Starting phenix.real_space_refine on Mon Dec 30 18:33:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ci1_16665/12_2024/8ci1_16665_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ci1_16665/12_2024/8ci1_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_16665/12_2024/8ci1_16665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ci1_16665/12_2024/8ci1_16665.map" model { file = "/net/cci-nas-00/data/ceres_data/8ci1_16665/12_2024/8ci1_16665_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ci1_16665/12_2024/8ci1_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-5532/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: 11.38, per 1000 atoms: 0.84 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: 3.21 Conformation dependent library (CDL) restraints added in 2.7 seconds 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3080 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 30 sheets defined 5.8% alpha, 43.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 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: 4.39 Time building geometry restraints manager: 3.73 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 208 or resid 401 throug \ h 403)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 208 or resid 401 throug \ h 403)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 208 or resid 401 throug \ h 403)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 208 or resid 401 throug \ h 403)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 208 or resid 401 throug \ h 403)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 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: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 37.090 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 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:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.150 ------------------------------------------------------------------------------- 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 13970 Z= 0.162 Angle : 0.467 5.079 18975 Z= 0.258 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 *********************** 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 : 1.619 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: 1.8581 time to fit residues: 643.8428 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 : 1.669 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9172 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 13970 Z= 0.289 Angle : 0.678 8.531 18975 Z= 0.335 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 *********************** 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 : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9406 (m110) cc_final: 0.9070 (m-40) REVERT: A 75 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.9099 (mtpp) REVERT: B 46 ASN cc_start: 0.9442 (m110) cc_final: 0.9130 (m-40) REVERT: B 75 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8782 (mtpp) REVERT: F 13 GLN cc_start: 0.8413 (tp40) cc_final: 0.7944 (tp-100) REVERT: F 16 ASP cc_start: 0.8755 (m-30) cc_final: 0.8529 (m-30) REVERT: F 85 ASN cc_start: 0.9285 (t0) cc_final: 0.8602 (t0) REVERT: F 87 LYS cc_start: 0.9346 (mttt) cc_final: 0.9007 (mttm) REVERT: G 13 GLN cc_start: 0.8313 (tp40) cc_final: 0.7859 (tp-100) REVERT: G 85 ASN cc_start: 0.9284 (t0) cc_final: 0.8905 (t0) REVERT: H 13 GLN cc_start: 0.8340 (tp40) cc_final: 0.7870 (tp-100) REVERT: H 16 ASP cc_start: 0.8718 (m-30) cc_final: 0.8463 (m-30) REVERT: I 13 GLN cc_start: 0.8343 (tp40) cc_final: 0.7908 (tp-100) REVERT: I 16 ASP cc_start: 0.8802 (m-30) cc_final: 0.8594 (m-30) REVERT: I 85 ASN cc_start: 0.9263 (t0) cc_final: 0.8726 (t0) REVERT: I 87 LYS cc_start: 0.9276 (mttt) cc_final: 0.8992 (mttm) REVERT: J 13 GLN cc_start: 0.8397 (tp40) cc_final: 0.7894 (tp-100) REVERT: J 16 ASP cc_start: 0.8852 (m-30) cc_final: 0.8643 (m-30) REVERT: J 85 ASN cc_start: 0.9301 (t0) cc_final: 0.8775 (t0) outliers start: 10 outliers final: 0 residues processed: 274 average time/residue: 2.0894 time to fit residues: 604.9336 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 : 1.450 ------------------------------------------------------------------------------- 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 80 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9156 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13970 Z= 0.178 Angle : 0.592 8.654 18975 Z= 0.294 Chirality : 0.046 0.336 2035 Planarity : 0.004 0.031 2430 Dihedral : 5.601 31.682 2315 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.39 % Allowed : 11.78 % Favored : 86.83 % 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: -0.23 (0.19), residues: 1645 helix: 3.51 (0.74), residues: 50 sheet: 0.70 (0.19), residues: 710 loop : -1.12 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 133 HIS 0.002 0.000 HIS A 62 PHE 0.026 0.001 PHE A 134 TYR 0.011 0.001 TYR B 117 ARG 0.008 0.001 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 256 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9405 (m110) cc_final: 0.9068 (m-40) REVERT: A 75 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.9069 (mtpp) REVERT: B 46 ASN cc_start: 0.9434 (m110) cc_final: 0.9096 (m-40) REVERT: F 13 GLN cc_start: 0.8447 (tp40) cc_final: 0.8016 (tp-100) REVERT: F 16 ASP cc_start: 0.8741 (m-30) cc_final: 0.8531 (m-30) REVERT: F 85 ASN cc_start: 0.9303 (t0) cc_final: 0.8903 (t0) REVERT: G 13 GLN cc_start: 0.8278 (tp40) cc_final: 0.8041 (tp-100) REVERT: G 85 ASN cc_start: 0.9286 (t0) cc_final: 0.8802 (t0) REVERT: G 87 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8772 (mttp) REVERT: H 13 GLN cc_start: 0.8393 (tp40) cc_final: 0.7857 (tp-100) REVERT: H 16 ASP cc_start: 0.8752 (m-30) cc_final: 0.8456 (m-30) REVERT: H 76 LYS cc_start: 0.9409 (mtmm) cc_final: 0.8963 (mtmm) REVERT: I 13 GLN cc_start: 0.8325 (tp40) cc_final: 0.7864 (tp-100) REVERT: I 16 ASP cc_start: 0.8811 (m-30) cc_final: 0.8600 (m-30) REVERT: I 76 LYS cc_start: 0.9391 (mtmm) cc_final: 0.8895 (mtmm) REVERT: I 85 ASN cc_start: 0.9268 (t0) cc_final: 0.9056 (t0) REVERT: J 13 GLN cc_start: 0.8437 (tp40) cc_final: 0.7910 (tp-100) REVERT: J 76 LYS cc_start: 0.9359 (mtmm) cc_final: 0.9003 (mtmm) REVERT: J 85 ASN cc_start: 0.9280 (t0) cc_final: 0.8760 (t0) outliers start: 20 outliers final: 1 residues processed: 264 average time/residue: 2.0473 time to fit residues: 571.6140 Evaluate side-chains 253 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 250 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain G residue 87 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.0770 chunk 109 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 97 optimal weight: 0.5980 chunk 146 optimal weight: 8.9990 chunk 154 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN J 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9169 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13970 Z= 0.215 Angle : 0.610 8.004 18975 Z= 0.304 Chirality : 0.046 0.350 2035 Planarity : 0.005 0.039 2430 Dihedral : 5.483 29.752 2315 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.98 % Allowed : 12.54 % 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: -0.27 (0.19), residues: 1645 helix: 3.30 (0.74), residues: 50 sheet: 0.72 (0.19), residues: 710 loop : -1.19 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 133 HIS 0.002 0.000 HIS A 62 PHE 0.026 0.001 PHE A 134 TYR 0.010 0.001 TYR E 117 ARG 0.009 0.001 ARG B 185 *********************** 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 270 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 256 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9414 (m110) cc_final: 0.9075 (m-40) REVERT: A 75 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.9049 (mtpp) REVERT: B 46 ASN cc_start: 0.9433 (m110) cc_final: 0.9093 (m-40) REVERT: F 13 GLN cc_start: 0.8457 (tp40) cc_final: 0.8020 (tp-100) REVERT: F 16 ASP cc_start: 0.8766 (m-30) cc_final: 0.8534 (m-30) REVERT: F 73 ASP cc_start: 0.8473 (t70) cc_final: 0.8244 (t0) REVERT: F 85 ASN cc_start: 0.9316 (t0) cc_final: 0.8888 (t0) REVERT: G 13 GLN cc_start: 0.8254 (tp40) cc_final: 0.8024 (tp-100) REVERT: G 73 ASP cc_start: 0.8481 (t70) cc_final: 0.7553 (t0) REVERT: G 85 ASN cc_start: 0.9313 (t0) cc_final: 0.8804 (t0) REVERT: G 87 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8787 (mttp) REVERT: H 13 GLN cc_start: 0.8373 (tp40) cc_final: 0.7868 (tp-100) REVERT: H 16 ASP cc_start: 0.8733 (m-30) cc_final: 0.8483 (m-30) REVERT: H 85 ASN cc_start: 0.9241 (t0) cc_final: 0.8740 (t0) REVERT: I 13 GLN cc_start: 0.8304 (tp40) cc_final: 0.7849 (tp-100) REVERT: I 16 ASP cc_start: 0.8818 (m-30) cc_final: 0.8607 (m-30) REVERT: I 76 LYS cc_start: 0.9386 (mtmm) cc_final: 0.8969 (mtmm) REVERT: I 85 ASN cc_start: 0.9301 (t0) cc_final: 0.9051 (t0) REVERT: J 13 GLN cc_start: 0.8325 (tp40) cc_final: 0.8026 (tp-100) REVERT: J 76 LYS cc_start: 0.9375 (mtmm) cc_final: 0.8964 (mtmm) REVERT: J 85 ASN cc_start: 0.9307 (t0) cc_final: 0.8795 (t0) outliers start: 14 outliers final: 5 residues processed: 263 average time/residue: 2.0605 time to fit residues: 573.2504 Evaluate side-chains 260 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 253 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 203 MET 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 128 optimal weight: 9.9990 chunk 87 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 39 optimal weight: 0.0040 overall best weight: 1.8398 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9182 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13970 Z= 0.235 Angle : 0.599 7.461 18975 Z= 0.300 Chirality : 0.045 0.315 2035 Planarity : 0.005 0.043 2430 Dihedral : 5.447 28.781 2315 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.32 % Allowed : 12.47 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.19), residues: 1645 helix: 3.22 (0.74), residues: 50 sheet: 0.75 (0.19), residues: 710 loop : -1.24 (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 0.027 0.001 PHE A 134 TYR 0.010 0.001 TYR G 94 ARG 0.010 0.001 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 256 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9408 (m110) cc_final: 0.9060 (m-40) REVERT: A 75 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9090 (mtpp) REVERT: B 46 ASN cc_start: 0.9431 (m110) cc_final: 0.9088 (m-40) REVERT: C 70 GLU cc_start: 0.8529 (mp0) cc_final: 0.8265 (mp0) REVERT: F 13 GLN cc_start: 0.8446 (tp40) cc_final: 0.7996 (tp-100) REVERT: F 16 ASP cc_start: 0.8759 (m-30) cc_final: 0.8492 (m-30) REVERT: F 73 ASP cc_start: 0.8532 (t70) cc_final: 0.8246 (t0) REVERT: F 85 ASN cc_start: 0.9332 (t0) cc_final: 0.8871 (t0) REVERT: G 13 GLN cc_start: 0.8221 (tp40) cc_final: 0.7983 (tp-100) REVERT: G 76 LYS cc_start: 0.9393 (mtmm) cc_final: 0.9041 (mtmm) REVERT: G 85 ASN cc_start: 0.9322 (t0) cc_final: 0.8994 (t0) REVERT: G 87 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8850 (mttp) REVERT: H 13 GLN cc_start: 0.8384 (tp40) cc_final: 0.7891 (tp-100) REVERT: H 16 ASP cc_start: 0.8748 (m-30) cc_final: 0.8467 (m-30) REVERT: H 85 ASN cc_start: 0.9247 (t0) cc_final: 0.8741 (t0) REVERT: I 13 GLN cc_start: 0.8359 (tp40) cc_final: 0.7906 (tp-100) REVERT: I 16 ASP cc_start: 0.8820 (m-30) cc_final: 0.8604 (m-30) REVERT: I 76 LYS cc_start: 0.9387 (mtmm) cc_final: 0.8934 (mtmm) REVERT: I 85 ASN cc_start: 0.9308 (t0) cc_final: 0.9047 (t0) REVERT: I 109 ASP cc_start: 0.8970 (p0) cc_final: 0.8715 (p0) REVERT: J 13 GLN cc_start: 0.8226 (tp40) cc_final: 0.7941 (tp-100) REVERT: J 76 LYS cc_start: 0.9385 (mtmm) cc_final: 0.8931 (mtmm) REVERT: J 85 ASN cc_start: 0.9306 (t0) cc_final: 0.8799 (t0) outliers start: 19 outliers final: 8 residues processed: 265 average time/residue: 2.0723 time to fit residues: 580.8493 Evaluate side-chains 262 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 252 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 203 MET 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 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 52 optimal weight: 0.7980 chunk 139 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN H 3 GLN J 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9170 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13970 Z= 0.200 Angle : 0.615 7.768 18975 Z= 0.308 Chirality : 0.044 0.288 2035 Planarity : 0.005 0.043 2430 Dihedral : 5.390 28.440 2315 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.05 % Allowed : 13.94 % Favored : 85.02 % 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: 3.24 (0.74), residues: 50 sheet: 0.79 (0.19), residues: 710 loop : -1.24 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 133 HIS 0.002 0.000 HIS A 62 PHE 0.027 0.001 PHE D 134 TYR 0.009 0.001 TYR E 117 ARG 0.010 0.001 ARG J 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 258 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9404 (m110) cc_final: 0.9061 (m-40) REVERT: A 75 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.9076 (mtpp) REVERT: B 46 ASN cc_start: 0.9438 (m110) cc_final: 0.9110 (m-40) REVERT: C 70 GLU cc_start: 0.8539 (mp0) cc_final: 0.8329 (mp0) REVERT: D 206 ARG cc_start: 0.8371 (mtm-85) cc_final: 0.8125 (mtm-85) REVERT: F 13 GLN cc_start: 0.8464 (tp40) cc_final: 0.8017 (tp-100) REVERT: F 16 ASP cc_start: 0.8759 (m-30) cc_final: 0.8493 (m-30) REVERT: F 73 ASP cc_start: 0.8541 (t70) cc_final: 0.8217 (t0) REVERT: F 85 ASN cc_start: 0.9334 (t0) cc_final: 0.8875 (t0) REVERT: G 13 GLN cc_start: 0.8198 (tp40) cc_final: 0.7957 (tp-100) REVERT: G 76 LYS cc_start: 0.9402 (mtmm) cc_final: 0.9067 (mtmm) REVERT: G 85 ASN cc_start: 0.9328 (t0) cc_final: 0.9064 (t0) REVERT: H 13 GLN cc_start: 0.8387 (tp40) cc_final: 0.7872 (tp-100) REVERT: H 16 ASP cc_start: 0.8764 (m-30) cc_final: 0.8477 (m-30) REVERT: H 85 ASN cc_start: 0.9252 (t0) cc_final: 0.8748 (t0) REVERT: I 13 GLN cc_start: 0.8367 (tp40) cc_final: 0.7953 (tp-100) REVERT: I 16 ASP cc_start: 0.8812 (m-30) cc_final: 0.8583 (m-30) REVERT: I 76 LYS cc_start: 0.9395 (mtmm) cc_final: 0.8948 (mtmm) REVERT: I 85 ASN cc_start: 0.9308 (t0) cc_final: 0.9055 (t0) REVERT: I 109 ASP cc_start: 0.8985 (p0) cc_final: 0.8699 (p0) REVERT: J 13 GLN cc_start: 0.8180 (tp40) cc_final: 0.7903 (tp-100) REVERT: J 76 LYS cc_start: 0.9390 (mtmm) cc_final: 0.8954 (mtmm) REVERT: J 85 ASN cc_start: 0.9290 (t0) cc_final: 0.8785 (t0) outliers start: 15 outliers final: 8 residues processed: 268 average time/residue: 2.0009 time to fit residues: 567.7519 Evaluate side-chains 261 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 252 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain G residue 95 CYS Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 11 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 149 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 88 optimal weight: 0.0870 chunk 113 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9206 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13970 Z= 0.289 Angle : 0.636 7.676 18975 Z= 0.320 Chirality : 0.046 0.282 2035 Planarity : 0.005 0.052 2430 Dihedral : 5.477 26.999 2315 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.46 % Allowed : 13.87 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.19), residues: 1645 helix: 2.87 (0.72), residues: 50 sheet: 0.76 (0.19), residues: 710 loop : -1.23 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 133 HIS 0.003 0.001 HIS A 62 PHE 0.027 0.001 PHE E 134 TYR 0.011 0.001 TYR I 94 ARG 0.013 0.001 ARG F 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 255 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9407 (m110) cc_final: 0.9054 (m-40) REVERT: A 75 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.9103 (mtpp) REVERT: B 46 ASN cc_start: 0.9442 (m110) cc_final: 0.9103 (m-40) REVERT: C 70 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: F 13 GLN cc_start: 0.8447 (tp40) cc_final: 0.8011 (tp-100) REVERT: F 16 ASP cc_start: 0.8738 (m-30) cc_final: 0.8409 (m-30) REVERT: F 73 ASP cc_start: 0.8607 (t70) cc_final: 0.8249 (t0) REVERT: F 85 ASN cc_start: 0.9355 (t0) cc_final: 0.8879 (t0) REVERT: G 13 GLN cc_start: 0.8200 (tp40) cc_final: 0.7958 (tp-100) REVERT: G 73 ASP cc_start: 0.8599 (t70) cc_final: 0.8245 (t0) REVERT: H 13 GLN cc_start: 0.8393 (tp40) cc_final: 0.7827 (tp-100) REVERT: H 16 ASP cc_start: 0.8710 (m-30) cc_final: 0.8422 (m-30) REVERT: H 85 ASN cc_start: 0.9272 (t0) cc_final: 0.8756 (t0) REVERT: I 13 GLN cc_start: 0.8424 (tp40) cc_final: 0.8053 (tp-100) REVERT: I 16 ASP cc_start: 0.8772 (m-30) cc_final: 0.8537 (m-30) REVERT: I 73 ASP cc_start: 0.8553 (t70) cc_final: 0.7519 (t0) REVERT: I 76 LYS cc_start: 0.9410 (mtmm) cc_final: 0.8903 (mtmm) REVERT: I 85 ASN cc_start: 0.9348 (t0) cc_final: 0.9076 (t0) REVERT: I 109 ASP cc_start: 0.9011 (p0) cc_final: 0.8725 (p0) REVERT: J 13 GLN cc_start: 0.8196 (tp40) cc_final: 0.7901 (tp-100) REVERT: J 73 ASP cc_start: 0.8603 (t70) cc_final: 0.8353 (t0) REVERT: J 85 ASN cc_start: 0.9299 (t0) cc_final: 0.8805 (t0) outliers start: 21 outliers final: 11 residues processed: 268 average time/residue: 2.0212 time to fit residues: 574.1031 Evaluate side-chains 264 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 251 time to evaluate : 1.501 ------------------------------------------------------------------------------- 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 F residue 95 CYS 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 H residue 120 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain J residue 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 95 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 98 optimal weight: 0.0470 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9172 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13970 Z= 0.193 Angle : 0.636 8.211 18975 Z= 0.320 Chirality : 0.044 0.262 2035 Planarity : 0.005 0.046 2430 Dihedral : 5.367 27.662 2315 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.05 % Allowed : 15.26 % 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: -0.21 (0.19), residues: 1645 helix: 3.10 (0.75), residues: 50 sheet: 0.86 (0.19), residues: 710 loop : -1.24 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 133 HIS 0.002 0.000 HIS A 62 PHE 0.029 0.001 PHE A 134 TYR 0.008 0.001 TYR C 117 ARG 0.011 0.001 ARG I 108 *********************** 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 271 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 256 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9402 (m110) cc_final: 0.9040 (m-40) REVERT: A 75 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.9044 (mtpp) REVERT: B 46 ASN cc_start: 0.9432 (m110) cc_final: 0.9083 (m-40) REVERT: C 70 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8404 (mp0) REVERT: F 13 GLN cc_start: 0.8426 (tp40) cc_final: 0.7954 (tp-100) REVERT: F 16 ASP cc_start: 0.8734 (m-30) cc_final: 0.8423 (m-30) REVERT: F 73 ASP cc_start: 0.8589 (t70) cc_final: 0.8232 (t0) REVERT: F 85 ASN cc_start: 0.9339 (t0) cc_final: 0.8850 (t0) REVERT: G 13 GLN cc_start: 0.8181 (tp40) cc_final: 0.7944 (tp-100) REVERT: G 73 ASP cc_start: 0.8596 (t70) cc_final: 0.8256 (t0) REVERT: H 13 GLN cc_start: 0.8376 (tp40) cc_final: 0.7837 (tp-100) REVERT: H 16 ASP cc_start: 0.8720 (m-30) cc_final: 0.8449 (m-30) REVERT: H 76 LYS cc_start: 0.9382 (mtmm) cc_final: 0.8941 (mtmm) REVERT: H 85 ASN cc_start: 0.9266 (t0) cc_final: 0.8760 (t0) REVERT: I 13 GLN cc_start: 0.8433 (tp40) cc_final: 0.8088 (tp-100) REVERT: I 16 ASP cc_start: 0.8755 (m-30) cc_final: 0.8535 (m-30) REVERT: I 73 ASP cc_start: 0.8538 (t70) cc_final: 0.7446 (t0) REVERT: I 76 LYS cc_start: 0.9410 (mtmm) cc_final: 0.8904 (mtmm) REVERT: I 85 ASN cc_start: 0.9320 (t0) cc_final: 0.9047 (t0) REVERT: I 109 ASP cc_start: 0.8997 (p0) cc_final: 0.8704 (p0) REVERT: J 13 GLN cc_start: 0.8163 (tp40) cc_final: 0.7894 (tp-100) REVERT: J 73 ASP cc_start: 0.8580 (t70) cc_final: 0.8320 (t0) REVERT: J 85 ASN cc_start: 0.9273 (t0) cc_final: 0.8777 (t0) outliers start: 15 outliers final: 9 residues processed: 265 average time/residue: 2.0753 time to fit residues: 583.0866 Evaluate side-chains 264 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 253 time to evaluate : 1.528 ------------------------------------------------------------------------------- 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 203 MET Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain F residue 95 CYS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 44 optimal weight: 0.0770 chunk 129 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9193 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13970 Z= 0.240 Angle : 0.632 8.277 18975 Z= 0.317 Chirality : 0.045 0.382 2035 Planarity : 0.005 0.064 2430 Dihedral : 5.348 26.258 2315 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.11 % Allowed : 15.26 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.19), residues: 1645 helix: 2.87 (0.74), residues: 50 sheet: 0.84 (0.19), residues: 710 loop : -1.24 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 133 HIS 0.002 0.000 HIS A 62 PHE 0.028 0.001 PHE E 134 TYR 0.008 0.001 TYR B 117 ARG 0.012 0.001 ARG H 108 *********************** 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 267 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 251 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9408 (m110) cc_final: 0.9061 (m-40) REVERT: A 75 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9049 (mtpp) REVERT: B 46 ASN cc_start: 0.9445 (m110) cc_final: 0.9093 (m-40) REVERT: C 70 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8409 (mp0) REVERT: F 13 GLN cc_start: 0.8403 (tp40) cc_final: 0.7831 (tp-100) REVERT: F 16 ASP cc_start: 0.8718 (m-30) cc_final: 0.8385 (m-30) REVERT: F 43 LYS cc_start: 0.8730 (mppt) cc_final: 0.8468 (mppt) REVERT: F 73 ASP cc_start: 0.8633 (t70) cc_final: 0.8287 (t0) REVERT: F 85 ASN cc_start: 0.9349 (t0) cc_final: 0.8853 (t0) REVERT: G 13 GLN cc_start: 0.8183 (tp40) cc_final: 0.7942 (tp-100) REVERT: G 73 ASP cc_start: 0.8628 (t70) cc_final: 0.8290 (t0) REVERT: H 13 GLN cc_start: 0.8362 (tp40) cc_final: 0.7799 (tp-100) REVERT: H 16 ASP cc_start: 0.8708 (m-30) cc_final: 0.8412 (m-30) REVERT: H 76 LYS cc_start: 0.9382 (mtmm) cc_final: 0.8938 (mtmm) REVERT: H 85 ASN cc_start: 0.9269 (t0) cc_final: 0.8757 (t0) REVERT: I 13 GLN cc_start: 0.8453 (tp40) cc_final: 0.8117 (tp-100) REVERT: I 16 ASP cc_start: 0.8765 (m-30) cc_final: 0.8549 (m-30) REVERT: I 73 ASP cc_start: 0.8573 (t70) cc_final: 0.7455 (t0) REVERT: I 76 LYS cc_start: 0.9414 (mtmm) cc_final: 0.8900 (mtmm) REVERT: I 85 ASN cc_start: 0.9341 (t0) cc_final: 0.9061 (t0) REVERT: I 109 ASP cc_start: 0.9005 (p0) cc_final: 0.8724 (p0) REVERT: J 13 GLN cc_start: 0.8203 (tp40) cc_final: 0.7934 (tp-100) REVERT: J 73 ASP cc_start: 0.8611 (t70) cc_final: 0.8328 (t0) REVERT: J 85 ASN cc_start: 0.9276 (t0) cc_final: 0.8787 (t0) outliers start: 16 outliers final: 9 residues processed: 261 average time/residue: 1.9984 time to fit residues: 552.0480 Evaluate side-chains 260 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 249 time to evaluate : 1.650 ------------------------------------------------------------------------------- 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 203 MET Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 12 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 159 optimal weight: 8.9990 chunk 146 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 98 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9182 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13970 Z= 0.223 Angle : 0.654 8.659 18975 Z= 0.330 Chirality : 0.045 0.376 2035 Planarity : 0.005 0.057 2430 Dihedral : 5.320 26.217 2315 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.84 % Allowed : 15.96 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.19), residues: 1645 helix: 2.77 (0.74), residues: 50 sheet: 0.87 (0.19), residues: 710 loop : -1.24 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 133 HIS 0.002 0.000 HIS A 62 PHE 0.028 0.001 PHE C 134 TYR 0.008 0.001 TYR B 117 ARG 0.013 0.001 ARG J 108 ********************** 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 262 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 250 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: 0.9401 (m110) cc_final: 0.9037 (m-40) REVERT: A 75 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.9039 (mtpp) REVERT: B 46 ASN cc_start: 0.9441 (m110) cc_final: 0.9091 (m-40) REVERT: C 70 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8424 (mp0) REVERT: F 13 GLN cc_start: 0.8399 (tp40) cc_final: 0.7833 (tp-100) REVERT: F 16 ASP cc_start: 0.8718 (m-30) cc_final: 0.8389 (m-30) REVERT: F 73 ASP cc_start: 0.8635 (t70) cc_final: 0.8292 (t0) REVERT: F 85 ASN cc_start: 0.9342 (t0) cc_final: 0.8838 (t0) REVERT: G 13 GLN cc_start: 0.8179 (tp40) cc_final: 0.7936 (tp-100) REVERT: G 73 ASP cc_start: 0.8633 (t70) cc_final: 0.8316 (t0) REVERT: H 13 GLN cc_start: 0.8351 (tp40) cc_final: 0.7793 (tp-100) REVERT: H 16 ASP cc_start: 0.8686 (m-30) cc_final: 0.8395 (m-30) REVERT: H 76 LYS cc_start: 0.9379 (mtmm) cc_final: 0.8934 (mtmm) REVERT: H 85 ASN cc_start: 0.9267 (t0) cc_final: 0.8763 (t0) REVERT: I 13 GLN cc_start: 0.8455 (tp40) cc_final: 0.8124 (tp-100) REVERT: I 16 ASP cc_start: 0.8765 (m-30) cc_final: 0.8550 (m-30) REVERT: I 73 ASP cc_start: 0.8571 (t70) cc_final: 0.7455 (t0) REVERT: I 76 LYS cc_start: 0.9409 (mtmm) cc_final: 0.8877 (mtmm) REVERT: I 85 ASN cc_start: 0.9332 (t0) cc_final: 0.9055 (t0) REVERT: I 109 ASP cc_start: 0.9004 (p0) cc_final: 0.8722 (p0) REVERT: J 13 GLN cc_start: 0.8165 (tp40) cc_final: 0.7908 (tp-100) REVERT: J 73 ASP cc_start: 0.8609 (t70) cc_final: 0.8330 (t0) REVERT: J 85 ASN cc_start: 0.9260 (t0) cc_final: 0.8765 (t0) outliers start: 12 outliers final: 10 residues processed: 258 average time/residue: 1.9980 time to fit residues: 545.6433 Evaluate side-chains 259 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 247 time to evaluate : 1.547 ------------------------------------------------------------------------------- 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 203 MET Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 53 optimal weight: 0.0470 chunk 130 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 overall best weight: 1.7682 ------------------------------------------------------------------------------- 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 = 0.060404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.042983 restraints weight = 82563.064| |-----------------------------------------------------------------------------| r_work (start): 0.2400 rms_B_bonded: 4.89 r_work: 0.2222 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2231 r_free = 0.2231 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2231 r_free = 0.2231 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13970 Z= 0.240 Angle : 0.646 8.341 18975 Z= 0.325 Chirality : 0.045 0.377 2035 Planarity : 0.005 0.057 2430 Dihedral : 5.310 25.541 2315 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.91 % Allowed : 15.75 % Favored : 83.34 % 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: 2.70 (0.74), residues: 50 sheet: 0.84 (0.19), residues: 710 loop : -1.25 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 133 HIS 0.002 0.000 HIS A 62 PHE 0.028 0.001 PHE A 134 TYR 0.008 0.001 TYR B 117 ARG 0.014 0.001 ARG I 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7767.88 seconds wall clock time: 138 minutes 53.45 seconds (8333.45 seconds total)