Starting phenix.real_space_refine on Wed Aug 7 20:22:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzz_23093/08_2024/7kzz_23093.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzz_23093/08_2024/7kzz_23093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzz_23093/08_2024/7kzz_23093.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzz_23093/08_2024/7kzz_23093.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzz_23093/08_2024/7kzz_23093.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzz_23093/08_2024/7kzz_23093.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.074 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: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 S 28 5.16 5 C 6668 2.51 5 N 1758 2.21 5 O 1998 1.98 5 H 10404 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 105": "OE1" <-> "OE2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ASP 159": "OD1" <-> "OD2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 209": "OD1" <-> "OD2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 229": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "E ASP 2": "OD1" <-> "OD2" Residue "E ASP 18": "OD1" <-> "OD2" Residue "E PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 124": "OD1" <-> "OD2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 49": "OE1" <-> "OE2" Residue "F TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 165": "OE1" <-> "OE2" Residue "F ASP 225": "OD1" <-> "OD2" Residue "F GLU 229": "OE1" <-> "OE2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A ASP 159": "OD1" <-> "OD2" Residue "A PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A ARG 229": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "C ASP 2": "OD1" <-> "OD2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 124": "OD1" <-> "OD2" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 161": "OD1" <-> "OD2" Residue "D GLU 165": "OE1" <-> "OE2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 225": "OD1" <-> "OD2" Residue "D GLU 229": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 20864 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 4376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 4376 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 6, 'TRANS': 274} Chain: "E" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 2915 Classifications: {'peptide': 192} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 181} Chain breaks: 1 Chain: "F" Number of atoms: 3137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3137 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 196} Chain breaks: 2 Chain: "A" Number of atoms: 4376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 4376 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 6, 'TRANS': 274} Chain: "C" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 2915 Classifications: {'peptide': 192} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 181} Chain breaks: 1 Chain: "D" Number of atoms: 3137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3137 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196} Chain breaks: 2 Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 9.77, per 1000 atoms: 0.47 Number of scatterers: 20864 At special positions: 0 Unit cell: (66.024, 158.248, 145.672, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 28 16.00 O 1998 8.00 N 1758 7.00 C 6668 6.00 H 10404 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 196 " distance=2.09 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.05 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 196 " distance=2.08 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 Time building additional restraints: 16.88 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 263 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS B 285 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 234 " pdb="ZN ZN A 302 " - pdb=" ND1 HIS A 250 " pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" ND1 HIS A 73 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 77 " pdb=" ZN A 304 " pdb="ZN ZN A 304 " - pdb=" NE2 HIS A 155 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 234 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 250 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" ND1 HIS B 73 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 77 " pdb=" ZN B 303 " pdb="ZN ZN B 303 " - pdb=" NE2 HIS B 155 " pdb=" ZN B 304 " pdb="ZN ZN B 304 " - pdb=" NE2 HIS B 263 " pdb="ZN ZN B 304 " - pdb=" NE2 HIS A 285 " 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2556 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 27 sheets defined 32.4% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'B' and resid 13 through 33 removed outlier: 4.341A pdb=" N ALA B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU B 25 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LEU B 31 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 66 Processing helix chain 'B' and resid 77 through 80 Processing helix chain 'B' and resid 81 through 106 removed outlier: 3.680A pdb=" N PHE B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 142 removed outlier: 3.557A pdb=" N SER B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 174 removed outlier: 3.764A pdb=" N PHE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 170 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 205 removed outlier: 4.230A pdb=" N ASP B 181 " --> pdb=" O TRP B 177 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 183 " --> pdb=" O TRP B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 224 removed outlier: 4.336A pdb=" N ILE B 220 " --> pdb=" O THR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 258 through 276 removed outlier: 3.594A pdb=" N THR B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LEU B 271 " --> pdb=" O ASP B 267 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.926A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 185 through 189 Processing helix chain 'F' and resid 65 through 68 Processing helix chain 'F' and resid 77 through 79 No H-bonds generated for 'chain 'F' and resid 77 through 79' Processing helix chain 'F' and resid 170 through 175 Processing helix chain 'A' and resid 13 through 30 removed outlier: 4.428A pdb=" N VAL A 19 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 66 Processing helix chain 'A' and resid 79 through 106 removed outlier: 3.512A pdb=" N LEU A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 142 removed outlier: 3.953A pdb=" N SER A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 170 removed outlier: 3.591A pdb=" N HIS A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 177 through 205 removed outlier: 4.468A pdb=" N ASP A 181 " --> pdb=" O TRP A 177 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN A 195 " --> pdb=" O TYR A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 224 removed outlier: 4.311A pdb=" N ILE A 220 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 258 through 276 removed outlier: 3.571A pdb=" N THR A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.937A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 Processing helix chain 'C' and resid 185 through 189 Processing helix chain 'D' and resid 65 through 68 Processing helix chain 'D' and resid 170 through 175 Processing sheet with id=AA1, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.948A pdb=" N GLY B 232 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR B 244 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.948A pdb=" N GLY B 232 " --> pdb=" O GLU B 252 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 5 through 8 Processing sheet with id=AA4, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.138A pdb=" N LEU E 12 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR E 104 " --> pdb=" O TYR E 87 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA E 85 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 90 through 91 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 120 removed outlier: 6.154A pdb=" N TYR E 175 " --> pdb=" O ASN E 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 131 through 132 Processing sheet with id=AA8, first strand: chain 'F' and resid 9 through 10 removed outlier: 3.637A pdb=" N LEU F 21 " --> pdb=" O MET F 86 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU F 23 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR F 81 " --> pdb=" O ASP F 76 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 60 through 63 removed outlier: 5.230A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA F 52 " --> pdb=" O TRP F 39 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE F 37 " --> pdb=" O ILE F 54 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 106 through 107 Processing sheet with id=AB2, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.611A pdb=" N LEU F 195 " --> pdb=" O VAL F 159 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.611A pdb=" N LEU F 195 " --> pdb=" O VAL F 159 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 213 through 215 removed outlier: 3.609A pdb=" N VAL F 224 " --> pdb=" O VAL F 215 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 232 through 234 removed outlier: 3.983A pdb=" N GLY A 232 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 252 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THR A 244 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 232 through 234 removed outlier: 3.983A pdb=" N GLY A 232 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 252 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 5 through 8 Processing sheet with id=AB8, first strand: chain 'C' and resid 37 through 39 removed outlier: 4.262A pdb=" N THR C 104 " --> pdb=" O TYR C 87 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=AC1, first strand: chain 'C' and resid 90 through 91 Processing sheet with id=AC2, first strand: chain 'C' and resid 118 through 120 removed outlier: 6.229A pdb=" N TYR C 175 " --> pdb=" O ASN C 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 131 through 132 Processing sheet with id=AC4, first strand: chain 'D' and resid 9 through 10 removed outlier: 3.567A pdb=" N LEU D 21 " --> pdb=" O MET D 86 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 23 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 60 through 63 removed outlier: 5.234A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA D 52 " --> pdb=" O TRP D 39 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE D 37 " --> pdb=" O ILE D 54 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 106 through 107 Processing sheet with id=AC7, first strand: chain 'D' and resid 137 through 141 removed outlier: 3.573A pdb=" N LEU D 195 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 137 through 141 removed outlier: 3.573A pdb=" N LEU D 195 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 213 through 215 removed outlier: 3.559A pdb=" N VAL D 224 " --> pdb=" O VAL D 215 " (cutoff:3.500A) 505 hydrogen bonds defined for protein. 1362 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: 7.06 Time building geometry restraints manager: 17.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 10394 1.13 - 1.30: 1818 1.30 - 1.48: 4293 1.48 - 1.65: 4541 1.65 - 1.83: 38 Bond restraints: 21084 Sorted by residual: bond pdb=" ND1 HIS B 234 " pdb=" HD1 HIS B 234 " ideal model delta sigma weight residual 0.860 1.034 -0.174 2.00e-02 2.50e+03 7.57e+01 bond pdb=" ND1 HIS A 234 " pdb=" HD1 HIS A 234 " ideal model delta sigma weight residual 0.860 1.033 -0.173 2.00e-02 2.50e+03 7.51e+01 bond pdb=" NH2 ARG B 217 " pdb="HH21 ARG B 217 " ideal model delta sigma weight residual 0.860 1.033 -0.173 2.00e-02 2.50e+03 7.51e+01 bond pdb=" NE2 HIS D 112 " pdb=" HE2 HIS D 112 " ideal model delta sigma weight residual 0.860 1.032 -0.172 2.00e-02 2.50e+03 7.38e+01 bond pdb=" NH2 ARG F 101 " pdb="HH21 ARG F 101 " ideal model delta sigma weight residual 0.860 1.032 -0.172 2.00e-02 2.50e+03 7.36e+01 ... (remaining 21079 not shown) Histogram of bond angle deviations from ideal: 94.16 - 102.36: 98 102.36 - 110.55: 19927 110.55 - 118.75: 9160 118.75 - 126.94: 8635 126.94 - 135.14: 220 Bond angle restraints: 38040 Sorted by residual: angle pdb=" CA PHE F 130 " pdb=" CB PHE F 130 " pdb=" CG PHE F 130 " ideal model delta sigma weight residual 113.80 123.39 -9.59 1.00e+00 1.00e+00 9.20e+01 angle pdb=" CA PHE D 130 " pdb=" CB PHE D 130 " pdb=" CG PHE D 130 " ideal model delta sigma weight residual 113.80 123.00 -9.20 1.00e+00 1.00e+00 8.47e+01 angle pdb=" OD1 ASP A 267 " pdb=" CG ASP A 267 " pdb=" OD2 ASP A 267 " ideal model delta sigma weight residual 122.90 101.34 21.56 2.40e+00 1.74e-01 8.07e+01 angle pdb=" OD1 ASP B 267 " pdb=" CG ASP B 267 " pdb=" OD2 ASP B 267 " ideal model delta sigma weight residual 122.90 101.56 21.34 2.40e+00 1.74e-01 7.90e+01 angle pdb=" OD1 ASP B 70 " pdb=" CG ASP B 70 " pdb=" OD2 ASP B 70 " ideal model delta sigma weight residual 122.90 104.23 18.67 2.40e+00 1.74e-01 6.05e+01 ... (remaining 38035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.37: 9377 26.37 - 52.74: 536 52.74 - 79.11: 97 79.11 - 105.48: 7 105.48 - 131.84: 1 Dihedral angle restraints: 10018 sinusoidal: 5342 harmonic: 4676 Sorted by residual: dihedral pdb=" CA GLU F 165 " pdb=" C GLU F 165 " pdb=" N PRO F 166 " pdb=" CA PRO F 166 " ideal model delta harmonic sigma weight residual 180.00 48.16 131.84 0 5.00e+00 4.00e-02 6.95e+02 dihedral pdb=" CA SER C 1 " pdb=" C SER C 1 " pdb=" N ASP C 2 " pdb=" CA ASP C 2 " ideal model delta harmonic sigma weight residual 180.00 -99.62 -80.38 0 5.00e+00 4.00e-02 2.58e+02 dihedral pdb=" CA VAL D 129 " pdb=" C VAL D 129 " pdb=" N PHE D 130 " pdb=" CA PHE D 130 " ideal model delta harmonic sigma weight residual 180.00 124.26 55.74 0 5.00e+00 4.00e-02 1.24e+02 ... (remaining 10015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 1243 0.139 - 0.278: 377 0.278 - 0.417: 59 0.417 - 0.556: 9 0.556 - 0.695: 4 Chirality restraints: 1692 Sorted by residual: chirality pdb=" CA TRP E 95 " pdb=" N TRP E 95 " pdb=" C TRP E 95 " pdb=" CB TRP E 95 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA TRP C 95 " pdb=" N TRP C 95 " pdb=" C TRP C 95 " pdb=" CB TRP C 95 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" CA LEU D 158 " pdb=" N LEU D 158 " pdb=" C LEU D 158 " pdb=" CB LEU D 158 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.99e+00 ... (remaining 1689 not shown) Planarity restraints: 3126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 33 " 0.340 2.00e-02 2.50e+03 1.29e-01 6.67e+02 pdb=" CG TRP B 33 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP B 33 " -0.068 2.00e-02 2.50e+03 pdb=" CD2 TRP B 33 " -0.159 2.00e-02 2.50e+03 pdb=" NE1 TRP B 33 " -0.146 2.00e-02 2.50e+03 pdb=" CE2 TRP B 33 " -0.093 2.00e-02 2.50e+03 pdb=" CE3 TRP B 33 " -0.127 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 33 " 0.017 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 33 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 33 " 0.081 2.00e-02 2.50e+03 pdb=" HD1 TRP B 33 " 0.117 2.00e-02 2.50e+03 pdb=" HE1 TRP B 33 " -0.023 2.00e-02 2.50e+03 pdb=" HE3 TRP B 33 " -0.136 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 33 " 0.055 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 33 " 0.020 2.00e-02 2.50e+03 pdb=" HH2 TRP B 33 " 0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 33 " 0.324 2.00e-02 2.50e+03 1.25e-01 6.23e+02 pdb=" CG TRP A 33 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP A 33 " -0.066 2.00e-02 2.50e+03 pdb=" CD2 TRP A 33 " -0.158 2.00e-02 2.50e+03 pdb=" NE1 TRP A 33 " -0.140 2.00e-02 2.50e+03 pdb=" CE2 TRP A 33 " -0.093 2.00e-02 2.50e+03 pdb=" CE3 TRP A 33 " -0.124 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 33 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 33 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 33 " 0.079 2.00e-02 2.50e+03 pdb=" HD1 TRP A 33 " 0.120 2.00e-02 2.50e+03 pdb=" HE1 TRP A 33 " -0.013 2.00e-02 2.50e+03 pdb=" HE3 TRP A 33 " -0.127 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 33 " 0.044 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 33 " 0.024 2.00e-02 2.50e+03 pdb=" HH2 TRP A 33 " 0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 41 " 1.120 9.50e-02 1.11e+02 4.01e-01 6.15e+02 pdb=" NE ARG F 41 " 0.076 2.00e-02 2.50e+03 pdb=" CZ ARG F 41 " 0.036 2.00e-02 2.50e+03 pdb=" NH1 ARG F 41 " 0.116 2.00e-02 2.50e+03 pdb=" NH2 ARG F 41 " -0.073 2.00e-02 2.50e+03 pdb="HH11 ARG F 41 " -0.121 2.00e-02 2.50e+03 pdb="HH12 ARG F 41 " -0.134 2.00e-02 2.50e+03 pdb="HH21 ARG F 41 " -0.231 2.00e-02 2.50e+03 pdb="HH22 ARG F 41 " 0.281 2.00e-02 2.50e+03 ... (remaining 3123 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1384 2.15 - 2.76: 37014 2.76 - 3.38: 59354 3.38 - 3.99: 79894 3.99 - 4.60: 117005 Nonbonded interactions: 294651 Sorted by model distance: nonbonded pdb=" O GLY A 119 " pdb=" HG SER A 123 " model vdw 1.541 2.450 nonbonded pdb=" HH TYR F 162 " pdb=" OE1 GLU F 165 " model vdw 1.547 2.450 nonbonded pdb=" OD2 ASP B 254 " pdb=" HG SER E 31 " model vdw 1.558 2.450 nonbonded pdb=" HG SER B 258 " pdb=" OE1 GLU B 261 " model vdw 1.558 2.450 nonbonded pdb=" O GLY B 119 " pdb=" HG SER B 123 " model vdw 1.561 2.450 ... (remaining 294646 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' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 3.030 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: 0.300 Extract box with map and model: 0.790 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 72.360 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 : 0.015 0.075 10680 Z= 0.975 Angle : 2.403 21.555 14538 Z= 1.559 Chirality : 0.135 0.695 1692 Planarity : 0.030 0.502 1830 Dihedral : 16.851 131.844 3766 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 3.21 % Allowed : 12.09 % Favored : 84.70 % Rotamer: Outliers : 3.85 % Allowed : 12.67 % Favored : 83.48 % Cbeta Deviations : 2.35 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 8.93 % Twisted General : 1.85 % 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: -4.38 (0.19), residues: 1340 helix: -3.12 (0.19), residues: 384 sheet: -2.93 (0.24), residues: 316 loop : -2.65 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.254 0.044 TRP B 33 HIS 0.027 0.008 HIS A 263 PHE 0.246 0.024 PHE C 120 TYR 0.200 0.046 TYR F 104 ARG 0.036 0.003 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 135 time to evaluate : 1.694 Fit side-chains revert: symmetry clash REVERT: B 122 VAL cc_start: 0.5077 (OUTLIER) cc_final: 0.4817 (p) REVERT: B 181 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.6904 (m-30) REVERT: F 90 ARG cc_start: 0.7694 (mtm-85) cc_final: 0.6897 (mtm180) REVERT: F 92 GLU cc_start: 0.7403 (pm20) cc_final: 0.6907 (pm20) REVERT: F 104 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.7376 (m-80) REVERT: A 122 VAL cc_start: 0.5129 (OUTLIER) cc_final: 0.4927 (p) REVERT: A 181 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.7072 (m-30) REVERT: D 72 THR cc_start: 0.8903 (m) cc_final: 0.8654 (p) REVERT: D 90 ARG cc_start: 0.7674 (mtm-85) cc_final: 0.6899 (mtm180) REVERT: D 92 GLU cc_start: 0.7417 (pm20) cc_final: 0.6914 (pm20) REVERT: D 104 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.7365 (m-10) outliers start: 44 outliers final: 15 residues processed: 170 average time/residue: 0.5527 time to fit residues: 128.8052 Evaluate side-chains 103 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 104 TYR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 104 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7567 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10680 Z= 0.274 Angle : 0.846 9.533 14538 Z= 0.445 Chirality : 0.047 0.200 1692 Planarity : 0.007 0.178 1830 Dihedral : 9.238 71.081 1496 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.90 % Allowed : 8.96 % Favored : 90.15 % Rotamer: Outliers : 3.06 % Allowed : 15.65 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.46 % 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: -3.29 (0.21), residues: 1340 helix: -1.76 (0.23), residues: 382 sheet: -2.46 (0.26), residues: 328 loop : -2.19 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 179 HIS 0.008 0.002 HIS D 112 PHE 0.016 0.002 PHE E 141 TYR 0.016 0.002 TYR F 55 ARG 0.004 0.001 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 107 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 SER cc_start: 0.8085 (OUTLIER) cc_final: 0.7868 (p) REVERT: B 181 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6764 (m-30) REVERT: D 72 THR cc_start: 0.8897 (m) cc_final: 0.8661 (p) outliers start: 35 outliers final: 17 residues processed: 131 average time/residue: 0.4951 time to fit residues: 94.4100 Evaluate side-chains 101 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 112 HIS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 112 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 0.0980 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7555 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10680 Z= 0.223 Angle : 0.700 9.507 14538 Z= 0.366 Chirality : 0.043 0.169 1692 Planarity : 0.004 0.063 1830 Dihedral : 7.136 54.898 1473 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.82 % Allowed : 9.18 % Favored : 90.00 % Rotamer: Outliers : 2.45 % Allowed : 16.17 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.31 % 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: -2.52 (0.22), residues: 1340 helix: -1.12 (0.25), residues: 382 sheet: -1.80 (0.26), residues: 364 loop : -1.81 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 179 HIS 0.007 0.001 HIS A 234 PHE 0.015 0.001 PHE B 277 TYR 0.014 0.001 TYR F 55 ARG 0.002 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 1.683 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: B 177 TRP cc_start: 0.3164 (m-10) cc_final: 0.2792 (m100) REVERT: B 181 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6778 (m-30) REVERT: B 194 GLN cc_start: 0.7784 (tm-30) cc_final: 0.7444 (tm-30) REVERT: F 92 GLU cc_start: 0.7285 (pp20) cc_final: 0.7078 (pp20) REVERT: D 72 THR cc_start: 0.8856 (m) cc_final: 0.8593 (p) outliers start: 28 outliers final: 15 residues processed: 131 average time/residue: 0.5165 time to fit residues: 97.5443 Evaluate side-chains 108 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 HIS Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain E residue 95 TRP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 112 HIS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain C residue 95 TRP Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 161 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 115 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10680 Z= 0.261 Angle : 0.665 9.638 14538 Z= 0.347 Chirality : 0.042 0.160 1692 Planarity : 0.004 0.056 1830 Dihedral : 6.625 48.311 1470 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.82 % Allowed : 8.96 % Favored : 90.22 % Rotamer: Outliers : 2.53 % Allowed : 16.26 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.15 % 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: -2.18 (0.23), residues: 1340 helix: -0.74 (0.26), residues: 388 sheet: -1.68 (0.26), residues: 364 loop : -1.63 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 179 HIS 0.006 0.001 HIS A 234 PHE 0.013 0.001 PHE E 141 TYR 0.010 0.001 TYR D 55 ARG 0.002 0.000 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 93 time to evaluate : 1.853 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: B 177 TRP cc_start: 0.3258 (m-10) cc_final: 0.2868 (m100) REVERT: B 181 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.6930 (m-30) REVERT: B 201 TYR cc_start: 0.8377 (t80) cc_final: 0.8169 (t80) REVERT: F 8 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8688 (m) REVERT: F 200 THR cc_start: 0.7334 (OUTLIER) cc_final: 0.7093 (t) REVERT: D 200 THR cc_start: 0.7162 (OUTLIER) cc_final: 0.6908 (t) outliers start: 29 outliers final: 17 residues processed: 119 average time/residue: 0.4935 time to fit residues: 85.4370 Evaluate side-chains 106 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 HIS Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain E residue 95 TRP Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 112 HIS Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 200 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 0.0570 chunk 116 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- 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: 0.7568 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10680 Z= 0.253 Angle : 0.646 9.654 14538 Z= 0.336 Chirality : 0.042 0.159 1692 Planarity : 0.004 0.052 1830 Dihedral : 6.307 44.768 1470 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.75 % Allowed : 8.73 % Favored : 90.52 % Rotamer: Outliers : 2.80 % Allowed : 16.61 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.15 % 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: -2.05 (0.23), residues: 1340 helix: -0.52 (0.26), residues: 388 sheet: -1.69 (0.27), residues: 342 loop : -1.60 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 171 HIS 0.006 0.001 HIS A 234 PHE 0.013 0.001 PHE A 277 TYR 0.011 0.001 TYR B 191 ARG 0.002 0.000 ARG D 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 98 time to evaluate : 1.791 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: B 177 TRP cc_start: 0.3219 (m-10) cc_final: 0.2903 (m100) REVERT: B 181 ASP cc_start: 0.7190 (OUTLIER) cc_final: 0.6884 (m-30) REVERT: F 8 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8668 (m) REVERT: F 200 THR cc_start: 0.7198 (OUTLIER) cc_final: 0.6964 (t) REVERT: D 200 THR cc_start: 0.7152 (OUTLIER) cc_final: 0.6918 (t) outliers start: 32 outliers final: 20 residues processed: 126 average time/residue: 0.4258 time to fit residues: 79.3338 Evaluate side-chains 112 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 HIS Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 112 HIS Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 160 LYS Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 200 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 124 optimal weight: 0.0370 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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: