Starting phenix.real_space_refine on Mon Aug 25 04:45:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sk7_40557/08_2025/8sk7_40557_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sk7_40557/08_2025/8sk7_40557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sk7_40557/08_2025/8sk7_40557_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sk7_40557/08_2025/8sk7_40557_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sk7_40557/08_2025/8sk7_40557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sk7_40557/08_2025/8sk7_40557.map" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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: 5 Type Number sf(0) Gaussians S 54 5.16 5 C 8280 2.51 5 N 2256 2.21 5 O 2547 1.98 5 H 12267 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25404 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 4928 Classifications: {'peptide': 321} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 304} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2469 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "X" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 948 Classifications: {'peptide': 65} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 64} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 4928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 4928 Classifications: {'peptide': 321} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 304} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2469 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "Y" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 948 Classifications: {'peptide': 65} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 64} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 4928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 4928 Classifications: {'peptide': 321} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 304} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "I" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2469 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "Z" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 948 Classifications: {'peptide': 65} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 64} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.52, per 1000 atoms: 0.14 Number of scatterers: 25404 At special positions: 0 Unit cell: (87.98, 90.47, 143.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 O 2547 8.00 N 2256 7.00 C 8280 6.00 H 12267 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS G 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 145 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS G 144 " - pdb=" SG CYS G 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS H 137 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 77 " distance=2.03 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 145 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 312 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS I 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 145 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 312 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 148 " 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 D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 401 " - " ASN A 171 " " NAG A 402 " - " ASN A 21 " " NAG A 403 " - " ASN A 278 " " NAG A 404 " - " ASN A 296 " " NAG B 401 " - " ASN B 171 " " NAG B 402 " - " ASN B 21 " " NAG B 403 " - " ASN B 278 " " NAG B 404 " - " ASN B 296 " " NAG C 401 " - " ASN C 171 " " NAG C 402 " - " ASN C 21 " " NAG C 403 " - " ASN C 278 " " NAG C 404 " - " ASN C 296 " " NAG D 1 " - " ASN A 97 " " NAG E 1 " - " ASN A 33 " " NAG F 1 " - " ASN B 97 " " NAG J 1 " - " ASN B 33 " " NAG K 1 " - " ASN C 97 " " NAG L 1 " - " ASN C 33 " Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 742.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3066 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 36 sheets defined 32.5% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 74 through 83 removed outlier: 5.994A pdb=" N SER A 79 " --> pdb=" O GLU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 116 Processing helix chain 'A' and resid 128 through 133 removed outlier: 4.430A pdb=" N TRP A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'G' and resid 37 through 58 Processing helix chain 'G' and resid 74 through 127 Processing helix chain 'G' and resid 145 through 154 Processing helix chain 'G' and resid 158 through 173 removed outlier: 3.831A pdb=" N TYR G 162 " --> pdb=" O ASP G 158 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU G 164 " --> pdb=" O PRO G 160 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU G 165 " --> pdb=" O LYS G 161 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 18 Processing helix chain 'X' and resid 39 through 54 Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 74 through 83 removed outlier: 6.005A pdb=" N SER B 79 " --> pdb=" O GLU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 128 through 133 removed outlier: 4.428A pdb=" N TRP B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 202 Processing helix chain 'H' and resid 37 through 58 Processing helix chain 'H' and resid 74 through 127 Processing helix chain 'H' and resid 145 through 154 Processing helix chain 'H' and resid 158 through 173 removed outlier: 3.831A pdb=" N TYR H 162 " --> pdb=" O ASP H 158 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU H 164 " --> pdb=" O PRO H 160 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLU H 165 " --> pdb=" O LYS H 161 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 18 Processing helix chain 'Y' and resid 39 through 54 Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 74 through 83 removed outlier: 5.998A pdb=" N SER C 79 " --> pdb=" O GLU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 116 Processing helix chain 'C' and resid 128 through 133 removed outlier: 4.431A pdb=" N TRP C 133 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 202 Processing helix chain 'I' and resid 37 through 58 Processing helix chain 'I' and resid 74 through 127 Processing helix chain 'I' and resid 145 through 154 Processing helix chain 'I' and resid 158 through 173 removed outlier: 3.830A pdb=" N TYR I 162 " --> pdb=" O ASP I 158 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU I 164 " --> pdb=" O PRO I 160 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N GLU I 165 " --> pdb=" O LYS I 161 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2 through 18 Processing helix chain 'Z' and resid 39 through 54 Processing sheet with id=AA1, first strand: chain 'G' and resid 32 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.182A pdb=" N ASP A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.359A pdb=" N LEU A 51 " --> pdb=" O HIS A 282 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N CYS A 284 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 60 through 62 removed outlier: 6.509A pdb=" N LEU A 60 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 120 through 125 removed outlier: 4.493A pdb=" N SER A 120 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TYR A 262 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LEU A 185 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU A 181 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU A 185 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU A 257 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 160 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP A 159 " --> pdb=" O GLY A 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 120 through 125 removed outlier: 4.493A pdb=" N SER A 120 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TYR A 262 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LEU A 185 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU A 181 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 142 through 147 removed outlier: 4.767A pdb=" N CYS A 145 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 152 " --> pdb=" O CYS A 145 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 170 through 175 Processing sheet with id=AB2, first strand: chain 'A' and resid 294 through 295 removed outlier: 4.134A pdb=" N CYS A 288 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'X' and resid 21 through 27 removed outlier: 6.818A pdb=" N LYS X 34 " --> pdb=" O GLU X 22 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL X 24 " --> pdb=" O LEU X 32 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU X 32 " --> pdb=" O VAL X 24 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL X 26 " --> pdb=" O LYS X 30 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS X 30 " --> pdb=" O VAL X 26 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE X 31 " --> pdb=" O GLU X 61 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLU X 63 " --> pdb=" O ILE X 31 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL X 33 " --> pdb=" O GLU X 63 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 32 through 36 Processing sheet with id=AB5, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB6, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB7, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB8, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.325A pdb=" N LEU B 51 " --> pdb=" O HIS B 282 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N CYS B 284 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 60 through 62 removed outlier: 6.504A pdb=" N LEU B 60 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 120 through 125 removed outlier: 4.493A pdb=" N SER B 120 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TYR B 262 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU B 185 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU B 181 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LEU B 185 " --> pdb=" O PRO B 260 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU B 257 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 160 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP B 159 " --> pdb=" O GLY B 139 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 120 through 125 removed outlier: 4.493A pdb=" N SER B 120 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TYR B 262 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU B 185 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU B 181 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 142 through 147 removed outlier: 4.750A pdb=" N CYS B 145 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 152 " --> pdb=" O CYS B 145 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 170 through 175 Processing sheet with id=AC5, first strand: chain 'B' and resid 294 through 295 removed outlier: 4.142A pdb=" N CYS B 288 " --> pdb=" O ILE B 295 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Y' and resid 21 through 27 removed outlier: 6.812A pdb=" N LYS Y 34 " --> pdb=" O GLU Y 22 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL Y 24 " --> pdb=" O LEU Y 32 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU Y 32 " --> pdb=" O VAL Y 24 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL Y 26 " --> pdb=" O LYS Y 30 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS Y 30 " --> pdb=" O VAL Y 26 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE Y 31 " --> pdb=" O GLU Y 61 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N GLU Y 63 " --> pdb=" O ILE Y 31 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL Y 33 " --> pdb=" O GLU Y 63 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 32 through 36 Processing sheet with id=AC8, first strand: chain 'C' and resid 24 through 26 removed outlier: 4.185A pdb=" N ASP C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AD1, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AD2, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.339A pdb=" N LEU C 51 " --> pdb=" O HIS C 282 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N CYS C 284 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 60 through 62 removed outlier: 6.513A pdb=" N LEU C 60 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 120 through 125 removed outlier: 4.493A pdb=" N SER C 120 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR C 262 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU C 185 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU C 181 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU C 185 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU C 257 " --> pdb=" O LEU C 160 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU C 160 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP C 159 " --> pdb=" O GLY C 139 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 120 through 125 removed outlier: 4.493A pdb=" N SER C 120 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR C 262 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU C 185 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU C 181 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 142 through 147 removed outlier: 4.764A pdb=" N CYS C 145 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 152 " --> pdb=" O CYS C 145 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 170 through 175 Processing sheet with id=AD8, first strand: chain 'C' and resid 294 through 295 removed outlier: 4.140A pdb=" N CYS C 288 " --> pdb=" O ILE C 295 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Z' and resid 21 through 27 removed outlier: 6.819A pdb=" N LYS Z 34 " --> pdb=" O GLU Z 22 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL Z 24 " --> pdb=" O LEU Z 32 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU Z 32 " --> pdb=" O VAL Z 24 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL Z 26 " --> pdb=" O LYS Z 30 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LYS Z 30 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE Z 31 " --> pdb=" O GLU Z 61 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLU Z 63 " --> pdb=" O ILE Z 31 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL Z 33 " --> pdb=" O GLU Z 63 " (cutoff:3.500A) 632 hydrogen bonds defined for protein. 1761 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: 5.24 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12267 1.03 - 1.23: 9 1.23 - 1.42: 5597 1.42 - 1.62: 7720 1.62 - 1.81: 78 Bond restraints: 25671 Sorted by residual: bond pdb=" N PHE H 9 " pdb=" CA PHE H 9 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N PHE I 9 " pdb=" CA PHE I 9 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N PHE G 9 " pdb=" CA PHE G 9 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N PHE I 9 " pdb=" H PHE I 9 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" N PHE H 9 " pdb=" H PHE H 9 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.34e+00 ... (remaining 25666 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 44629 1.25 - 2.50: 1332 2.50 - 3.75: 89 3.75 - 5.00: 18 5.00 - 6.25: 6 Bond angle restraints: 46074 Sorted by residual: angle pdb=" C3 BMA F 3 " pdb=" C2 BMA F 3 " pdb=" O2 BMA F 3 " ideal model delta sigma weight residual 112.95 106.70 6.25 3.00e+00 1.11e-01 4.34e+00 angle pdb=" C3 BMA K 3 " pdb=" C2 BMA K 3 " pdb=" O2 BMA K 3 " ideal model delta sigma weight residual 112.95 106.74 6.21 3.00e+00 1.11e-01 4.28e+00 angle pdb=" C3 BMA D 3 " pdb=" C2 BMA D 3 " pdb=" O2 BMA D 3 " ideal model delta sigma weight residual 112.95 106.77 6.18 3.00e+00 1.11e-01 4.25e+00 angle pdb=" C1 BMA D 3 " pdb=" O5 BMA D 3 " pdb=" C5 BMA D 3 " ideal model delta sigma weight residual 118.82 113.54 5.28 3.00e+00 1.11e-01 3.10e+00 angle pdb=" C1 BMA F 3 " pdb=" O5 BMA F 3 " pdb=" C5 BMA F 3 " ideal model delta sigma weight residual 118.82 113.56 5.26 3.00e+00 1.11e-01 3.07e+00 ... (remaining 46069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.00: 11856 21.00 - 42.01: 389 42.01 - 63.01: 258 63.01 - 84.02: 43 84.02 - 105.02: 12 Dihedral angle restraints: 12558 sinusoidal: 6924 harmonic: 5634 Sorted by residual: dihedral pdb=" CA ILE A 258 " pdb=" C ILE A 258 " pdb=" N ALA A 259 " pdb=" CA ALA A 259 " ideal model delta harmonic sigma weight residual -180.00 -159.35 -20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ILE B 258 " pdb=" C ILE B 258 " pdb=" N ALA B 259 " pdb=" CA ALA B 259 " ideal model delta harmonic sigma weight residual 180.00 -159.55 -20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ILE C 258 " pdb=" C ILE C 258 " pdb=" N ALA C 259 " pdb=" CA ALA C 259 " ideal model delta harmonic sigma weight residual 180.00 -159.70 -20.30 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 12555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1825 0.060 - 0.120: 243 0.120 - 0.180: 20 0.180 - 0.241: 0 0.241 - 0.301: 9 Chirality restraints: 2097 Sorted by residual: chirality pdb=" C1 NAG A 401 " pdb=" ND2 ASN A 171 " pdb=" C2 NAG A 401 " pdb=" O5 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 171 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C1 NAG B 401 " pdb=" ND2 ASN B 171 " pdb=" C2 NAG B 401 " pdb=" O5 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 2094 not shown) Planarity restraints: 3912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 97 " -0.010 2.00e-02 2.50e+03 7.84e-03 9.23e-01 pdb=" CG ASN C 97 " 0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN C 97 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C 97 " 0.010 2.00e-02 2.50e+03 pdb="HD21 ASN C 97 " 0.003 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 97 " 0.010 2.00e-02 2.50e+03 7.69e-03 8.88e-01 pdb=" CG ASN A 97 " -0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN A 97 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 97 " -0.010 2.00e-02 2.50e+03 pdb="HD21 ASN A 97 " -0.003 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 97 " -0.009 2.00e-02 2.50e+03 7.48e-03 8.40e-01 pdb=" CG ASN B 97 " 0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN B 97 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 97 " 0.010 2.00e-02 2.50e+03 pdb="HD21 ASN B 97 " 0.003 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.011 2.00e-02 2.50e+03 ... (remaining 3909 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.20: 1358 2.20 - 2.80: 52084 2.80 - 3.40: 69252 3.40 - 4.00: 94405 4.00 - 4.60: 146851 Nonbonded interactions: 363950 Sorted by model distance: nonbonded pdb=" HG1 THR A 290 " pdb=" O GLY A 293 " model vdw 1.606 2.450 nonbonded pdb=" HG1 THR B 290 " pdb=" O GLY B 293 " model vdw 1.616 2.450 nonbonded pdb=" HG1 THR C 290 " pdb=" O GLY C 293 " model vdw 1.620 2.450 nonbonded pdb="HH12 ARG C 317 " pdb=" OD1 ASP I 90 " model vdw 1.630 2.450 nonbonded pdb="HH12 ARG B 317 " pdb=" OD1 ASP H 90 " model vdw 1.644 2.450 ... (remaining 363945 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'L' } 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=1.00 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: 2.380 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: 0.150 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 20.360 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 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 : 0.004 0.033 13446 Z= 0.178 Angle : 0.560 7.261 18288 Z= 0.277 Chirality : 0.045 0.301 2097 Planarity : 0.002 0.019 2301 Dihedral : 11.939 105.022 5235 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.45 % Allowed : 1.79 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.20), residues: 1635 helix: 3.59 (0.22), residues: 450 sheet: 0.19 (0.31), residues: 291 loop : -0.52 (0.18), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 218 TYR 0.008 0.001 TYR A 167 PHE 0.014 0.001 PHE H 110 TRP 0.006 0.001 TRP I 92 HIS 0.004 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00371 (13404) covalent geometry : angle 0.52656 (18177) SS BOND : bond 0.00254 ( 15) SS BOND : angle 0.71343 ( 30) hydrogen bonds : bond 0.16164 ( 608) hydrogen bonds : angle 6.85187 ( 1761) link_BETA1-4 : bond 0.00306 ( 9) link_BETA1-4 : angle 2.62143 ( 27) link_NAG-ASN : bond 0.00276 ( 18) link_NAG-ASN : angle 3.03843 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 255 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 261 average time/residue: 1.5306 time to fit residues: 431.7711 Evaluate side-chains 126 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain I residue 22 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN B 237 ASN C 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.079382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.060918 restraints weight = 84559.023| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.80 r_work: 0.2797 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13446 Z= 0.287 Angle : 0.624 5.999 18288 Z= 0.329 Chirality : 0.045 0.265 2097 Planarity : 0.004 0.027 2301 Dihedral : 7.633 52.477 2347 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.93 % Allowed : 10.04 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.20), residues: 1635 helix: 2.88 (0.22), residues: 465 sheet: 0.00 (0.31), residues: 297 loop : -0.71 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 217 TYR 0.009 0.001 TYR A 167 PHE 0.017 0.002 PHE I 110 TRP 0.012 0.002 TRP H 26 HIS 0.004 0.001 HIS G 142 Details of bonding type rmsd covalent geometry : bond 0.00639 (13404) covalent geometry : angle 0.60294 (18177) SS BOND : bond 0.00455 ( 15) SS BOND : angle 1.11580 ( 30) hydrogen bonds : bond 0.04476 ( 608) hydrogen bonds : angle 5.34242 ( 1761) link_BETA1-4 : bond 0.00384 ( 9) link_BETA1-4 : angle 2.42592 ( 27) link_NAG-ASN : bond 0.00437 ( 18) link_NAG-ASN : angle 2.42280 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8320 (m-30) cc_final: 0.8029 (m-30) REVERT: G 30 GLN cc_start: 0.9518 (mt0) cc_final: 0.9318 (mt0) REVERT: B 24 ASP cc_start: 0.8459 (m-30) cc_final: 0.8163 (m-30) REVERT: B 307 ILE cc_start: 0.8375 (mp) cc_final: 0.8168 (mp) REVERT: Y 34 LYS cc_start: 0.8611 (mttt) cc_final: 0.8399 (mttm) REVERT: Y 63 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7747 (tt0) REVERT: C 24 ASP cc_start: 0.8327 (m-30) cc_final: 0.7994 (m-30) REVERT: C 307 ILE cc_start: 0.8418 (mt) cc_final: 0.8215 (mp) REVERT: I 57 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8614 (mt-10) REVERT: I 74 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8191 (mt-10) outliers start: 26 outliers final: 6 residues processed: 160 average time/residue: 1.0831 time to fit residues: 191.0440 Evaluate side-chains 132 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain I residue 74 GLU Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 46 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 156 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.077702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.059530 restraints weight = 84658.702| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.77 r_work: 0.2766 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13446 Z= 0.274 Angle : 0.569 6.069 18288 Z= 0.301 Chirality : 0.043 0.250 2097 Planarity : 0.004 0.063 2301 Dihedral : 5.961 40.558 2337 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.64 % Allowed : 10.34 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.20), residues: 1635 helix: 2.75 (0.22), residues: 465 sheet: -0.27 (0.31), residues: 297 loop : -0.80 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG X 55 TYR 0.009 0.001 TYR B 239 PHE 0.016 0.001 PHE I 110 TRP 0.007 0.001 TRP G 14 HIS 0.005 0.001 HIS G 142 Details of bonding type rmsd covalent geometry : bond 0.00613 (13404) covalent geometry : angle 0.55014 (18177) SS BOND : bond 0.00445 ( 15) SS BOND : angle 1.02225 ( 30) hydrogen bonds : bond 0.04384 ( 608) hydrogen bonds : angle 5.07994 ( 1761) link_BETA1-4 : bond 0.00414 ( 9) link_BETA1-4 : angle 2.10591 ( 27) link_NAG-ASN : bond 0.00434 ( 18) link_NAG-ASN : angle 2.21831 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8400 (m-30) cc_final: 0.8069 (m-30) REVERT: G 69 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8459 (mm-30) REVERT: B 24 ASP cc_start: 0.8480 (m-30) cc_final: 0.8201 (m-30) REVERT: H 125 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8464 (mm-40) REVERT: Y 63 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7941 (tt0) REVERT: C 24 ASP cc_start: 0.8385 (m-30) cc_final: 0.8043 (m-30) REVERT: C 154 TYR cc_start: 0.8547 (m-80) cc_final: 0.8307 (m-80) REVERT: I 57 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8553 (mt-10) REVERT: I 69 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8672 (mm-30) REVERT: I 74 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.7912 (mt-10) outliers start: 22 outliers final: 9 residues processed: 140 average time/residue: 1.0197 time to fit residues: 159.3996 Evaluate side-chains 125 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain I residue 74 GLU Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 87 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.079402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.061302 restraints weight = 83499.149| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.76 r_work: 0.2811 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13446 Z= 0.119 Angle : 0.498 4.786 18288 Z= 0.260 Chirality : 0.042 0.258 2097 Planarity : 0.003 0.023 2301 Dihedral : 5.188 39.640 2337 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.04 % Allowed : 11.09 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.20), residues: 1635 helix: 2.93 (0.22), residues: 465 sheet: -0.18 (0.31), residues: 291 loop : -0.82 (0.18), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 76 TYR 0.007 0.001 TYR G 24 PHE 0.012 0.001 PHE H 110 TRP 0.004 0.001 TRP H 92 HIS 0.003 0.001 HIS I 25 Details of bonding type rmsd covalent geometry : bond 0.00266 (13404) covalent geometry : angle 0.48035 (18177) SS BOND : bond 0.00273 ( 15) SS BOND : angle 0.90830 ( 30) hydrogen bonds : bond 0.03673 ( 608) hydrogen bonds : angle 4.73091 ( 1761) link_BETA1-4 : bond 0.00316 ( 9) link_BETA1-4 : angle 1.95106 ( 27) link_NAG-ASN : bond 0.00225 ( 18) link_NAG-ASN : angle 1.97808 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8411 (m-30) cc_final: 0.8050 (m-30) REVERT: G 69 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8398 (mm-30) REVERT: B 24 ASP cc_start: 0.8479 (m-30) cc_final: 0.8190 (m-30) REVERT: H 97 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8314 (mm-30) REVERT: H 125 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8534 (mm-40) REVERT: Y 34 LYS cc_start: 0.8544 (mttp) cc_final: 0.8150 (mttm) REVERT: Y 63 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7827 (tt0) REVERT: C 24 ASP cc_start: 0.8355 (m-30) cc_final: 0.7994 (m-30) REVERT: C 154 TYR cc_start: 0.8430 (m-80) cc_final: 0.8180 (m-80) REVERT: C 250 MET cc_start: 0.8989 (mtp) cc_final: 0.8772 (mtt) REVERT: I 57 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8686 (mt-10) REVERT: I 69 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8583 (mm-30) REVERT: I 97 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8218 (mm-30) outliers start: 14 outliers final: 9 residues processed: 139 average time/residue: 1.0451 time to fit residues: 161.8914 Evaluate side-chains 129 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.078125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.060068 restraints weight = 83641.267| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.75 r_work: 0.2790 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13446 Z= 0.216 Angle : 0.517 5.141 18288 Z= 0.270 Chirality : 0.042 0.245 2097 Planarity : 0.003 0.028 2301 Dihedral : 5.247 41.596 2337 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.26 % Allowed : 10.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.20), residues: 1635 helix: 2.96 (0.22), residues: 465 sheet: -0.36 (0.31), residues: 297 loop : -0.88 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 217 TYR 0.007 0.001 TYR A 167 PHE 0.014 0.001 PHE H 110 TRP 0.006 0.001 TRP B 133 HIS 0.003 0.001 HIS G 25 Details of bonding type rmsd covalent geometry : bond 0.00484 (13404) covalent geometry : angle 0.49925 (18177) SS BOND : bond 0.00401 ( 15) SS BOND : angle 0.98247 ( 30) hydrogen bonds : bond 0.03774 ( 608) hydrogen bonds : angle 4.71523 ( 1761) link_BETA1-4 : bond 0.00275 ( 9) link_BETA1-4 : angle 1.99347 ( 27) link_NAG-ASN : bond 0.00361 ( 18) link_NAG-ASN : angle 1.99077 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8429 (m-30) cc_final: 0.8090 (m-30) REVERT: G 69 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8446 (mm-30) REVERT: B 24 ASP cc_start: 0.8482 (m-30) cc_final: 0.8186 (m-30) REVERT: H 120 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8439 (mp0) REVERT: H 125 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8534 (mm-40) REVERT: Y 34 LYS cc_start: 0.8538 (mttp) cc_final: 0.8143 (mttm) REVERT: Y 63 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7838 (tt0) REVERT: C 24 ASP cc_start: 0.8371 (m-30) cc_final: 0.8024 (m-30) REVERT: C 154 TYR cc_start: 0.8491 (m-80) cc_final: 0.8239 (m-80) REVERT: I 57 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8635 (mt-10) REVERT: I 69 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8602 (mm-30) REVERT: I 97 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8187 (mm-30) REVERT: I 149 MET cc_start: 0.8748 (mmp) cc_final: 0.8545 (mmm) outliers start: 17 outliers final: 10 residues processed: 135 average time/residue: 1.0633 time to fit residues: 159.0179 Evaluate side-chains 129 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 63 optimal weight: 0.3980 chunk 106 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.078422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.060370 restraints weight = 83906.425| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.75 r_work: 0.2799 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13446 Z= 0.174 Angle : 0.502 4.846 18288 Z= 0.262 Chirality : 0.041 0.245 2097 Planarity : 0.003 0.026 2301 Dihedral : 5.105 42.091 2337 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.34 % Allowed : 10.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.20), residues: 1635 helix: 3.01 (0.22), residues: 465 sheet: -0.41 (0.30), residues: 297 loop : -0.90 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG X 55 TYR 0.008 0.001 TYR G 24 PHE 0.012 0.001 PHE H 110 TRP 0.006 0.001 TRP B 133 HIS 0.003 0.001 HIS G 25 Details of bonding type rmsd covalent geometry : bond 0.00392 (13404) covalent geometry : angle 0.48543 (18177) SS BOND : bond 0.00334 ( 15) SS BOND : angle 1.03264 ( 30) hydrogen bonds : bond 0.03611 ( 608) hydrogen bonds : angle 4.61628 ( 1761) link_BETA1-4 : bond 0.00272 ( 9) link_BETA1-4 : angle 1.94586 ( 27) link_NAG-ASN : bond 0.00276 ( 18) link_NAG-ASN : angle 1.91245 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8422 (m-30) cc_final: 0.8080 (m-30) REVERT: A 307 ILE cc_start: 0.8462 (mp) cc_final: 0.8242 (mp) REVERT: G 69 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8420 (mm-30) REVERT: B 24 ASP cc_start: 0.8549 (m-30) cc_final: 0.8247 (m-30) REVERT: H 120 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8448 (mt-10) REVERT: H 125 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8564 (mm-40) REVERT: Y 34 LYS cc_start: 0.8537 (mttp) cc_final: 0.8099 (mttm) REVERT: Y 63 GLU cc_start: 0.8496 (mt-10) cc_final: 0.7864 (tt0) REVERT: C 24 ASP cc_start: 0.8361 (m-30) cc_final: 0.8013 (m-30) REVERT: C 154 TYR cc_start: 0.8459 (m-80) cc_final: 0.8181 (m-80) REVERT: I 57 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8643 (mt-10) REVERT: I 69 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8557 (mm-30) REVERT: I 120 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7901 (mp0) REVERT: I 149 MET cc_start: 0.8711 (mmp) cc_final: 0.8475 (mmm) outliers start: 18 outliers final: 14 residues processed: 135 average time/residue: 1.0983 time to fit residues: 165.0725 Evaluate side-chains 132 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain Z residue 7 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 115 optimal weight: 0.6980 chunk 152 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.079200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.061123 restraints weight = 83121.588| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.76 r_work: 0.2814 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13446 Z= 0.120 Angle : 0.481 4.583 18288 Z= 0.249 Chirality : 0.041 0.244 2097 Planarity : 0.003 0.023 2301 Dihedral : 4.827 41.147 2337 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.49 % Allowed : 10.79 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.20), residues: 1635 helix: 3.14 (0.22), residues: 465 sheet: -0.38 (0.30), residues: 297 loop : -0.89 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 55 TYR 0.008 0.001 TYR G 24 PHE 0.010 0.001 PHE H 110 TRP 0.004 0.001 TRP H 92 HIS 0.003 0.001 HIS G 25 Details of bonding type rmsd covalent geometry : bond 0.00271 (13404) covalent geometry : angle 0.46530 (18177) SS BOND : bond 0.00261 ( 15) SS BOND : angle 0.93697 ( 30) hydrogen bonds : bond 0.03425 ( 608) hydrogen bonds : angle 4.46219 ( 1761) link_BETA1-4 : bond 0.00319 ( 9) link_BETA1-4 : angle 1.87310 ( 27) link_NAG-ASN : bond 0.00212 ( 18) link_NAG-ASN : angle 1.79710 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8414 (m-30) cc_final: 0.8064 (m-30) REVERT: A 307 ILE cc_start: 0.8414 (mp) cc_final: 0.8193 (mp) REVERT: G 69 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8426 (mm-30) REVERT: B 24 ASP cc_start: 0.8547 (m-30) cc_final: 0.8246 (m-30) REVERT: H 57 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8604 (mt-10) REVERT: H 120 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8428 (mt-10) REVERT: Y 34 LYS cc_start: 0.8534 (mttp) cc_final: 0.8137 (mttm) REVERT: Y 63 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7898 (tt0) REVERT: C 24 ASP cc_start: 0.8345 (m-30) cc_final: 0.7986 (m-30) REVERT: I 57 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8705 (mt-10) REVERT: I 69 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8581 (mm-30) REVERT: I 106 ARG cc_start: 0.8730 (tpm170) cc_final: 0.8386 (mmm160) REVERT: I 120 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7895 (mp0) REVERT: I 149 MET cc_start: 0.8712 (mmp) cc_final: 0.8460 (mmm) outliers start: 20 outliers final: 15 residues processed: 138 average time/residue: 0.9784 time to fit residues: 150.7981 Evaluate side-chains 131 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 26 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 112 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.078765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.060638 restraints weight = 83288.499| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.78 r_work: 0.2806 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13446 Z= 0.150 Angle : 0.488 4.758 18288 Z= 0.253 Chirality : 0.041 0.237 2097 Planarity : 0.002 0.025 2301 Dihedral : 4.818 41.579 2337 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.41 % Allowed : 11.31 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.20), residues: 1635 helix: 3.23 (0.22), residues: 465 sheet: -0.49 (0.30), residues: 297 loop : -0.91 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 170 TYR 0.008 0.001 TYR G 24 PHE 0.012 0.001 PHE H 110 TRP 0.005 0.001 TRP H 92 HIS 0.003 0.001 HIS G 25 Details of bonding type rmsd covalent geometry : bond 0.00337 (13404) covalent geometry : angle 0.47254 (18177) SS BOND : bond 0.00341 ( 15) SS BOND : angle 0.94856 ( 30) hydrogen bonds : bond 0.03414 ( 608) hydrogen bonds : angle 4.43578 ( 1761) link_BETA1-4 : bond 0.00221 ( 9) link_BETA1-4 : angle 1.88588 ( 27) link_NAG-ASN : bond 0.00248 ( 18) link_NAG-ASN : angle 1.76222 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8415 (m-30) cc_final: 0.8065 (m-30) REVERT: G 69 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8335 (mt-10) REVERT: B 24 ASP cc_start: 0.8550 (m-30) cc_final: 0.8280 (m-30) REVERT: H 57 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8609 (mt-10) REVERT: H 120 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8339 (mt-10) REVERT: Y 34 LYS cc_start: 0.8523 (mttp) cc_final: 0.8062 (mttm) REVERT: Y 63 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7872 (tt0) REVERT: C 24 ASP cc_start: 0.8349 (m-30) cc_final: 0.7993 (m-30) REVERT: I 57 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8632 (mt-10) REVERT: I 69 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8553 (mm-30) REVERT: I 106 ARG cc_start: 0.8734 (tpm170) cc_final: 0.8393 (mmm160) REVERT: I 120 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: I 149 MET cc_start: 0.8711 (mmp) cc_final: 0.8460 (mmm) outliers start: 19 outliers final: 14 residues processed: 132 average time/residue: 1.1270 time to fit residues: 165.0059 Evaluate side-chains 134 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 26 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 94 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.078306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.060232 restraints weight = 83590.843| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.77 r_work: 0.2794 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13446 Z= 0.182 Angle : 0.500 5.062 18288 Z= 0.259 Chirality : 0.041 0.235 2097 Planarity : 0.003 0.026 2301 Dihedral : 4.900 42.540 2337 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.41 % Allowed : 11.90 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.20), residues: 1635 helix: 3.20 (0.22), residues: 465 sheet: -0.56 (0.32), residues: 267 loop : -0.90 (0.18), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 217 TYR 0.008 0.001 TYR G 24 PHE 0.012 0.001 PHE H 110 TRP 0.006 0.001 TRP G 26 HIS 0.004 0.001 HIS G 25 Details of bonding type rmsd covalent geometry : bond 0.00412 (13404) covalent geometry : angle 0.48377 (18177) SS BOND : bond 0.00349 ( 15) SS BOND : angle 1.06464 ( 30) hydrogen bonds : bond 0.03442 ( 608) hydrogen bonds : angle 4.46171 ( 1761) link_BETA1-4 : bond 0.00261 ( 9) link_BETA1-4 : angle 1.93620 ( 27) link_NAG-ASN : bond 0.00298 ( 18) link_NAG-ASN : angle 1.80726 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8447 (m-30) cc_final: 0.8095 (m-30) REVERT: A 307 ILE cc_start: 0.8490 (mp) cc_final: 0.8260 (mp) REVERT: G 69 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8343 (mt-10) REVERT: B 24 ASP cc_start: 0.8557 (m-30) cc_final: 0.8281 (m-30) REVERT: H 57 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8618 (mt-10) REVERT: H 120 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8341 (mt-10) REVERT: Y 34 LYS cc_start: 0.8590 (mttp) cc_final: 0.8103 (mttm) REVERT: Y 63 GLU cc_start: 0.8554 (mt-10) cc_final: 0.7888 (tt0) REVERT: C 24 ASP cc_start: 0.8376 (m-30) cc_final: 0.8018 (m-30) REVERT: I 57 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8638 (mt-10) REVERT: I 69 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8566 (mm-30) REVERT: I 106 ARG cc_start: 0.8768 (tpm170) cc_final: 0.8420 (mmm160) REVERT: I 120 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7891 (mp0) REVERT: I 149 MET cc_start: 0.8735 (mmp) cc_final: 0.8473 (mmm) REVERT: Z 4 GLU cc_start: 0.8984 (tt0) cc_final: 0.8673 (tm-30) outliers start: 19 outliers final: 16 residues processed: 130 average time/residue: 1.1153 time to fit residues: 161.7030 Evaluate side-chains 135 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 26 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 12 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.078680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.060581 restraints weight = 83216.473| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.76 r_work: 0.2801 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13446 Z= 0.144 Angle : 0.493 4.771 18288 Z= 0.256 Chirality : 0.041 0.239 2097 Planarity : 0.003 0.025 2301 Dihedral : 4.832 42.155 2337 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.49 % Allowed : 11.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.20), residues: 1635 helix: 3.25 (0.22), residues: 465 sheet: -0.56 (0.32), residues: 267 loop : -0.90 (0.18), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG X 55 TYR 0.008 0.001 TYR G 24 PHE 0.011 0.001 PHE H 110 TRP 0.005 0.001 TRP B 133 HIS 0.004 0.001 HIS G 25 Details of bonding type rmsd covalent geometry : bond 0.00326 (13404) covalent geometry : angle 0.47774 (18177) SS BOND : bond 0.00316 ( 15) SS BOND : angle 1.08082 ( 30) hydrogen bonds : bond 0.03381 ( 608) hydrogen bonds : angle 4.42331 ( 1761) link_BETA1-4 : bond 0.00272 ( 9) link_BETA1-4 : angle 1.91755 ( 27) link_NAG-ASN : bond 0.00249 ( 18) link_NAG-ASN : angle 1.77804 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8445 (m-30) cc_final: 0.8092 (m-30) REVERT: A 307 ILE cc_start: 0.8480 (mp) cc_final: 0.8250 (mp) REVERT: G 69 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8351 (mt-10) REVERT: B 24 ASP cc_start: 0.8541 (m-30) cc_final: 0.8267 (m-30) REVERT: H 57 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8618 (mt-10) REVERT: H 120 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8418 (mp0) REVERT: Y 34 LYS cc_start: 0.8544 (mttp) cc_final: 0.8035 (mttm) REVERT: Y 63 GLU cc_start: 0.8550 (mt-10) cc_final: 0.7890 (tt0) REVERT: C 24 ASP cc_start: 0.8373 (m-30) cc_final: 0.8014 (m-30) REVERT: I 57 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8640 (mt-10) REVERT: I 69 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8552 (mm-30) REVERT: I 106 ARG cc_start: 0.8774 (tpm170) cc_final: 0.8424 (mmm160) REVERT: I 120 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: I 149 MET cc_start: 0.8746 (mmp) cc_final: 0.8501 (mmm) REVERT: Z 4 GLU cc_start: 0.8973 (tt0) cc_final: 0.8670 (tm-30) outliers start: 20 outliers final: 16 residues processed: 131 average time/residue: 1.0317 time to fit residues: 150.5992 Evaluate side-chains 136 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Y residue 26 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 26 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 71 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.077059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.058561 restraints weight = 81855.599| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 3.00 r_work: 0.2675 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13446 Z= 0.121 Angle : 0.480 4.726 18288 Z= 0.248 Chirality : 0.041 0.239 2097 Planarity : 0.002 0.026 2301 Dihedral : 4.643 41.344 2337 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.56 % Allowed : 11.68 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.20), residues: 1635 helix: 3.35 (0.22), residues: 465 sheet: -0.54 (0.32), residues: 267 loop : -0.87 (0.18), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 55 TYR 0.008 0.001 TYR G 24 PHE 0.010 0.001 PHE H 110 TRP 0.004 0.001 TRP H 92 HIS 0.004 0.001 HIS G 25 Details of bonding type rmsd covalent geometry : bond 0.00273 (13404) covalent geometry : angle 0.46473 (18177) SS BOND : bond 0.00264 ( 15) SS BOND : angle 1.02931 ( 30) hydrogen bonds : bond 0.03266 ( 608) hydrogen bonds : angle 4.34393 ( 1761) link_BETA1-4 : bond 0.00286 ( 9) link_BETA1-4 : angle 1.86803 ( 27) link_NAG-ASN : bond 0.00212 ( 18) link_NAG-ASN : angle 1.69535 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7228.34 seconds wall clock time: 123 minutes 10.62 seconds (7390.62 seconds total)