Starting phenix.real_space_refine on Fri Aug 9 07:07:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sk7_40557/08_2024/8sk7_40557_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sk7_40557/08_2024/8sk7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sk7_40557/08_2024/8sk7_40557.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sk7_40557/08_2024/8sk7_40557.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sk7_40557/08_2024/8sk7_40557_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sk7_40557/08_2024/8sk7_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 Residue "A TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 11.87, per 1000 atoms: 0.47 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 - 3.50 Amino acid : False - 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: 20.49 Conformation dependent library (CDL) restraints added in 2.3 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: 2.34 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: 9.88 Time building geometry restraints manager: 21.46 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: 100.45 - 107.15: 474 107.15 - 113.85: 30281 113.85 - 120.56: 8005 120.56 - 127.26: 7158 127.26 - 133.96: 156 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 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: 0.380 Extract box with map and model: 1.060 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 80.250 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.110 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:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.940 ------------------------------------------------------------------------------- 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 13404 Z= 0.245 Angle : 0.527 6.251 18177 Z= 0.270 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 *********************** 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 fitting. rotamer outliers: 6 poor density : 255 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: 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: 2.7023 time to fit residues: 767.4394 Evaluate side-chains 126 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 2.014 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 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 13404 Z= 0.340 Angle : 0.570 4.007 18177 Z= 0.307 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 *********************** 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 fitting. rotamer outliers: 20 poor density : 139 time to evaluate : 1.978 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 outliers start: 20 outliers final: 6 residues processed: 155 average time/residue: 1.9482 time to fit residues: 337.1274 Evaluate side-chains 130 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 1.323 ------------------------------------------------------------------------------- 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 148 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: