Starting phenix.real_space_refine on Sat May 24 10:22:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sk7_40557/05_2025/8sk7_40557_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sk7_40557/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sk7_40557/05_2025/8sk7_40557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sk7_40557/05_2025/8sk7_40557.map" model { file = "/net/cci-nas-00/data/ceres_data/8sk7_40557/05_2025/8sk7_40557_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sk7_40557/05_2025/8sk7_40557_trim.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.11, per 1000 atoms: 0.48 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: 6.57 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.39 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: 9.65 Time building geometry restraints manager: 7.90 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'Y' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'K' } 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: 10.050 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: 0.000 Extract box with map and model: 0.820 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 53.390 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.970 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.006 0.001 TRP I 92 HIS 0.004 0.001 HIS A 18 PHE 0.014 0.001 PHE H 110 TYR 0.008 0.001 TYR A 167 ARG 0.002 0.000 ARG B 218 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 18) link_NAG-ASN : angle 3.03843 ( 54) link_BETA1-4 : bond 0.00306 ( 9) link_BETA1-4 : angle 2.62143 ( 27) hydrogen bonds : bond 0.16164 ( 608) hydrogen bonds : angle 6.85187 ( 1761) SS BOND : bond 0.00254 ( 15) SS BOND : angle 0.71343 ( 30) covalent geometry : bond 0.00371 (13404) covalent geometry : angle 0.52656 (18177) *********************** 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 : 2.052 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: 2.7413 time to fit residues: 777.3562 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 : 1.978 ------------------------------------------------------------------------------- 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 136 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3298 r_free = 0.3298 target = 0.080177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.061789 restraints weight = 83404.826| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.77 r_work: 0.2819 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13446 Z= 0.231 Angle : 0.592 5.636 18288 Z= 0.311 Chirality : 0.044 0.263 2097 Planarity : 0.003 0.024 2301 Dihedral : 7.802 55.901 2347 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.20), residues: 1635 helix: 2.99 (0.22), residues: 465 sheet: 0.10 (0.31), residues: 297 loop : -0.66 (0.18), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 26 HIS 0.004 0.001 HIS G 142 PHE 0.015 0.001 PHE H 110 TYR 0.007 0.001 TYR A 167 ARG 0.002 0.001 ARG G 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 18) link_NAG-ASN : angle 2.39383 ( 54) link_BETA1-4 : bond 0.00507 ( 9) link_BETA1-4 : angle 2.39600 ( 27) hydrogen bonds : bond 0.04576 ( 608) hydrogen bonds : angle 5.35046 ( 1761) SS BOND : bond 0.00385 ( 15) SS BOND : angle 0.99882 ( 30) covalent geometry : bond 0.00512 (13404) covalent geometry : angle 0.57009 (18177) *********************** 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 159 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 2.198 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: 0.8186 (m-30) cc_final: 0.7891 (m-30) REVERT: B 24 ASP cc_start: 0.8391 (m-30) cc_final: 0.8096 (m-30) REVERT: Y 34 LYS cc_start: 0.8604 (mttt) cc_final: 0.8403 (mttm) REVERT: Y 63 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7740 (tt0) REVERT: C 24 ASP cc_start: 0.8308 (m-30) cc_final: 0.7971 (m-30) REVERT: C 307 ILE cc_start: 0.8362 (mt) cc_final: 0.8157 (mp) REVERT: I 57 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8600 (mt-10) REVERT: I 74 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8195 (mt-10) outliers start: 20 outliers final: 6 residues processed: 155 average time/residue: 2.2472 time to fit residues: 387.6811 Evaluate side-chains 131 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 2.326 ------------------------------------------------------------------------------- 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 65 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 155 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3299 r_free = 0.3299 target = 0.079970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.061703 restraints weight = 83536.280| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.80 r_work: 0.2827 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 13446 Z= 0.165 Angle : 0.523 5.319 18288 Z= 0.274 Chirality : 0.043 0.257 2097 Planarity : 0.003 0.024 2301 Dihedral : 5.830 34.881 2337 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.71 % Allowed : 10.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.20), residues: 1635 helix: 2.99 (0.22), residues: 465 sheet: -0.04 (0.31), residues: 297 loop : -0.71 (0.18), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 92 HIS 0.004 0.001 HIS G 142 PHE 0.014 0.001 PHE H 110 TYR 0.008 0.001 TYR H 24 ARG 0.002 0.000 ARG Y 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 18) link_NAG-ASN : angle 2.13871 ( 54) link_BETA1-4 : bond 0.00351 ( 9) link_BETA1-4 : angle 2.10994 ( 27) hydrogen bonds : bond 0.04095 ( 608) hydrogen bonds : angle 5.00546 ( 1761) SS BOND : bond 0.00321 ( 15) SS BOND : angle 0.83960 ( 30) covalent geometry : bond 0.00368 (13404) covalent geometry : angle 0.50360 (18177) *********************** 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 155 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 2.088 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: 0.8310 (m-30) cc_final: 0.7975 (m-30) REVERT: A 307 ILE cc_start: 0.8421 (mt) cc_final: 0.8202 (mp) REVERT: G 69 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8493 (mm-30) REVERT: B 24 ASP cc_start: 0.8451 (m-30) cc_final: 0.8128 (m-30) REVERT: H 125 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8396 (mm-40) REVERT: Y 63 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7845 (tt0) REVERT: C 24 ASP cc_start: 0.8314 (m-30) cc_final: 0.7971 (m-30) REVERT: C 250 MET cc_start: 0.9023 (mtp) cc_final: 0.8779 (mtt) REVERT: I 57 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8519 (mt-10) REVERT: I 74 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7913 (mt-10) outliers start: 23 outliers final: 8 residues processed: 150 average time/residue: 2.2482 time to fit residues: 375.2089 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 : 1.956 ------------------------------------------------------------------------------- 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 45 ILE Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain I residue 22 TYR 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 18 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.3291 r_free = 0.3291 target = 0.079490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.061261 restraints weight = 84250.054| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.79 r_work: 0.2810 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 13446 Z= 0.168 Angle : 0.508 5.049 18288 Z= 0.267 Chirality : 0.042 0.249 2097 Planarity : 0.003 0.045 2301 Dihedral : 5.276 37.473 2337 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.12 % Allowed : 11.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.20), residues: 1635 helix: 3.05 (0.22), residues: 465 sheet: -0.13 (0.31), residues: 297 loop : -0.75 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 26 HIS 0.003 0.001 HIS G 25 PHE 0.014 0.001 PHE I 110 TYR 0.007 0.001 TYR G 24 ARG 0.006 0.000 ARG X 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 18) link_NAG-ASN : angle 2.00718 ( 54) link_BETA1-4 : bond 0.00291 ( 9) link_BETA1-4 : angle 1.98391 ( 27) hydrogen bonds : bond 0.03824 ( 608) hydrogen bonds : angle 4.82131 ( 1761) SS BOND : bond 0.00311 ( 15) SS BOND : angle 0.90342 ( 30) covalent geometry : bond 0.00373 (13404) covalent geometry : angle 0.49090 (18177) *********************** 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 137 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 2.001 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: 0.8357 (m-30) cc_final: 0.8003 (m-30) REVERT: A 307 ILE cc_start: 0.8452 (mt) cc_final: 0.8235 (mp) REVERT: G 69 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8479 (mm-30) REVERT: B 24 ASP cc_start: 0.8468 (m-30) cc_final: 0.8154 (m-30) REVERT: Y 34 LYS cc_start: 0.8516 (mttp) cc_final: 0.8102 (mttm) REVERT: Y 63 GLU cc_start: 0.8449 (mt-10) cc_final: 0.7817 (tt0) REVERT: C 24 ASP cc_start: 0.8333 (m-30) cc_final: 0.7958 (m-30) REVERT: I 57 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8608 (mt-10) REVERT: I 97 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8177 (mm-30) outliers start: 15 outliers final: 8 residues processed: 135 average time/residue: 2.1360 time to fit residues: 321.4974 Evaluate side-chains 122 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 1.895 ------------------------------------------------------------------------------- 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 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 9 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 138 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3287 r_free = 0.3287 target = 0.079186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.061039 restraints weight = 84008.030| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.78 r_work: 0.2810 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13446 Z= 0.168 Angle : 0.499 4.774 18288 Z= 0.261 Chirality : 0.042 0.244 2097 Planarity : 0.003 0.025 2301 Dihedral : 5.077 39.308 2337 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.19 % Allowed : 11.01 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.20), residues: 1635 helix: 3.04 (0.22), residues: 465 sheet: -0.21 (0.31), residues: 297 loop : -0.80 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 14 HIS 0.003 0.001 HIS H 142 PHE 0.014 0.001 PHE H 110 TYR 0.007 0.001 TYR G 24 ARG 0.005 0.000 ARG X 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 18) link_NAG-ASN : angle 1.91359 ( 54) link_BETA1-4 : bond 0.00366 ( 9) link_BETA1-4 : angle 1.89207 ( 27) hydrogen bonds : bond 0.03697 ( 608) hydrogen bonds : angle 4.67472 ( 1761) SS BOND : bond 0.00323 ( 15) SS BOND : angle 0.96252 ( 30) covalent geometry : bond 0.00374 (13404) covalent geometry : angle 0.48289 (18177) *********************** 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: 16 poor density : 124 time to evaluate : 2.075 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: 0.8387 (m-30) cc_final: 0.8059 (m-30) REVERT: A 307 ILE cc_start: 0.8445 (mt) cc_final: 0.8229 (mp) REVERT: G 69 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8438 (mm-30) REVERT: B 24 ASP cc_start: 0.8462 (m-30) cc_final: 0.8163 (m-30) REVERT: B 307 ILE cc_start: 0.8474 (mp) cc_final: 0.8220 (mp) REVERT: Y 34 LYS cc_start: 0.8559 (mttp) cc_final: 0.8087 (mttm) REVERT: Y 63 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7812 (tt0) REVERT: C 24 ASP cc_start: 0.8308 (m-30) cc_final: 0.7932 (m-30) REVERT: C 250 MET cc_start: 0.9025 (mtp) cc_final: 0.8799 (mtt) REVERT: I 57 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8683 (mt-10) REVERT: I 97 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8171 (mm-30) REVERT: I 120 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7945 (mp0) outliers start: 16 outliers final: 8 residues processed: 136 average time/residue: 2.1806 time to fit residues: 331.2762 Evaluate side-chains 124 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 2.250 ------------------------------------------------------------------------------- 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 148 CYS Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain I residue 120 GLU 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 0 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3301 r_free = 0.3301 target = 0.079937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.061796 restraints weight = 82879.367| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.78 r_work: 0.2829 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13446 Z= 0.112 Angle : 0.477 4.622 18288 Z= 0.248 Chirality : 0.041 0.244 2097 Planarity : 0.003 0.023 2301 Dihedral : 4.784 38.565 2337 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.89 % Allowed : 11.46 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.20), residues: 1635 helix: 3.21 (0.22), residues: 465 sheet: -0.21 (0.31), residues: 297 loop : -0.84 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 92 HIS 0.002 0.001 HIS G 25 PHE 0.012 0.001 PHE H 110 TYR 0.007 0.001 TYR I 24 ARG 0.003 0.000 ARG X 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 18) link_NAG-ASN : angle 1.79370 ( 54) link_BETA1-4 : bond 0.00340 ( 9) link_BETA1-4 : angle 1.82746 ( 27) hydrogen bonds : bond 0.03480 ( 608) hydrogen bonds : angle 4.50626 ( 1761) SS BOND : bond 0.00270 ( 15) SS BOND : angle 0.84809 ( 30) covalent geometry : bond 0.00251 (13404) covalent geometry : angle 0.46202 (18177) *********************** 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 136 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 1.965 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: 0.8404 (m-30) cc_final: 0.8068 (m-30) REVERT: A 307 ILE cc_start: 0.8418 (mt) cc_final: 0.8204 (mp) REVERT: G 69 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8527 (mm-30) REVERT: B 24 ASP cc_start: 0.8475 (m-30) cc_final: 0.8169 (m-30) REVERT: B 307 ILE cc_start: 0.8433 (mp) cc_final: 0.8168 (mp) REVERT: Y 34 LYS cc_start: 0.8514 (mttp) cc_final: 0.8023 (mttm) REVERT: Y 63 GLU cc_start: 0.8491 (mt-10) cc_final: 0.7837 (tt0) REVERT: C 24 ASP cc_start: 0.8312 (m-30) cc_final: 0.7924 (m-30) REVERT: C 250 MET cc_start: 0.9031 (mtp) cc_final: 0.8803 (mtt) REVERT: I 57 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8703 (mt-10) REVERT: I 120 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7875 (mp0) outliers start: 12 outliers final: 8 residues processed: 132 average time/residue: 2.1356 time to fit residues: 314.8482 Evaluate side-chains 126 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 2.180 ------------------------------------------------------------------------------- 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 148 CYS Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.0970 chunk 16 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.079214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.061200 restraints weight = 83487.512| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.76 r_work: 0.2820 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13446 Z= 0.157 Angle : 0.485 4.494 18288 Z= 0.252 Chirality : 0.041 0.238 2097 Planarity : 0.002 0.022 2301 Dihedral : 4.811 39.842 2337 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.12 % Allowed : 11.83 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.20), residues: 1635 helix: 3.26 (0.22), residues: 465 sheet: -0.30 (0.31), residues: 297 loop : -0.87 (0.18), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 14 HIS 0.002 0.001 HIS I 25 PHE 0.013 0.001 PHE H 110 TYR 0.007 0.001 TYR C 108 ARG 0.002 0.000 ARG X 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 18) link_NAG-ASN : angle 1.80197 ( 54) link_BETA1-4 : bond 0.00275 ( 9) link_BETA1-4 : angle 1.85710 ( 27) hydrogen bonds : bond 0.03483 ( 608) hydrogen bonds : angle 4.48526 ( 1761) SS BOND : bond 0.00323 ( 15) SS BOND : angle 0.90829 ( 30) covalent geometry : bond 0.00351 (13404) covalent geometry : angle 0.47001 (18177) *********************** 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 132 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 1.989 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: 0.8407 (m-30) cc_final: 0.8062 (m-30) REVERT: A 307 ILE cc_start: 0.8417 (mt) cc_final: 0.8207 (mp) REVERT: G 69 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8470 (mm-30) REVERT: B 24 ASP cc_start: 0.8492 (m-30) cc_final: 0.8184 (m-30) REVERT: B 307 ILE cc_start: 0.8449 (mp) cc_final: 0.8191 (mp) REVERT: H 120 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8435 (mt-10) REVERT: Y 34 LYS cc_start: 0.8508 (mttp) cc_final: 0.8054 (mttm) REVERT: Y 63 GLU cc_start: 0.8512 (mt-10) cc_final: 0.7864 (tt0) REVERT: C 24 ASP cc_start: 0.8303 (m-30) cc_final: 0.7942 (m-30) REVERT: I 57 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8696 (mt-10) REVERT: I 120 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7880 (mp0) outliers start: 15 outliers final: 10 residues processed: 128 average time/residue: 2.1620 time to fit residues: 310.0482 Evaluate side-chains 125 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 2.148 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 119 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 82 optimal weight: 0.0470 chunk 101 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.2082 ------------------------------------------------------------------------------- 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 = 0.3291 r_free = 0.3291 target = 0.079423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.061390 restraints weight = 83504.810| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.78 r_work: 0.2820 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13446 Z= 0.136 Angle : 0.484 4.522 18288 Z= 0.251 Chirality : 0.041 0.239 2097 Planarity : 0.002 0.025 2301 Dihedral : 4.737 40.150 2337 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.26 % Allowed : 11.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.20), residues: 1635 helix: 3.29 (0.22), residues: 465 sheet: -0.33 (0.31), residues: 297 loop : -0.88 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 14 HIS 0.002 0.001 HIS C 190 PHE 0.012 0.001 PHE H 110 TYR 0.007 0.001 TYR C 108 ARG 0.003 0.000 ARG X 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 18) link_NAG-ASN : angle 1.76097 ( 54) link_BETA1-4 : bond 0.00293 ( 9) link_BETA1-4 : angle 1.83899 ( 27) hydrogen bonds : bond 0.03398 ( 608) hydrogen bonds : angle 4.43004 ( 1761) SS BOND : bond 0.00275 ( 15) SS BOND : angle 0.92826 ( 30) covalent geometry : bond 0.00306 (13404) covalent geometry : angle 0.46870 (18177) *********************** 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 134 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 1.942 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: 0.8408 (m-30) cc_final: 0.8066 (m-30) REVERT: A 307 ILE cc_start: 0.8406 (mt) cc_final: 0.8189 (mp) REVERT: G 69 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8470 (mm-30) REVERT: B 24 ASP cc_start: 0.8559 (m-30) cc_final: 0.8252 (m-30) REVERT: B 307 ILE cc_start: 0.8481 (mp) cc_final: 0.8223 (mp) REVERT: H 120 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8483 (mp0) REVERT: Y 34 LYS cc_start: 0.8504 (mttp) cc_final: 0.8052 (mttm) REVERT: Y 47 MET cc_start: 0.8542 (mmt) cc_final: 0.8178 (mmt) REVERT: Y 63 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7856 (tt0) REVERT: C 24 ASP cc_start: 0.8297 (m-30) cc_final: 0.7937 (m-30) REVERT: I 57 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8702 (mt-10) REVERT: I 120 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: I 149 MET cc_start: 0.8673 (mmp) cc_final: 0.8430 (mmm) outliers start: 17 outliers final: 14 residues processed: 130 average time/residue: 2.2480 time to fit residues: 326.4581 Evaluate side-chains 128 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 2.080 ------------------------------------------------------------------------------- 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 H residue 45 ILE 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 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 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 40 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 131 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3301 r_free = 0.3301 target = 0.079883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.061853 restraints weight = 83400.173| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.78 r_work: 0.2830 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13446 Z= 0.112 Angle : 0.474 6.465 18288 Z= 0.244 Chirality : 0.041 0.237 2097 Planarity : 0.002 0.023 2301 Dihedral : 4.584 39.427 2337 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.12 % Allowed : 11.68 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.20), residues: 1635 helix: 3.38 (0.22), residues: 465 sheet: -0.35 (0.30), residues: 297 loop : -0.86 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 92 HIS 0.002 0.001 HIS G 25 PHE 0.010 0.001 PHE H 110 TYR 0.008 0.001 TYR C 108 ARG 0.002 0.000 ARG X 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 18) link_NAG-ASN : angle 1.69891 ( 54) link_BETA1-4 : bond 0.00289 ( 9) link_BETA1-4 : angle 1.80776 ( 27) hydrogen bonds : bond 0.03295 ( 608) hydrogen bonds : angle 4.35250 ( 1761) SS BOND : bond 0.00243 ( 15) SS BOND : angle 0.87909 ( 30) covalent geometry : bond 0.00251 (13404) covalent geometry : angle 0.46000 (18177) *********************** 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 130 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.987 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: 0.8403 (m-30) cc_final: 0.8061 (m-30) REVERT: A 307 ILE cc_start: 0.8396 (mt) cc_final: 0.8182 (mp) REVERT: G 69 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8451 (mm-30) REVERT: B 307 ILE cc_start: 0.8417 (mp) cc_final: 0.8154 (mp) REVERT: H 120 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8438 (mt-10) REVERT: Y 63 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8041 (tt0) REVERT: C 24 ASP cc_start: 0.8332 (m-30) cc_final: 0.7970 (m-30) REVERT: C 250 MET cc_start: 0.8976 (mtp) cc_final: 0.8746 (mtt) REVERT: I 57 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8707 (mt-10) REVERT: I 106 ARG cc_start: 0.8753 (tpm170) cc_final: 0.8425 (mmm160) REVERT: I 120 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: I 149 MET cc_start: 0.8699 (mmp) cc_final: 0.8461 (mmm) REVERT: Z 4 GLU cc_start: 0.8976 (tt0) cc_final: 0.8695 (tm-30) REVERT: Z 30 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7424 (ttmm) outliers start: 15 outliers final: 13 residues processed: 125 average time/residue: 2.2223 time to fit residues: 309.1857 Evaluate side-chains 127 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 2.218 ------------------------------------------------------------------------------- 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 B residue 171 ASN Chi-restraints excluded: chain H residue 45 ILE 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 33 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 152 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 70 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3308 r_free = 0.3308 target = 0.080235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.062144 restraints weight = 83574.802| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.78 r_work: 0.2834 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13446 Z= 0.097 Angle : 0.474 5.566 18288 Z= 0.244 Chirality : 0.041 0.237 2097 Planarity : 0.002 0.025 2301 Dihedral : 4.500 38.644 2337 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.34 % Allowed : 11.53 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.20), residues: 1635 helix: 3.43 (0.22), residues: 465 sheet: -0.35 (0.31), residues: 291 loop : -0.87 (0.18), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 26 HIS 0.003 0.000 HIS G 25 PHE 0.010 0.001 PHE H 110 TYR 0.007 0.001 TYR C 108 ARG 0.002 0.000 ARG X 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 18) link_NAG-ASN : angle 1.65712 ( 54) link_BETA1-4 : bond 0.00321 ( 9) link_BETA1-4 : angle 1.78857 ( 27) hydrogen bonds : bond 0.03238 ( 608) hydrogen bonds : angle 4.31225 ( 1761) SS BOND : bond 0.00273 ( 15) SS BOND : angle 1.02564 ( 30) covalent geometry : bond 0.00219 (13404) covalent geometry : angle 0.45969 (18177) ********************** 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 135 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 2.208 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: 0.8399 (m-30) cc_final: 0.8055 (m-30) REVERT: A 307 ILE cc_start: 0.8373 (mt) cc_final: 0.8156 (mp) REVERT: G 69 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8467 (mm-30) REVERT: B 307 ILE cc_start: 0.8415 (mp) cc_final: 0.8154 (mp) REVERT: H 57 GLU cc_start: 0.9026 (tt0) cc_final: 0.8791 (mt-10) REVERT: H 120 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8415 (mt-10) REVERT: Y 34 LYS cc_start: 0.8430 (mttp) cc_final: 0.8036 (mttm) REVERT: Y 63 GLU cc_start: 0.8521 (mt-10) cc_final: 0.7918 (tt0) REVERT: C 24 ASP cc_start: 0.8328 (m-30) cc_final: 0.7962 (m-30) REVERT: C 250 MET cc_start: 0.8985 (mtp) cc_final: 0.8754 (mtt) REVERT: I 57 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8694 (mt-10) REVERT: I 106 ARG cc_start: 0.8761 (tpm170) cc_final: 0.8417 (mmm160) REVERT: I 120 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7901 (mp0) REVERT: I 149 MET cc_start: 0.8699 (mmp) cc_final: 0.8454 (mmm) REVERT: Z 4 GLU cc_start: 0.8971 (tt0) cc_final: 0.8692 (tm-30) REVERT: Z 30 LYS cc_start: 0.7741 (ttpp) cc_final: 0.7439 (ttmm) outliers start: 18 outliers final: 15 residues processed: 130 average time/residue: 2.1710 time to fit residues: 315.6088 Evaluate side-chains 130 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 2.251 ------------------------------------------------------------------------------- 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 H residue 45 ILE 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 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 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 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.0060 chunk 9 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 135 optimal weight: 0.0970 chunk 80 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.080464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.062439 restraints weight = 82932.844| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.78 r_work: 0.2839 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13446 Z= 0.097 Angle : 0.465 4.820 18288 Z= 0.239 Chirality : 0.041 0.234 2097 Planarity : 0.002 0.024 2301 Dihedral : 4.324 37.245 2337 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.26 % Allowed : 11.68 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.20), residues: 1635 helix: 3.55 (0.22), residues: 465 sheet: -0.37 (0.31), residues: 291 loop : -0.84 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 26 HIS 0.002 0.000 HIS I 25 PHE 0.010 0.001 PHE H 110 TYR 0.008 0.001 TYR B 154 ARG 0.002 0.000 ARG X 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 18) link_NAG-ASN : angle 1.58637 ( 54) link_BETA1-4 : bond 0.00306 ( 9) link_BETA1-4 : angle 1.77221 ( 27) hydrogen bonds : bond 0.03154 ( 608) hydrogen bonds : angle 4.23867 ( 1761) SS BOND : bond 0.00278 ( 15) SS BOND : angle 0.97897 ( 30) covalent geometry : bond 0.00217 (13404) covalent geometry : angle 0.45186 (18177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14471.02 seconds wall clock time: 249 minutes 10.12 seconds (14950.12 seconds total)