (mtm180) REVERT: D 172 GLU cc_start: 0.8676 (tp30) cc_final: 0.8296 (tp30) REVERT: E 70 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8703 (mp0) REVERT: E 98 ARG cc_start: 0.9363 (mtm180) cc_final: 0.9109 (mtm180) REVERT: E 172 GLU cc_start: 0.9030 (tt0) cc_final: 0.8622 (tp30) REVERT: E 206 ARG cc_start: 0.8364 (mtm-85) cc_final: 0.7833 (mtm-85) REVERT: F 13 GLN cc_start: 0.8511 (tp40) cc_final: 0.8043 (tp-100) REVERT: F 16 ASP cc_start: 0.8942 (m-30) cc_final: 0.8545 (m-30) REVERT: F 73 ASP cc_start: 0.8174 (t70) cc_final: 0.7723 (t0) REVERT: F 85 ASN cc_start: 0.9359 (t0) cc_final: 0.8838 (t0) REVERT: G 13 GLN cc_start: 0.8345 (tp40) cc_final: 0.7759 (tp-100) REVERT: G 16 ASP cc_start: 0.8898 (m-30) cc_final: 0.8473 (m-30) REVERT: G 43 LYS cc_start: 0.8709 (mppt) cc_final: 0.8378 (mppt) REVERT: G 73 ASP cc_start: 0.8291 (t70) cc_final: 0.7281 (t0) REVERT: G 76 LYS cc_start: 0.9574 (mptt) cc_final: 0.9272 (mtmm) REVERT: G 85 ASN cc_start: 0.9337 (t0) cc_final: 0.8957 (t0) REVERT: G 87 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8469 (mttp) REVERT: H 13 GLN cc_start: 0.8364 (tp40) cc_final: 0.7904 (tp-100) REVERT: H 16 ASP cc_start: 0.8973 (m-30) cc_final: 0.8583 (m-30) REVERT: H 39 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8151 (tp-100) REVERT: H 43 LYS cc_start: 0.8413 (mppt) cc_final: 0.8104 (mppt) REVERT: H 85 ASN cc_start: 0.9274 (t0) cc_final: 0.8726 (t0) REVERT: I 13 GLN cc_start: 0.8325 (tp40) cc_final: 0.7970 (tp-100) REVERT: I 16 ASP cc_start: 0.9037 (m-30) cc_final: 0.8699 (m-30) REVERT: I 39 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8207 (tp-100) REVERT: I 43 LYS cc_start: 0.8670 (mppt) cc_final: 0.8283 (mppt) REVERT: I 73 ASP cc_start: 0.8275 (t70) cc_final: 0.7705 (t0) REVERT: I 85 ASN cc_start: 0.9381 (t0) cc_final: 0.9052 (t0) REVERT: I 109 ASP cc_start: 0.9252 (p0) cc_final: 0.8959 (p0) REVERT: J 13 GLN cc_start: 0.8408 (tp40) cc_final: 0.7894 (tp-100) REVERT: J 16 ASP cc_start: 0.8996 (m-30) cc_final: 0.8611 (m-30) REVERT: J 43 LYS cc_start: 0.8811 (mppt) cc_final: 0.8507 (mppt) REVERT: J 73 ASP cc_start: 0.8244 (t70) cc_final: 0.7915 (t0) REVERT: J 85 ASN cc_start: 0.9289 (t0) cc_final: 0.8721 (t0) outliers start: 18 outliers final: 10 residues processed: 270 average time/residue: 1.8340 time to fit residues: 525.3461 Evaluate side-chains 268 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 254 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 95 CYS Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 95 CYS Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain J residue 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: 3.9990 chunk 49 optimal weight: 0.5980 chunk 44 optimal weight: 0.0060 chunk 101 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 144 optimal weight: 0.0970 chunk 156 optimal weight: 2.9990 chunk 39 optimal weight: 0.0970 chunk 34 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN H 3 GLN J 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.061680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.044079 restraints weight = 87701.788| |-----------------------------------------------------------------------------| r_work (start): 0.2448 rms_B_bonded: 5.03 r_work: 0.2275 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2280 r_free = 0.2280 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 = 0.2280 r_free = 0.2280 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 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 : 0.002 0.037 14005 Z= 0.102 Angle : 0.597 8.494 19065 Z= 0.291 Chirality : 0.043 0.312 2035 Planarity : 0.005 0.046 2430 Dihedral : 5.122 27.556 2315 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.32 % Allowed : 13.80 % Favored : 84.88 % 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: -0.20 (0.19), residues: 1645 helix: 2.41 (0.75), residues: 55 sheet: 0.90 (0.19), residues: 710 loop : -1.23 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 133 HIS 0.000 0.000 HIS C 62 PHE 0.027 0.001 PHE B 134 TYR 0.009 0.001 TYR C 117 ARG 0.012 0.001 ARG F 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 15) link_NAG-ASN : angle 1.88621 ( 45) link_BETA1-4 : bond 0.01851 ( 5) link_BETA1-4 : angle 5.40376 ( 15) hydrogen bonds : bond 0.02570 ( 395) hydrogen bonds : angle 3.99017 ( 1200) SS BOND : bond 0.00249 ( 15) SS BOND : angle 1.17712 ( 30) covalent geometry : bond 0.00236 (13970) covalent geometry : angle 0.56985 (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 284 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 265 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9380 (m110) cc_final: 0.8979 (m-40) REVERT: A 98 ARG cc_start: 0.9318 (mtm110) cc_final: 0.9066 (mtm110) REVERT: A 172 GLU cc_start: 0.9129 (tt0) cc_final: 0.8659 (tp30) REVERT: A 185 ARG cc_start: 0.8943 (mtm110) cc_final: 0.8713 (mtp-110) REVERT: B 46 ASN cc_start: 0.9377 (m110) cc_final: 0.8974 (m-40) REVERT: B 98 ARG cc_start: 0.9362 (mtm110) cc_final: 0.9072 (mtm180) REVERT: B 172 GLU cc_start: 0.9107 (tt0) cc_final: 0.8639 (tp30) REVERT: C 70 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8724 (mp0) REVERT: C 172 GLU cc_start: 0.9052 (tt0) cc_final: 0.8585 (tp30) REVERT: D 70 GLU cc_start: 0.8426 (mp0) cc_final: 0.8074 (mp0) REVERT: D 98 ARG cc_start: 0.9290 (mtm180) cc_final: 0.9084 (mtm180) REVERT: D 172 GLU cc_start: 0.8712 (tp30) cc_final: 0.8339 (tp30) REVERT: D 206 ARG cc_start: 0.8378 (mtm-85) cc_final: 0.8055 (mtm-85) REVERT: E 70 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8710 (mp0) REVERT: E 98 ARG cc_start: 0.9331 (mtm180) cc_final: 0.9071 (mtm180) REVERT: E 172 GLU cc_start: 0.9027 (tt0) cc_final: 0.8666 (tp30) REVERT: F 13 GLN cc_start: 0.8460 (tp40) cc_final: 0.7975 (tp-100) REVERT: F 16 ASP cc_start: 0.8925 (m-30) cc_final: 0.8521 (m-30) REVERT: F 39 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8097 (tp-100) REVERT: F 73 ASP cc_start: 0.8165 (t70) cc_final: 0.7725 (t0) REVERT: F 85 ASN cc_start: 0.9356 (t0) cc_final: 0.8851 (t0) REVERT: G 13 GLN cc_start: 0.8325 (tp40) cc_final: 0.7722 (tp-100) REVERT: G 16 ASP cc_start: 0.8905 (m-30) cc_final: 0.8487 (m-30) REVERT: G 73 ASP cc_start: 0.8298 (t70) cc_final: 0.7285 (t0) REVERT: G 76 LYS cc_start: 0.9566 (mptt) cc_final: 0.9263 (mtmm) REVERT: G 85 ASN cc_start: 0.9331 (t0) cc_final: 0.9071 (t0) REVERT: H 13 GLN cc_start: 0.8321 (tp40) cc_final: 0.7774 (tp-100) REVERT: H 16 ASP cc_start: 0.8997 (m-30) cc_final: 0.8545 (m-30) REVERT: H 39 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8332 (tp-100) REVERT: H 43 LYS cc_start: 0.8433 (mppt) cc_final: 0.8175 (mppt) REVERT: H 85 ASN cc_start: 0.9274 (t0) cc_final: 0.8737 (t0) REVERT: I 13 GLN cc_start: 0.8358 (tp40) cc_final: 0.8000 (tp-100) REVERT: I 16 ASP cc_start: 0.9012 (m-30) cc_final: 0.8659 (m-30) REVERT: I 39 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8242 (tp-100) REVERT: I 43 LYS cc_start: 0.8679 (mppt) cc_final: 0.8273 (mppt) REVERT: I 73 ASP cc_start: 0.8272 (t70) cc_final: 0.7705 (t0) REVERT: I 85 ASN cc_start: 0.9382 (t0) cc_final: 0.9010 (t0) REVERT: I 109 ASP cc_start: 0.9275 (p0) cc_final: 0.8984 (p0) REVERT: J 13 GLN cc_start: 0.8374 (tp40) cc_final: 0.7846 (tp-100) REVERT: J 16 ASP cc_start: 0.8989 (m-30) cc_final: 0.8586 (m-30) REVERT: J 39 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8221 (tp-100) REVERT: J 43 LYS cc_start: 0.8858 (mppt) cc_final: 0.8312 (mppt) REVERT: J 44 GLU cc_start: 0.8572 (mp0) cc_final: 0.8322 (pm20) REVERT: J 73 ASP cc_start: 0.8251 (t70) cc_final: 0.7922 (t0) REVERT: J 85 ASN cc_start: 0.9287 (t0) cc_final: 0.8713 (t0) outliers start: 19 outliers final: 12 residues processed: 275 average time/residue: 1.7928 time to fit residues: 523.3912 Evaluate side-chains 276 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 262 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 95 CYS Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 95 CYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 114 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 31 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 118 optimal weight: 0.0060 overall best weight: 0.7600 ------------------------------------------------------------------------------- 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 = 0.2891 r_free = 0.2891 target = 0.061404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.043774 restraints weight = 89774.928| |-----------------------------------------------------------------------------| r_work (start): 0.2441 rms_B_bonded: 5.06 r_work: 0.2269 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2270 r_free = 0.2270 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2270 r_free = 0.2270 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14005 Z= 0.108 Angle : 0.603 8.470 19065 Z= 0.296 Chirality : 0.044 0.393 2035 Planarity : 0.005 0.048 2430 Dihedral : 5.019 25.908 2315 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.05 % Allowed : 14.70 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.15 (0.19), residues: 1645 helix: 2.39 (0.75), residues: 55 sheet: 0.94 (0.19), residues: 710 loop : -1.21 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 133 HIS 0.001 0.000 HIS C 62 PHE 0.030 0.001 PHE A 134 TYR 0.009 0.001 TYR C 117 ARG 0.011 0.001 ARG I 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 15) link_NAG-ASN : angle 1.83990 ( 45) link_BETA1-4 : bond 0.01785 ( 5) link_BETA1-4 : angle 5.41293 ( 15) hydrogen bonds : bond 0.02729 ( 395) hydrogen bonds : angle 3.98339 ( 1200) SS BOND : bond 0.00362 ( 15) SS BOND : angle 0.46354 ( 30) covalent geometry : bond 0.00253 (13970) covalent geometry : angle 0.57806 (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 280 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 265 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9372 (m110) cc_final: 0.8968 (m-40) REVERT: A 98 ARG cc_start: 0.9311 (mtm110) cc_final: 0.9057 (mtm110) REVERT: A 172 GLU cc_start: 0.9127 (tt0) cc_final: 0.8668 (tp30) REVERT: B 46 ASN cc_start: 0.9360 (m110) cc_final: 0.8953 (m-40) REVERT: B 98 ARG cc_start: 0.9351 (mtm110) cc_final: 0.9057 (mtm180) REVERT: B 172 GLU cc_start: 0.9107 (tt0) cc_final: 0.8666 (tp30) REVERT: C 70 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8724 (mp0) REVERT: C 172 GLU cc_start: 0.9052 (tt0) cc_final: 0.8576 (tp30) REVERT: D 70 GLU cc_start: 0.8466 (mp0) cc_final: 0.8080 (mp0) REVERT: D 98 ARG cc_start: 0.9290 (mtm180) cc_final: 0.9084 (mtm180) REVERT: D 172 GLU cc_start: 0.8741 (tp30) cc_final: 0.8368 (tp30) REVERT: E 98 ARG cc_start: 0.9337 (mtm180) cc_final: 0.9077 (mtm180) REVERT: E 172 GLU cc_start: 0.9035 (tt0) cc_final: 0.8698 (tp30) REVERT: F 13 GLN cc_start: 0.8466 (tp40) cc_final: 0.7988 (tp40) REVERT: F 16 ASP cc_start: 0.8919 (m-30) cc_final: 0.8502 (m-30) REVERT: F 39 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8059 (tp-100) REVERT: F 73 ASP cc_start: 0.8205 (t70) cc_final: 0.7778 (t0) REVERT: F 85 ASN cc_start: 0.9350 (t0) cc_final: 0.8838 (t0) REVERT: G 13 GLN cc_start: 0.8333 (tp40) cc_final: 0.7739 (tp-100) REVERT: G 16 ASP cc_start: 0.8869 (m-30) cc_final: 0.8414 (m-30) REVERT: G 43 LYS cc_start: 0.8719 (mppt) cc_final: 0.8449 (mppt) REVERT: G 73 ASP cc_start: 0.8320 (t70) cc_final: 0.7276 (t0) REVERT: G 76 LYS cc_start: 0.9570 (mptt) cc_final: 0.9254 (mtmm) REVERT: G 85 ASN cc_start: 0.9333 (t0) cc_final: 0.9055 (t0) REVERT: H 13 GLN cc_start: 0.8329 (tp40) cc_final: 0.7825 (tp-100) REVERT: H 16 ASP cc_start: 0.8990 (m-30) cc_final: 0.8575 (m-30) REVERT: H 39 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8344 (tp-100) REVERT: H 43 LYS cc_start: 0.8444 (mppt) cc_final: 0.8163 (mppt) REVERT: H 85 ASN cc_start: 0.9283 (t0) cc_final: 0.8749 (t0) REVERT: I 13 GLN cc_start: 0.8381 (tp40) cc_final: 0.8023 (tp-100) REVERT: I 16 ASP cc_start: 0.8989 (m-30) cc_final: 0.8642 (m-30) REVERT: I 39 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8281 (tp-100) REVERT: I 43 LYS cc_start: 0.8733 (mppt) cc_final: 0.8291 (mppt) REVERT: I 73 ASP cc_start: 0.8281 (t70) cc_final: 0.7717 (t0) REVERT: I 85 ASN cc_start: 0.9365 (t0) cc_final: 0.9016 (t0) REVERT: I 109 ASP cc_start: 0.9288 (p0) cc_final: 0.9003 (p0) REVERT: J 13 GLN cc_start: 0.8411 (tp40) cc_final: 0.7876 (tp-100) REVERT: J 16 ASP cc_start: 0.8979 (m-30) cc_final: 0.8580 (m-30) REVERT: J 39 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8278 (tp-100) REVERT: J 43 LYS cc_start: 0.8932 (mppt) cc_final: 0.8400 (mppt) REVERT: J 44 GLU cc_start: 0.8659 (mp0) cc_final: 0.8414 (pm20) REVERT: J 73 ASP cc_start: 0.8252 (t70) cc_final: 0.7991 (t0) REVERT: J 85 ASN cc_start: 0.9289 (t0) cc_final: 0.8728 (t0) outliers start: 15 outliers final: 9 residues processed: 274 average time/residue: 1.7891 time to fit residues: 520.5741 Evaluate side-chains 271 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 261 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 95 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain J residue 95 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 122 optimal weight: 9.9990 chunk 44 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 146 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN F 3 GLN H 3 GLN J 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.060855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.043410 restraints weight = 77222.649| |-----------------------------------------------------------------------------| r_work (start): 0.2431 rms_B_bonded: 4.78 r_work: 0.2263 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2266 r_free = 0.2266 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2266 r_free = 0.2266 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9071 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14005 Z= 0.121 Angle : 0.619 8.598 19065 Z= 0.304 Chirality : 0.044 0.397 2035 Planarity : 0.005 0.052 2430 Dihedral : 5.023 24.850 2315 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.91 % Allowed : 15.26 % Favored : 83.83 % 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: -0.13 (0.20), residues: 1645 helix: 2.39 (0.76), residues: 55 sheet: 0.93 (0.19), residues: 710 loop : -1.17 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP D 133 HIS 0.002 0.000 HIS C 62 PHE 0.028 0.001 PHE D 134 TYR 0.009 0.001 TYR E 117 ARG 0.012 0.001 ARG G 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 15) link_NAG-ASN : angle 1.83911 ( 45) link_BETA1-4 : bond 0.01751 ( 5) link_BETA1-4 : angle 5.48436 ( 15) hydrogen bonds : bond 0.02909 ( 395) hydrogen bonds : angle 4.02641 ( 1200) SS BOND : bond 0.00261 ( 15) SS BOND : angle 0.43443 ( 30) covalent geometry : bond 0.00287 (13970) covalent geometry : angle 0.59407 (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 272 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 259 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9370 (m110) cc_final: 0.8956 (m-40) REVERT: A 98 ARG cc_start: 0.9310 (mtm110) cc_final: 0.9053 (mtm110) REVERT: A 172 GLU cc_start: 0.9106 (tt0) cc_final: 0.8649 (tp30) REVERT: B 46 ASN cc_start: 0.9367 (m110) cc_final: 0.8955 (m-40) REVERT: B 98 ARG cc_start: 0.9345 (mtm110) cc_final: 0.9049 (mtm180) REVERT: B 172 GLU cc_start: 0.9099 (tt0) cc_final: 0.8666 (tp30) REVERT: C 70 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8719 (mp0) REVERT: C 172 GLU cc_start: 0.9074 (tt0) cc_final: 0.8629 (tp30) REVERT: D 70 GLU cc_start: 0.8497 (mp0) cc_final: 0.8077 (mp0) REVERT: D 98 ARG cc_start: 0.9302 (mtm180) cc_final: 0.9095 (mtm180) REVERT: D 172 GLU cc_start: 0.8752 (tp30) cc_final: 0.8384 (tp30) REVERT: E 98 ARG cc_start: 0.9336 (mtm180) cc_final: 0.9071 (mtm180) REVERT: E 172 GLU cc_start: 0.9032 (tt0) cc_final: 0.8698 (tp30) REVERT: F 13 GLN cc_start: 0.8448 (tp40) cc_final: 0.7950 (tp-100) REVERT: F 16 ASP cc_start: 0.8922 (m-30) cc_final: 0.8510 (m-30) REVERT: F 39 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8111 (tp-100) REVERT: F 44 GLU cc_start: 0.8370 (mp0) cc_final: 0.8071 (pm20) REVERT: F 73 ASP cc_start: 0.8245 (t70) cc_final: 0.7795 (t0) REVERT: F 85 ASN cc_start: 0.9353 (t0) cc_final: 0.8823 (t0) REVERT: G 13 GLN cc_start: 0.8322 (tp40) cc_final: 0.7722 (tp-100) REVERT: G 16 ASP cc_start: 0.8855 (m-30) cc_final: 0.8389 (m-30) REVERT: G 43 LYS cc_start: 0.8726 (mppt) cc_final: 0.8472 (mppt) REVERT: G 73 ASP cc_start: 0.8355 (t70) cc_final: 0.7268 (t0) REVERT: G 76 LYS cc_start: 0.9569 (mptt) cc_final: 0.9250 (mtmm) REVERT: H 13 GLN cc_start: 0.8323 (tp40) cc_final: 0.7822 (tp-100) REVERT: H 16 ASP cc_start: 0.8956 (m-30) cc_final: 0.8529 (m-30) REVERT: H 39 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8391 (tp-100) REVERT: H 43 LYS cc_start: 0.8491 (mppt) cc_final: 0.8242 (mppt) REVERT: H 85 ASN cc_start: 0.9291 (t0) cc_final: 0.8763 (t0) REVERT: I 13 GLN cc_start: 0.8447 (tp40) cc_final: 0.8072 (tp-100) REVERT: I 16 ASP cc_start: 0.8986 (m-30) cc_final: 0.8647 (m-30) REVERT: I 39 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8321 (tp-100) REVERT: I 43 LYS cc_start: 0.8801 (mppt) cc_final: 0.8296 (mppt) REVERT: I 73 ASP cc_start: 0.8297 (t70) cc_final: 0.7728 (t0) REVERT: I 85 ASN cc_start: 0.9387 (t0) cc_final: 0.9015 (t0) REVERT: I 109 ASP cc_start: 0.9293 (p0) cc_final: 0.8999 (p0) REVERT: J 13 GLN cc_start: 0.8433 (tp40) cc_final: 0.7894 (tp-100) REVERT: J 16 ASP cc_start: 0.8955 (m-30) cc_final: 0.8544 (m-30) REVERT: J 39 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8316 (tp-100) REVERT: J 43 LYS cc_start: 0.8980 (mppt) cc_final: 0.8461 (mppt) REVERT: J 44 GLU cc_start: 0.8684 (mp0) cc_final: 0.8447 (pm20) REVERT: J 73 ASP cc_start: 0.8283 (t70) cc_final: 0.7918 (t0) REVERT: J 85 ASN cc_start: 0.9283 (t0) cc_final: 0.8723 (t0) outliers start: 13 outliers final: 12 residues processed: 268 average time/residue: 1.9314 time to fit residues: 549.0447 Evaluate side-chains 271 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 258 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 95 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 114 CYS 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: 4.9990 chunk 116 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.2875 r_free = 0.2875 target = 0.060717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.043298 restraints weight = 75729.517| |-----------------------------------------------------------------------------| r_work (start): 0.2426 rms_B_bonded: 4.74 r_work: 0.2256 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2256 ------------------------------------------------------------------------------- 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 = 0.44 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 = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14005 Z= 0.121 Angle : 0.618 8.631 19065 Z= 0.304 Chirality : 0.044 0.403 2035 Planarity : 0.005 0.056 2430 Dihedral : 5.017 24.419 2315 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.98 % Allowed : 15.33 % Favored : 83.69 % 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: -0.11 (0.20), residues: 1645 helix: 2.41 (0.76), residues: 55 sheet: 0.94 (0.19), residues: 710 loop : -1.16 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 133 HIS 0.002 0.000 HIS C 62 PHE 0.028 0.001 PHE C 134 TYR 0.009 0.001 TYR E 117 ARG 0.013 0.001 ARG J 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 15) link_NAG-ASN : angle 1.83256 ( 45) link_BETA1-4 : bond 0.01756 ( 5) link_BETA1-4 : angle 5.50446 ( 15) hydrogen bonds : bond 0.02927 ( 395) hydrogen bonds : angle 4.03495 ( 1200) SS BOND : bond 0.00219 ( 15) SS BOND : angle 0.40834 ( 30) covalent geometry : bond 0.00288 (13970) covalent geometry : angle 0.59315 (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 276 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 262 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9360 (m110) cc_final: 0.8949 (m-40) REVERT: A 98 ARG cc_start: 0.9323 (mtm110) cc_final: 0.9064 (mtm110) REVERT: A 172 GLU cc_start: 0.9121 (tt0) cc_final: 0.8653 (tp30) REVERT: B 46 ASN cc_start: 0.9351 (m110) cc_final: 0.8942 (m-40) REVERT: B 98 ARG cc_start: 0.9351 (mtm110) cc_final: 0.9053 (mtm180) REVERT: B 172 GLU cc_start: 0.9103 (tt0) cc_final: 0.8667 (tp30) REVERT: C 70 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8745 (mp0) REVERT: C 172 GLU cc_start: 0.9067 (tt0) cc_final: 0.8637 (tp30) REVERT: D 70 GLU cc_start: 0.8513 (mp0) cc_final: 0.8089 (mp0) REVERT: D 98 ARG cc_start: 0.9311 (mtm180) cc_final: 0.9105 (mtm180) REVERT: D 172 GLU cc_start: 0.8782 (tp30) cc_final: 0.8415 (tp30) REVERT: E 70 GLU cc_start: 0.8919 (mp0) cc_final: 0.8707 (mp0) REVERT: E 98 ARG cc_start: 0.9339 (mtm180) cc_final: 0.9075 (mtm180) REVERT: E 172 GLU cc_start: 0.9053 (tt0) cc_final: 0.8670 (tp30) REVERT: F 13 GLN cc_start: 0.8439 (tp40) cc_final: 0.7862 (tp-100) REVERT: F 16 ASP cc_start: 0.8919 (m-30) cc_final: 0.8470 (m-30) REVERT: F 39 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8104 (tp-100) REVERT: F 43 LYS cc_start: 0.8476 (mppt) cc_final: 0.7882 (mppt) REVERT: F 44 GLU cc_start: 0.8389 (mp0) cc_final: 0.8092 (pm20) REVERT: F 73 ASP cc_start: 0.8261 (t70) cc_final: 0.7802 (t0) REVERT: F 85 ASN cc_start: 0.9350 (t0) cc_final: 0.8842 (t0) REVERT: G 13 GLN cc_start: 0.8319 (tp40) cc_final: 0.7698 (tp-100) REVERT: G 16 ASP cc_start: 0.8841 (m-30) cc_final: 0.8387 (m-30) REVERT: G 43 LYS cc_start: 0.8731 (mppt) cc_final: 0.8317 (mppt) REVERT: G 73 ASP cc_start: 0.8358 (t70) cc_final: 0.7306 (t0) REVERT: G 76 LYS cc_start: 0.9573 (mptt) cc_final: 0.9261 (mtmm) REVERT: H 13 GLN cc_start: 0.8305 (tp40) cc_final: 0.7798 (tp-100) REVERT: H 16 ASP cc_start: 0.8946 (m-30) cc_final: 0.8518 (m-30) REVERT: H 39 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8233 (tp-100) REVERT: H 43 LYS cc_start: 0.8486 (mppt) cc_final: 0.8155 (mppt) REVERT: H 73 ASP cc_start: 0.8193 (t70) cc_final: 0.7392 (t0) REVERT: H 76 LYS cc_start: 0.9502 (mtmm) cc_final: 0.9015 (mtmm) REVERT: H 85 ASN cc_start: 0.9286 (t0) cc_final: 0.8758 (t0) REVERT: I 13 GLN cc_start: 0.8440 (tp40) cc_final: 0.8084 (tp-100) REVERT: I 16 ASP cc_start: 0.8983 (m-30) cc_final: 0.8642 (m-30) REVERT: I 39 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8306 (tp-100) REVERT: I 43 LYS cc_start: 0.8793 (mppt) cc_final: 0.8274 (mppt) REVERT: I 73 ASP cc_start: 0.8304 (t70) cc_final: 0.7740 (t0) REVERT: I 85 ASN cc_start: 0.9364 (t0) cc_final: 0.9011 (t0) REVERT: I 109 ASP cc_start: 0.9303 (p0) cc_final: 0.9011 (p0) REVERT: J 13 GLN cc_start: 0.8448 (tp40) cc_final: 0.7904 (tp-100) REVERT: J 16 ASP cc_start: 0.8934 (m-30) cc_final: 0.8515 (m-30) REVERT: J 39 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8291 (tp-100) REVERT: J 43 LYS cc_start: 0.8999 (mppt) cc_final: 0.8473 (mppt) REVERT: J 44 GLU cc_start: 0.8708 (mp0) cc_final: 0.8468 (pm20) REVERT: J 73 ASP cc_start: 0.8295 (t70) cc_final: 0.7932 (t0) REVERT: J 85 ASN cc_start: 0.9265 (t0) cc_final: 0.8698 (t0) outliers start: 14 outliers final: 11 residues processed: 272 average time/residue: 1.9146 time to fit residues: 551.9642 Evaluate side-chains 270 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 258 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 12 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 55 optimal weight: 0.0980 chunk 120 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 0.0070 chunk 132 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 34 optimal weight: 0.0270 chunk 113 optimal weight: 3.9990 overall best weight: 1.0058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 52 ASN F 3 GLN H 3 GLN J 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.060866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.043626 restraints weight = 67598.014| |-----------------------------------------------------------------------------| r_work (start): 0.2438 rms_B_bonded: 4.54 r_work: 0.2278 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2280 r_free = 0.2280 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2280 r_free = 0.2280 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14005 Z= 0.116 Angle : 0.618 8.597 19065 Z= 0.304 Chirality : 0.044 0.402 2035 Planarity : 0.005 0.056 2430 Dihedral : 4.978 24.579 2315 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.77 % Allowed : 15.40 % Favored : 83.83 % 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: -0.10 (0.20), residues: 1645 helix: 2.27 (0.75), residues: 55 sheet: 0.95 (0.19), residues: 710 loop : -1.14 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 133 HIS 0.001 0.000 HIS C 62 PHE 0.030 0.001 PHE A 134 TYR 0.008 0.001 TYR C 117 ARG 0.013 0.001 ARG I 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 15) link_NAG-ASN : angle 1.82061 ( 45) link_BETA1-4 : bond 0.01786 ( 5) link_BETA1-4 : angle 5.48976 ( 15) hydrogen bonds : bond 0.02823 ( 395) hydrogen bonds : angle 4.02456 ( 1200) SS BOND : bond 0.00201 ( 15) SS BOND : angle 0.40663 ( 30) covalent geometry : bond 0.00275 (13970) covalent geometry : angle 0.59305 (18975) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11306.17 seconds wall clock time: 194 minutes 47.43 seconds (11687.43 seconds total)