Starting phenix.real_space_refine on Sun Mar 17 05:52:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/03_2024/5bkk_9407_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/03_2024/5bkk_9407.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/03_2024/5bkk_9407_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/03_2024/5bkk_9407_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/03_2024/5bkk_9407_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/03_2024/5bkk_9407.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/03_2024/5bkk_9407.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/03_2024/5bkk_9407_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/03_2024/5bkk_9407_updated.pdb" } resolution = 3.5 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= 0.005 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 K 3 8.98 5 S 68 5.16 5 C 10617 2.51 5 N 2897 2.21 5 O 3246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 42": "OE1" <-> "OE2" Residue "A PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A ASP 254": "OD1" <-> "OD2" Residue "A ASP 284": "OD1" <-> "OD2" Residue "A ASP 300": "OD1" <-> "OD2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "A ASP 309": "OD1" <-> "OD2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 316": "OD1" <-> "OD2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B ASP 169": "OD1" <-> "OD2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 245": "OD1" <-> "OD2" Residue "B TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B ASP 282": "OD1" <-> "OD2" Residue "B ASP 300": "OD1" <-> "OD2" Residue "B GLU 301": "OE1" <-> "OE2" Residue "C PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C ASP 64": "OD1" <-> "OD2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C ASP 145": "OD1" <-> "OD2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C ASP 188": "OD1" <-> "OD2" Residue "C ASP 202": "OD1" <-> "OD2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 248": "OE1" <-> "OE2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D ASP 188": "OD1" <-> "OD2" Residue "D ARG 199": "NH1" <-> "NH2" Residue "D GLU 203": "OE1" <-> "OE2" Residue "D ASP 226": "OD1" <-> "OD2" Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D GLU 271": "OE1" <-> "OE2" Residue "D ASP 284": "OD1" <-> "OD2" Residue "D ASP 287": "OD1" <-> "OD2" Residue "D ASP 300": "OD1" <-> "OD2" Residue "D ASP 309": "OD1" <-> "OD2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E GLU 210": "OE1" <-> "OE2" Residue "E ARG 213": "NH1" <-> "NH2" Residue "E ASP 226": "OD1" <-> "OD2" Residue "E GLU 248": "OE1" <-> "OE2" Residue "E GLU 271": "OE1" <-> "OE2" Residue "E GLU 301": "OE1" <-> "OE2" Residue "E ASP 305": "OD1" <-> "OD2" Residue "E ASP 309": "OD1" <-> "OD2" Residue "E PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 326": "OE1" <-> "OE2" Residue "E GLU 328": "OE1" <-> "OE2" Residue "F PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 145": "OD1" <-> "OD2" Residue "F ASP 169": "OD1" <-> "OD2" Residue "F GLU 186": "OE1" <-> "OE2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "F ASP 245": "OD1" <-> "OD2" Residue "F TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 254": "OD1" <-> "OD2" Residue "F ARG 263": "NH1" <-> "NH2" Residue "F ASP 316": "OD1" <-> "OD2" Residue "F GLU 328": "OE1" <-> "OE2" Residue "G PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 144": "OE1" <-> "OE2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "G ASP 184": "OD1" <-> "OD2" Residue "G ASP 202": "OD1" <-> "OD2" Residue "G GLU 210": "OE1" <-> "OE2" Residue "G ARG 213": "NH1" <-> "NH2" Residue "G ASP 245": "OD1" <-> "OD2" Residue "G GLU 266": "OE1" <-> "OE2" Residue "G GLU 276": "OE1" <-> "OE2" Residue "G ASP 282": "OD1" <-> "OD2" Residue "G ASP 284": "OD1" <-> "OD2" Residue "G ASP 305": "OD1" <-> "OD2" Residue "G PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "H PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 144": "OE1" <-> "OE2" Residue "H ARG 199": "NH1" <-> "NH2" Residue "H GLU 203": "OE1" <-> "OE2" Residue "H PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 263": "NH1" <-> "NH2" Residue "H GLU 266": "OE1" <-> "OE2" Residue "H GLU 271": "OE1" <-> "OE2" Residue "H GLU 276": "OE1" <-> "OE2" Residue "H ASP 300": "OD1" <-> "OD2" Residue "H ASP 305": "OD1" <-> "OD2" Residue "H TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 316": "OD1" <-> "OD2" Residue "H GLU 328": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16831 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2467 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "B" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "C" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2464 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "E" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2464 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "G" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2464 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' K': 1, 'PGW': 1, 'YQ4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' K': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PGW:plan-1': 1, 'PGW:plan-2': 1, 'PGW:plan-3': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 8.91, per 1000 atoms: 0.53 Number of scatterers: 16831 At special positions: 0 Unit cell: (147.96, 147.96, 119.464, 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) K 3 19.00 S 68 16.00 O 3246 8.00 N 2897 7.00 C 10617 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 6.45 Conformation dependent library (CDL) restraints added in 3.0 seconds 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 16 sheets defined 39.7% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain 'A' and resid 22 through 41 removed outlier: 3.530A pdb=" N PHE A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 70 through 106 removed outlier: 4.158A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 128 No H-bonds generated for 'chain 'A' and resid 125 through 128' Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.758A pdb=" N LYS A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 154 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 173 removed outlier: 4.345A pdb=" N LYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 188 through 201 removed outlier: 3.954A pdb=" N ILE A 192 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 223 Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 248 through 255 removed outlier: 3.555A pdb=" N GLN A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 285 through 288 No H-bonds generated for 'chain 'A' and resid 285 through 288' Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.659A pdb=" N GLU A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'B' and resid 147 through 154 removed outlier: 3.611A pdb=" N LYS B 150 " --> pdb=" O ASN B 147 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU B 153 " --> pdb=" O LYS B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 170 No H-bonds generated for 'chain 'B' and resid 167 through 170' Processing helix chain 'B' and resid 188 through 199 removed outlier: 3.742A pdb=" N HIS B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 223 Processing helix chain 'B' and resid 231 through 237 Processing helix chain 'B' and resid 249 through 255 removed outlier: 3.561A pdb=" N ASP B 254 " --> pdb=" O MET B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 334 removed outlier: 3.721A pdb=" N GLU B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 41 removed outlier: 3.954A pdb=" N PHE C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 57 Processing helix chain 'C' and resid 70 through 106 Processing helix chain 'C' and resid 125 through 131 removed outlier: 4.003A pdb=" N CYS C 130 " --> pdb=" O SER C 126 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 131 " --> pdb=" O THR C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 155 removed outlier: 3.549A pdb=" N LYS C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 170 No H-bonds generated for 'chain 'C' and resid 167 through 170' Processing helix chain 'C' and resid 189 through 201 removed outlier: 3.518A pdb=" N LYS C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 223 removed outlier: 4.388A pdb=" N GLU C 218 " --> pdb=" O GLU C 215 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG C 221 " --> pdb=" O GLU C 218 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET C 222 " --> pdb=" O GLN C 219 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 223 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 239 Processing helix chain 'C' and resid 248 through 255 Processing helix chain 'C' and resid 280 through 283 No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 285 through 288 No H-bonds generated for 'chain 'C' and resid 285 through 288' Processing helix chain 'C' and resid 324 through 333 removed outlier: 3.625A pdb=" N GLU C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN C 332 " --> pdb=" O GLU C 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 128 No H-bonds generated for 'chain 'D' and resid 125 through 128' Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 146 through 154 removed outlier: 3.774A pdb=" N LYS D 150 " --> pdb=" O ASN D 147 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL D 152 " --> pdb=" O ARG D 149 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG D 154 " --> pdb=" O LYS D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 170 No H-bonds generated for 'chain 'D' and resid 167 through 170' Processing helix chain 'D' and resid 189 through 199 Processing helix chain 'D' and resid 217 through 223 removed outlier: 3.924A pdb=" N MET D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 240 removed outlier: 3.643A pdb=" N SER D 240 " --> pdb=" O GLY D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 255 removed outlier: 3.521A pdb=" N ASP D 254 " --> pdb=" O MET D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 283 No H-bonds generated for 'chain 'D' and resid 280 through 283' Processing helix chain 'D' and resid 285 through 289 removed outlier: 3.647A pdb=" N THR D 289 " --> pdb=" O ILE D 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 285 through 289' Processing helix chain 'D' and resid 324 through 334 removed outlier: 3.793A pdb=" N GLU D 328 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 42 removed outlier: 4.165A pdb=" N ILE E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 70 through 106 Processing helix chain 'E' and resid 131 through 133 No H-bonds generated for 'chain 'E' and resid 131 through 133' Processing helix chain 'E' and resid 147 through 155 removed outlier: 3.645A pdb=" N LYS E 151 " --> pdb=" O ASN E 147 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 170 No H-bonds generated for 'chain 'E' and resid 167 through 170' Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 188 through 201 removed outlier: 3.722A pdb=" N HIS E 193 " --> pdb=" O SER E 189 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 223 removed outlier: 3.571A pdb=" N ARG E 221 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 239 Processing helix chain 'E' and resid 248 through 255 removed outlier: 3.561A pdb=" N ASP E 254 " --> pdb=" O MET E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 283 No H-bonds generated for 'chain 'E' and resid 280 through 283' Processing helix chain 'E' and resid 285 through 289 Processing helix chain 'E' and resid 324 through 328 removed outlier: 3.871A pdb=" N GLU E 328 " --> pdb=" O PRO E 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 324 through 328' Processing helix chain 'E' and resid 330 through 333 No H-bonds generated for 'chain 'E' and resid 330 through 333' Processing helix chain 'F' and resid 125 through 128 No H-bonds generated for 'chain 'F' and resid 125 through 128' Processing helix chain 'F' and resid 130 through 133 removed outlier: 3.851A pdb=" N GLU F 133 " --> pdb=" O CYS F 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 130 through 133' Processing helix chain 'F' and resid 148 through 154 Processing helix chain 'F' and resid 167 through 170 No H-bonds generated for 'chain 'F' and resid 167 through 170' Processing helix chain 'F' and resid 188 through 201 removed outlier: 3.725A pdb=" N ILE F 192 " --> pdb=" O ASP F 188 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS F 200 " --> pdb=" O LEU F 196 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE F 201 " --> pdb=" O GLY F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 223 Processing helix chain 'F' and resid 231 through 240 removed outlier: 3.661A pdb=" N MET F 239 " --> pdb=" O SER F 235 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER F 240 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 255 removed outlier: 3.508A pdb=" N ASP F 254 " --> pdb=" O MET F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 334 removed outlier: 3.949A pdb=" N GLU F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 41 removed outlier: 3.513A pdb=" N THR G 35 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA G 36 " --> pdb=" O TYR G 33 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY G 37 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N HIS G 39 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 57 Processing helix chain 'G' and resid 70 through 104 Processing helix chain 'G' and resid 125 through 128 No H-bonds generated for 'chain 'G' and resid 125 through 128' Processing helix chain 'G' and resid 146 through 155 removed outlier: 3.629A pdb=" N LYS G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 170 No H-bonds generated for 'chain 'G' and resid 167 through 170' Processing helix chain 'G' and resid 188 through 199 removed outlier: 3.507A pdb=" N HIS G 193 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 223 removed outlier: 4.561A pdb=" N GLU G 218 " --> pdb=" O GLU G 215 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG G 221 " --> pdb=" O GLU G 218 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET G 222 " --> pdb=" O GLN G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 237 Processing helix chain 'G' and resid 248 through 255 Processing helix chain 'G' and resid 280 through 283 No H-bonds generated for 'chain 'G' and resid 280 through 283' Processing helix chain 'G' and resid 285 through 288 No H-bonds generated for 'chain 'G' and resid 285 through 288' Processing helix chain 'G' and resid 324 through 333 removed outlier: 3.803A pdb=" N ARG G 329 " --> pdb=" O GLU G 325 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU G 330 " --> pdb=" O GLU G 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 130 Processing helix chain 'H' and resid 147 through 155 removed outlier: 3.599A pdb=" N LYS H 150 " --> pdb=" O ASN H 147 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL H 152 " --> pdb=" O ARG H 149 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU H 153 " --> pdb=" O LYS H 150 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG H 154 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 170 No H-bonds generated for 'chain 'H' and resid 167 through 170' Processing helix chain 'H' and resid 189 through 201 removed outlier: 3.668A pdb=" N ILE H 201 " --> pdb=" O GLY H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 223 removed outlier: 4.507A pdb=" N GLU H 218 " --> pdb=" O GLU H 215 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG H 221 " --> pdb=" O GLU H 218 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET H 222 " --> pdb=" O GLN H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 240 removed outlier: 3.655A pdb=" N SER H 240 " --> pdb=" O GLY H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 255 Processing helix chain 'H' and resid 324 through 331 removed outlier: 3.663A pdb=" N GLU H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG H 329 " --> pdb=" O GLU H 325 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 158 through 161 removed outlier: 6.298A pdb=" N VAL A 118 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU A 142 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE A 120 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL A 119 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL A 181 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N CYS A 121 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL A 183 " --> pdb=" O CYS A 121 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG A 206 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL A 183 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE A 208 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN A 227 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 262 through 268 removed outlier: 6.919A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE A 293 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 227 through 230 removed outlier: 3.539A pdb=" N ILE B 229 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 119 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASN B 158 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ALA B 143 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL B 160 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 262 through 268 removed outlier: 3.528A pdb=" N GLY B 295 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 227 through 229 removed outlier: 6.524A pdb=" N ASN C 158 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ALA C 143 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL C 160 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 262 through 267 removed outlier: 3.666A pdb=" N ILE C 317 " --> pdb=" O GLY C 297 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE C 321 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE C 293 " --> pdb=" O ILE C 321 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 206 through 209 removed outlier: 6.946A pdb=" N VAL D 119 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASN D 158 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ALA D 143 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL D 160 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 262 through 268 removed outlier: 3.524A pdb=" N GLY D 295 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ILE D 293 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 227 through 229 removed outlier: 6.598A pdb=" N ASN E 158 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ALA E 143 " --> pdb=" O ASN E 158 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL E 160 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 265 through 268 removed outlier: 3.853A pdb=" N ILE E 317 " --> pdb=" O GLY E 297 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY E 295 " --> pdb=" O LEU E 319 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE E 321 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ILE E 293 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL E 296 " --> pdb=" O ILE E 303 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 227 through 229 removed outlier: 3.688A pdb=" N ILE F 229 " --> pdb=" O ALA F 209 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL F 119 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASN F 158 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ALA F 143 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL F 160 " --> pdb=" O ALA F 143 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 262 through 268 removed outlier: 6.981A pdb=" N ILE F 321 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ILE F 293 " --> pdb=" O ILE F 321 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 227 through 230 removed outlier: 6.685A pdb=" N ASN G 158 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ALA G 143 " --> pdb=" O ASN G 158 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL G 160 " --> pdb=" O ALA G 143 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 262 through 268 removed outlier: 7.117A pdb=" N ILE G 321 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE G 293 " --> pdb=" O ILE G 321 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 180 through 183 removed outlier: 6.328A pdb=" N ASN H 158 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ALA H 143 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL H 160 " --> pdb=" O ALA H 143 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 262 through 268 removed outlier: 6.998A pdb=" N ILE H 321 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE H 293 " --> pdb=" O ILE H 321 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1590 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.59 Time building geometry restraints manager: 7.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5596 1.34 - 1.46: 2021 1.46 - 1.57: 9335 1.57 - 1.69: 3 1.69 - 1.81: 112 Bond restraints: 17067 Sorted by residual: bond pdb=" C1 PGW A 401 " pdb=" O01 PGW A 401 " ideal model delta sigma weight residual 1.332 1.455 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C19 PGW A 401 " pdb=" O03 PGW A 401 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" CA LEU A 275 " pdb=" C LEU A 275 " ideal model delta sigma weight residual 1.525 1.547 -0.022 1.22e-02 6.72e+03 3.30e+00 bond pdb=" C13 YQ4 A 403 " pdb=" N01 YQ4 A 403 " ideal model delta sigma weight residual 1.481 1.517 -0.036 2.00e-02 2.50e+03 3.30e+00 bond pdb=" C13 YQ4 A 403 " pdb=" C14 YQ4 A 403 " ideal model delta sigma weight residual 1.539 1.574 -0.035 2.00e-02 2.50e+03 3.11e+00 ... (remaining 17062 not shown) Histogram of bond angle deviations from ideal: 99.29 - 106.22: 314 106.22 - 113.16: 9421 113.16 - 120.09: 6267 120.09 - 127.02: 6943 127.02 - 133.96: 128 Bond angle restraints: 23073 Sorted by residual: angle pdb=" N LEU H 275 " pdb=" CA LEU H 275 " pdb=" C LEU H 275 " ideal model delta sigma weight residual 112.41 118.31 -5.90 1.30e+00 5.92e-01 2.06e+01 angle pdb=" C SER C 273 " pdb=" N LYS C 274 " pdb=" CA LYS C 274 " ideal model delta sigma weight residual 121.54 129.94 -8.40 1.91e+00 2.74e-01 1.94e+01 angle pdb=" N VAL G 60 " pdb=" CA VAL G 60 " pdb=" C VAL G 60 " ideal model delta sigma weight residual 111.67 107.96 3.71 9.50e-01 1.11e+00 1.53e+01 angle pdb=" C11 YQ4 A 403 " pdb=" C12 YQ4 A 403 " pdb=" N01 YQ4 A 403 " ideal model delta sigma weight residual 109.57 120.44 -10.87 3.00e+00 1.11e-01 1.31e+01 angle pdb=" C SER D 273 " pdb=" N LYS D 274 " pdb=" CA LYS D 274 " ideal model delta sigma weight residual 121.54 127.89 -6.35 1.91e+00 2.74e-01 1.11e+01 ... (remaining 23068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.80: 10094 32.80 - 65.61: 249 65.61 - 98.41: 30 98.41 - 131.22: 2 131.22 - 164.02: 1 Dihedral angle restraints: 10376 sinusoidal: 4224 harmonic: 6152 Sorted by residual: dihedral pdb=" CA SER D 273 " pdb=" C SER D 273 " pdb=" N LYS D 274 " pdb=" CA LYS D 274 " ideal model delta harmonic sigma weight residual 180.00 156.38 23.62 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ASP D 284 " pdb=" C ASP D 284 " pdb=" N ILE D 285 " pdb=" CA ILE D 285 " ideal model delta harmonic sigma weight residual -180.00 -156.81 -23.19 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" C01 PGW A 401 " pdb=" C19 PGW A 401 " pdb=" O03 PGW A 401 " pdb=" O04 PGW A 401 " ideal model delta sinusoidal sigma weight residual 9.00 173.02 -164.02 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 10373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2032 0.057 - 0.113: 540 0.113 - 0.170: 105 0.170 - 0.227: 8 0.227 - 0.283: 2 Chirality restraints: 2687 Sorted by residual: chirality pdb=" CB ILE H 334 " pdb=" CA ILE H 334 " pdb=" CG1 ILE H 334 " pdb=" CG2 ILE H 334 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CB ILE F 317 " pdb=" CA ILE F 317 " pdb=" CG1 ILE F 317 " pdb=" CG2 ILE F 317 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB ILE F 285 " pdb=" CA ILE F 285 " pdb=" CG1 ILE F 285 " pdb=" CG2 ILE F 285 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2684 not shown) Planarity restraints: 2993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 69 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO C 70 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 70 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 70 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 274 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.18e+00 pdb=" C LYS H 274 " 0.035 2.00e-02 2.50e+03 pdb=" O LYS H 274 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU H 275 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 267 " -0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO A 268 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 268 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 268 " -0.027 5.00e-02 4.00e+02 ... (remaining 2990 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 5089 2.82 - 3.40: 17415 3.40 - 3.98: 31642 3.98 - 4.56: 44265 4.56 - 5.14: 67740 Nonbonded interactions: 166151 Sorted by model distance: nonbonded pdb=" O VAL G 60 " pdb=" K K G 402 " model vdw 2.242 2.850 nonbonded pdb=" OG SER F 279 " pdb=" O ARG F 308 " model vdw 2.273 2.440 nonbonded pdb=" OG SER E 126 " pdb=" OD2 ASP E 184 " model vdw 2.289 2.440 nonbonded pdb=" OH TYR C 62 " pdb=" OG1 THR E 56 " model vdw 2.298 2.440 nonbonded pdb=" OG SER C 126 " pdb=" OD2 ASP C 184 " model vdw 2.301 2.440 ... (remaining 166146 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 274 or (resid 275 and (name N or name CA or nam \ e C or name O or name CB )) or resid 276 through 336)) selection = chain 'C' selection = (chain 'E' and resid 20 through 336) selection = (chain 'G' and resid 20 through 336) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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 group one per residue 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: 0.770 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: 0.020 Extract box with map and model: 3.870 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 44.310 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 0.123 17067 Z= 0.304 Angle : 0.719 10.866 23073 Z= 0.402 Chirality : 0.053 0.283 2687 Planarity : 0.005 0.051 2993 Dihedral : 14.929 164.021 6424 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.11 % Allowed : 6.16 % Favored : 93.73 % 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: -4.88 (0.13), residues: 2140 helix: -3.78 (0.09), residues: 976 sheet: -1.91 (0.26), residues: 316 loop : -2.83 (0.17), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 52 HIS 0.006 0.001 HIS A 117 PHE 0.010 0.001 PHE A 87 TYR 0.012 0.002 TYR E 33 ARG 0.003 0.000 ARG D 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 453 time to evaluate : 2.005 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8256 (mm) cc_final: 0.8036 (mm) REVERT: A 114 LYS cc_start: 0.7929 (mmtp) cc_final: 0.7498 (mmmt) REVERT: A 149 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7880 (ttp-170) REVERT: A 200 LYS cc_start: 0.8285 (ttmt) cc_final: 0.8081 (ttmm) REVERT: A 239 MET cc_start: 0.8335 (mtt) cc_final: 0.8106 (mtt) REVERT: B 210 GLU cc_start: 0.7860 (tt0) cc_final: 0.7653 (tt0) REVERT: C 93 ARG cc_start: 0.7625 (mmt180) cc_final: 0.7350 (mmt180) REVERT: D 200 LYS cc_start: 0.7933 (mmtt) cc_final: 0.7724 (mtmt) REVERT: D 239 MET cc_start: 0.7936 (mtt) cc_final: 0.7618 (mtt) REVERT: E 35 THR cc_start: 0.7684 (p) cc_final: 0.7278 (p) REVERT: E 84 ILE cc_start: 0.8978 (mm) cc_final: 0.8562 (mt) REVERT: E 94 LEU cc_start: 0.8554 (tt) cc_final: 0.8299 (tt) REVERT: E 98 LEU cc_start: 0.9036 (tp) cc_final: 0.8705 (tp) REVERT: E 241 ARG cc_start: 0.6839 (mtt180) cc_final: 0.6497 (mtt-85) REVERT: F 125 GLU cc_start: 0.8767 (tp30) cc_final: 0.8403 (tp30) REVERT: G 92 GLU cc_start: 0.7938 (tp30) cc_final: 0.7270 (tp30) REVERT: H 203 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6738 (tp30) REVERT: H 239 MET cc_start: 0.8725 (mtt) cc_final: 0.8511 (mtt) outliers start: 2 outliers final: 0 residues processed: 454 average time/residue: 0.3553 time to fit residues: 226.0757 Evaluate side-chains 344 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 0.1980 chunk 54 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 85 optimal weight: 0.2980 chunk 166 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN C 39 HIS C 332 ASN D 286 HIS E 39 HIS E 158 ASN E 227 GLN E 286 HIS F 286 HIS G 219 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17067 Z= 0.271 Angle : 0.509 7.748 23073 Z= 0.270 Chirality : 0.046 0.150 2687 Planarity : 0.004 0.063 2993 Dihedral : 7.755 149.206 2426 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.45 % Allowed : 11.24 % Favored : 86.31 % 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: -3.52 (0.15), residues: 2140 helix: -2.31 (0.13), residues: 982 sheet: -1.68 (0.26), residues: 312 loop : -2.42 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 52 HIS 0.007 0.001 HIS E 286 PHE 0.012 0.001 PHE E 75 TYR 0.022 0.001 TYR F 333 ARG 0.006 0.000 ARG F 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 359 time to evaluate : 1.872 Fit side-chains REVERT: A 24 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7655 (mp) REVERT: A 114 LYS cc_start: 0.7942 (mmtp) cc_final: 0.7470 (mmmt) REVERT: A 210 GLU cc_start: 0.7689 (tt0) cc_final: 0.7215 (tt0) REVERT: B 210 GLU cc_start: 0.7837 (tt0) cc_final: 0.7559 (tt0) REVERT: C 93 ARG cc_start: 0.7668 (mmt180) cc_final: 0.7333 (mmt180) REVERT: C 135 ARG cc_start: 0.7218 (mtt90) cc_final: 0.6950 (mtm-85) REVERT: C 301 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6310 (pm20) REVERT: D 154 ARG cc_start: 0.6994 (mtt180) cc_final: 0.6751 (mtm-85) REVERT: D 239 MET cc_start: 0.8019 (mtt) cc_final: 0.7780 (mtt) REVERT: D 266 GLU cc_start: 0.8350 (pm20) cc_final: 0.8120 (mp0) REVERT: E 73 MET cc_start: 0.8077 (mtm) cc_final: 0.7792 (mtm) REVERT: E 84 ILE cc_start: 0.9014 (mm) cc_final: 0.8610 (mt) REVERT: E 94 LEU cc_start: 0.8621 (tt) cc_final: 0.8231 (tt) REVERT: E 241 ARG cc_start: 0.6896 (mtt180) cc_final: 0.6592 (mtt-85) REVERT: F 125 GLU cc_start: 0.8876 (tp30) cc_final: 0.8585 (tp30) REVERT: F 300 ASP cc_start: 0.7511 (m-30) cc_final: 0.7193 (t70) REVERT: G 92 GLU cc_start: 0.7979 (tp30) cc_final: 0.7509 (tp30) REVERT: G 300 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.7139 (t0) REVERT: H 203 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6699 (mm-30) REVERT: H 239 MET cc_start: 0.8544 (mtt) cc_final: 0.8195 (mtt) outliers start: 45 outliers final: 29 residues processed: 381 average time/residue: 0.3468 time to fit residues: 189.8191 Evaluate side-chains 357 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 325 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 282 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 192 optimal weight: 1.9990 chunk 208 optimal weight: 7.9990 chunk 171 optimal weight: 3.9990 chunk 191 optimal weight: 0.2980 chunk 65 optimal weight: 5.9990 chunk 154 optimal weight: 0.4980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17067 Z= 0.222 Angle : 0.474 7.401 23073 Z= 0.247 Chirality : 0.046 0.155 2687 Planarity : 0.003 0.054 2993 Dihedral : 7.314 135.962 2426 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.35 % Allowed : 14.57 % Favored : 83.09 % 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: -2.72 (0.16), residues: 2140 helix: -1.57 (0.14), residues: 1006 sheet: -1.51 (0.26), residues: 312 loop : -2.01 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 52 HIS 0.004 0.001 HIS A 117 PHE 0.012 0.001 PHE G 75 TYR 0.022 0.001 TYR F 333 ARG 0.005 0.000 ARG F 241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 340 time to evaluate : 1.907 Fit side-chains REVERT: A 114 LYS cc_start: 0.7926 (mmtp) cc_final: 0.7445 (mmmt) REVERT: A 145 ASP cc_start: 0.7911 (m-30) cc_final: 0.7633 (m-30) REVERT: A 210 GLU cc_start: 0.7616 (tt0) cc_final: 0.7256 (tt0) REVERT: B 169 ASP cc_start: 0.8973 (t70) cc_final: 0.8653 (t0) REVERT: B 210 GLU cc_start: 0.7793 (tt0) cc_final: 0.7459 (tt0) REVERT: B 250 MET cc_start: 0.8713 (ttm) cc_final: 0.8473 (mtp) REVERT: C 93 ARG cc_start: 0.7756 (mmt180) cc_final: 0.7410 (mmt180) REVERT: C 135 ARG cc_start: 0.7118 (mtt90) cc_final: 0.6885 (mtm-85) REVERT: C 301 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6261 (pm20) REVERT: D 239 MET cc_start: 0.8044 (mtt) cc_final: 0.7833 (mtt) REVERT: D 266 GLU cc_start: 0.8347 (pm20) cc_final: 0.7759 (mp0) REVERT: E 73 MET cc_start: 0.8103 (mtm) cc_final: 0.7809 (mtm) REVERT: E 84 ILE cc_start: 0.9001 (mm) cc_final: 0.8584 (mt) REVERT: E 241 ARG cc_start: 0.6876 (mtt180) cc_final: 0.6474 (mtt-85) REVERT: E 288 VAL cc_start: 0.8076 (p) cc_final: 0.7847 (m) REVERT: F 125 GLU cc_start: 0.8860 (tp30) cc_final: 0.8458 (tp30) REVERT: F 323 LYS cc_start: 0.8891 (mttt) cc_final: 0.8608 (mtpp) REVERT: G 25 LEU cc_start: 0.8094 (mp) cc_final: 0.7713 (mt) REVERT: G 248 GLU cc_start: 0.7596 (tt0) cc_final: 0.7084 (tt0) REVERT: G 300 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.7046 (t0) REVERT: H 203 GLU cc_start: 0.6853 (mm-30) cc_final: 0.6516 (tp30) REVERT: H 239 MET cc_start: 0.8539 (mtt) cc_final: 0.8159 (mtt) outliers start: 43 outliers final: 35 residues processed: 357 average time/residue: 0.3246 time to fit residues: 166.9868 Evaluate side-chains 355 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 318 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 245 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 92 optimal weight: 0.1980 chunk 129 optimal weight: 0.1980 chunk 193 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 101 optimal weight: 0.0980 chunk 183 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17067 Z= 0.120 Angle : 0.436 7.092 23073 Z= 0.225 Chirality : 0.044 0.145 2687 Planarity : 0.003 0.047 2993 Dihedral : 6.738 125.032 2426 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.07 % Allowed : 15.33 % Favored : 82.60 % 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: -1.95 (0.17), residues: 2140 helix: -0.84 (0.16), residues: 1000 sheet: -1.10 (0.28), residues: 304 loop : -1.78 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 52 HIS 0.002 0.000 HIS G 39 PHE 0.012 0.001 PHE G 75 TYR 0.021 0.001 TYR F 333 ARG 0.006 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 345 time to evaluate : 1.940 Fit side-chains REVERT: A 114 LYS cc_start: 0.7986 (mmtp) cc_final: 0.7481 (mmmt) REVERT: A 145 ASP cc_start: 0.7844 (m-30) cc_final: 0.7577 (m-30) REVERT: B 169 ASP cc_start: 0.8929 (t70) cc_final: 0.8651 (t0) REVERT: B 210 GLU cc_start: 0.7715 (tt0) cc_final: 0.7427 (tt0) REVERT: B 250 MET cc_start: 0.8680 (ttm) cc_final: 0.8454 (mtp) REVERT: C 135 ARG cc_start: 0.7129 (mtt90) cc_final: 0.6896 (mtm-85) REVERT: D 239 MET cc_start: 0.7916 (mtt) cc_final: 0.7683 (mtt) REVERT: D 266 GLU cc_start: 0.8341 (pm20) cc_final: 0.7890 (mp0) REVERT: E 73 MET cc_start: 0.8191 (mtm) cc_final: 0.7955 (mtm) REVERT: E 84 ILE cc_start: 0.9007 (mm) cc_final: 0.8571 (mt) REVERT: E 241 ARG cc_start: 0.6814 (mtt180) cc_final: 0.6515 (mtt-85) REVERT: E 288 VAL cc_start: 0.8039 (p) cc_final: 0.7795 (m) REVERT: F 125 GLU cc_start: 0.8821 (tp30) cc_final: 0.8449 (tp30) REVERT: F 300 ASP cc_start: 0.7381 (m-30) cc_final: 0.7099 (t70) REVERT: F 323 LYS cc_start: 0.8903 (mttt) cc_final: 0.8632 (mtpp) REVERT: G 25 LEU cc_start: 0.7993 (mp) cc_final: 0.7775 (mt) REVERT: G 248 GLU cc_start: 0.7674 (tt0) cc_final: 0.7369 (tt0) REVERT: H 203 GLU cc_start: 0.6885 (mm-30) cc_final: 0.6524 (tp30) REVERT: H 239 MET cc_start: 0.8501 (mtt) cc_final: 0.8183 (mtt) outliers start: 38 outliers final: 27 residues processed: 358 average time/residue: 0.3193 time to fit residues: 165.8000 Evaluate side-chains 355 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 328 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 282 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 152 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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 0.060 17067 Z= 0.358 Angle : 0.529 7.533 23073 Z= 0.275 Chirality : 0.048 0.265 2687 Planarity : 0.004 0.051 2993 Dihedral : 6.812 128.261 2426 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.84 % Allowed : 16.31 % Favored : 80.85 % 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: -1.96 (0.17), residues: 2140 helix: -0.80 (0.15), residues: 1010 sheet: -1.20 (0.27), residues: 312 loop : -1.80 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 52 HIS 0.007 0.001 HIS A 117 PHE 0.010 0.001 PHE A 75 TYR 0.023 0.002 TYR F 333 ARG 0.006 0.000 ARG F 241 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 343 time to evaluate : 1.875 Fit side-chains REVERT: A 114 LYS cc_start: 0.7924 (mmtp) cc_final: 0.7482 (mmmt) REVERT: B 210 GLU cc_start: 0.7776 (tt0) cc_final: 0.7556 (tt0) REVERT: C 96 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7454 (mt-10) REVERT: D 215 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8542 (pm20) REVERT: D 239 MET cc_start: 0.8119 (mtt) cc_final: 0.7861 (mtt) REVERT: D 266 GLU cc_start: 0.8382 (pm20) cc_final: 0.7919 (mp0) REVERT: D 328 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7769 (mm-30) REVERT: E 73 MET cc_start: 0.8324 (mtm) cc_final: 0.8059 (mtm) REVERT: E 84 ILE cc_start: 0.8993 (mm) cc_final: 0.8574 (mt) REVERT: E 241 ARG cc_start: 0.6735 (mtt180) cc_final: 0.6420 (mtt-85) REVERT: F 125 GLU cc_start: 0.8903 (tp30) cc_final: 0.8507 (tp30) REVERT: F 215 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8272 (pm20) REVERT: F 300 ASP cc_start: 0.7468 (m-30) cc_final: 0.7168 (t70) REVERT: F 323 LYS cc_start: 0.8899 (mttt) cc_final: 0.8569 (mtpp) REVERT: G 248 GLU cc_start: 0.7624 (tt0) cc_final: 0.7123 (tt0) REVERT: H 203 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6615 (tp30) REVERT: H 239 MET cc_start: 0.8579 (mtt) cc_final: 0.8182 (mtt) outliers start: 52 outliers final: 44 residues processed: 371 average time/residue: 0.3117 time to fit residues: 167.6826 Evaluate side-chains 360 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 314 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 282 ASP Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 319 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 0.0170 chunk 50 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 170 optimal weight: 0.3980 chunk 94 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17067 Z= 0.151 Angle : 0.454 8.080 23073 Z= 0.233 Chirality : 0.045 0.159 2687 Planarity : 0.003 0.048 2993 Dihedral : 6.498 118.580 2426 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.40 % Allowed : 17.84 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.50 (0.18), residues: 2140 helix: -0.40 (0.16), residues: 1004 sheet: -0.96 (0.28), residues: 304 loop : -1.62 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 52 HIS 0.002 0.001 HIS A 117 PHE 0.012 0.001 PHE G 75 TYR 0.022 0.001 TYR F 333 ARG 0.008 0.000 ARG D 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 339 time to evaluate : 1.843 Fit side-chains REVERT: A 114 LYS cc_start: 0.8041 (mmtp) cc_final: 0.7516 (mmmt) REVERT: A 210 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: B 169 ASP cc_start: 0.8964 (t70) cc_final: 0.8645 (t0) REVERT: B 210 GLU cc_start: 0.7794 (tt0) cc_final: 0.7513 (tt0) REVERT: B 215 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8435 (pm20) REVERT: D 239 MET cc_start: 0.7999 (mtt) cc_final: 0.7721 (mtt) REVERT: D 266 GLU cc_start: 0.8367 (pm20) cc_final: 0.7913 (mp0) REVERT: D 328 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7754 (mm-30) REVERT: E 73 MET cc_start: 0.8275 (mtm) cc_final: 0.8024 (mtm) REVERT: E 84 ILE cc_start: 0.9007 (mm) cc_final: 0.8581 (mt) REVERT: E 169 ASP cc_start: 0.8571 (m-30) cc_final: 0.8368 (m-30) REVERT: E 241 ARG cc_start: 0.6700 (mtt180) cc_final: 0.6354 (mtt-85) REVERT: F 125 GLU cc_start: 0.8812 (tp30) cc_final: 0.8518 (tp30) REVERT: F 150 LYS cc_start: 0.7947 (mtmt) cc_final: 0.7610 (mmmt) REVERT: F 300 ASP cc_start: 0.7379 (m-30) cc_final: 0.7118 (t70) REVERT: F 323 LYS cc_start: 0.8937 (mttt) cc_final: 0.8561 (mtpp) REVERT: G 25 LEU cc_start: 0.7727 (mp) cc_final: 0.7485 (mt) REVERT: G 248 GLU cc_start: 0.7752 (tt0) cc_final: 0.7240 (tt0) REVERT: H 203 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6560 (tp30) REVERT: H 239 MET cc_start: 0.8545 (mtt) cc_final: 0.8158 (mtt) outliers start: 44 outliers final: 36 residues processed: 356 average time/residue: 0.3172 time to fit residues: 164.3217 Evaluate side-chains 357 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 319 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 282 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 172 optimal weight: 0.5980 chunk 114 optimal weight: 8.9990 chunk 204 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17067 Z= 0.171 Angle : 0.460 8.566 23073 Z= 0.235 Chirality : 0.045 0.141 2687 Planarity : 0.003 0.047 2993 Dihedral : 6.376 116.349 2426 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.67 % Allowed : 18.22 % Favored : 79.11 % 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: -1.29 (0.18), residues: 2140 helix: -0.24 (0.16), residues: 1008 sheet: -0.86 (0.28), residues: 304 loop : -1.49 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 52 HIS 0.009 0.001 HIS G 39 PHE 0.011 0.001 PHE G 75 TYR 0.024 0.001 TYR F 333 ARG 0.007 0.000 ARG F 241 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 332 time to evaluate : 1.734 Fit side-chains REVERT: A 114 LYS cc_start: 0.8026 (mmtp) cc_final: 0.7499 (mmmt) REVERT: A 210 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7851 (tt0) REVERT: B 210 GLU cc_start: 0.7799 (tt0) cc_final: 0.7531 (tt0) REVERT: D 239 MET cc_start: 0.8047 (mtt) cc_final: 0.7772 (mtt) REVERT: D 266 GLU cc_start: 0.8356 (pm20) cc_final: 0.7914 (mp0) REVERT: D 328 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7792 (mm-30) REVERT: E 73 MET cc_start: 0.8279 (mtm) cc_final: 0.8027 (mtm) REVERT: E 84 ILE cc_start: 0.9001 (mm) cc_final: 0.8578 (mt) REVERT: E 241 ARG cc_start: 0.6736 (mtt180) cc_final: 0.6373 (mtt-85) REVERT: E 264 MET cc_start: 0.7828 (ttm) cc_final: 0.7611 (ttm) REVERT: F 125 GLU cc_start: 0.8817 (tp30) cc_final: 0.8473 (tp30) REVERT: F 150 LYS cc_start: 0.7902 (mtmt) cc_final: 0.7566 (mmmt) REVERT: F 300 ASP cc_start: 0.7268 (m-30) cc_final: 0.7036 (t70) REVERT: F 323 LYS cc_start: 0.8928 (mttt) cc_final: 0.8534 (mtpp) REVERT: G 25 LEU cc_start: 0.7715 (mp) cc_final: 0.7512 (mt) REVERT: G 248 GLU cc_start: 0.7697 (tt0) cc_final: 0.7215 (tt0) REVERT: G 276 GLU cc_start: 0.6963 (mm-30) cc_final: 0.6716 (mm-30) REVERT: H 203 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6543 (tp30) REVERT: H 239 MET cc_start: 0.8565 (mtt) cc_final: 0.8175 (mtt) outliers start: 49 outliers final: 38 residues processed: 352 average time/residue: 0.3013 time to fit residues: 154.3940 Evaluate side-chains 358 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 319 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 282 ASP Chi-restraints excluded: chain H residue 319 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.0170 chunk 129 optimal weight: 0.8980 chunk 139 optimal weight: 0.0270 chunk 101 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 185 optimal weight: 4.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17067 Z= 0.125 Angle : 0.455 11.231 23073 Z= 0.229 Chirality : 0.045 0.318 2687 Planarity : 0.003 0.045 2993 Dihedral : 6.182 110.409 2426 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.13 % Allowed : 19.48 % Favored : 78.40 % 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: -1.03 (0.18), residues: 2140 helix: -0.02 (0.17), residues: 1004 sheet: -0.71 (0.29), residues: 304 loop : -1.36 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 52 HIS 0.009 0.001 HIS G 39 PHE 0.016 0.001 PHE C 75 TYR 0.025 0.001 TYR F 333 ARG 0.007 0.000 ARG F 241 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 335 time to evaluate : 1.883 Fit side-chains REVERT: A 114 LYS cc_start: 0.8005 (mmtp) cc_final: 0.7464 (mmmt) REVERT: A 210 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: B 210 GLU cc_start: 0.7741 (tt0) cc_final: 0.7520 (tt0) REVERT: C 71 LEU cc_start: 0.7862 (tp) cc_final: 0.7476 (mp) REVERT: D 215 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8409 (pm20) REVERT: D 239 MET cc_start: 0.8078 (mtt) cc_final: 0.7787 (mtt) REVERT: D 266 GLU cc_start: 0.8348 (pm20) cc_final: 0.7919 (mp0) REVERT: D 328 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7752 (mm-30) REVERT: E 73 MET cc_start: 0.8252 (mtm) cc_final: 0.7993 (mtm) REVERT: E 84 ILE cc_start: 0.8982 (mm) cc_final: 0.8570 (mt) REVERT: E 241 ARG cc_start: 0.6732 (mtt180) cc_final: 0.6363 (mtt-85) REVERT: E 264 MET cc_start: 0.7811 (ttm) cc_final: 0.7572 (ttm) REVERT: F 125 GLU cc_start: 0.8792 (tp30) cc_final: 0.8306 (tp30) REVERT: F 300 ASP cc_start: 0.7264 (m-30) cc_final: 0.7022 (t70) REVERT: F 323 LYS cc_start: 0.8891 (mttt) cc_final: 0.8630 (mtpp) REVERT: H 203 GLU cc_start: 0.6865 (mm-30) cc_final: 0.6525 (tp30) REVERT: H 239 MET cc_start: 0.8555 (mtt) cc_final: 0.8177 (mtt) outliers start: 39 outliers final: 32 residues processed: 349 average time/residue: 0.3196 time to fit residues: 161.6832 Evaluate side-chains 352 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 318 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 282 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 189 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17067 Z= 0.181 Angle : 0.479 10.778 23073 Z= 0.240 Chirality : 0.045 0.260 2687 Planarity : 0.003 0.047 2993 Dihedral : 6.139 109.306 2426 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.24 % Allowed : 19.69 % Favored : 78.07 % 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: -0.91 (0.18), residues: 2140 helix: 0.09 (0.17), residues: 992 sheet: -0.67 (0.29), residues: 304 loop : -1.30 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 52 HIS 0.009 0.001 HIS G 39 PHE 0.017 0.001 PHE G 75 TYR 0.024 0.001 TYR F 333 ARG 0.007 0.000 ARG F 241 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 325 time to evaluate : 1.899 Fit side-chains REVERT: A 114 LYS cc_start: 0.8014 (mmtp) cc_final: 0.7483 (mmmt) REVERT: A 210 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: B 169 ASP cc_start: 0.9027 (t0) cc_final: 0.8749 (t0) REVERT: B 210 GLU cc_start: 0.7787 (tt0) cc_final: 0.7520 (tt0) REVERT: C 71 LEU cc_start: 0.7889 (tp) cc_final: 0.7491 (mp) REVERT: D 215 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8435 (pm20) REVERT: D 239 MET cc_start: 0.8040 (mtt) cc_final: 0.7799 (mtt) REVERT: D 266 GLU cc_start: 0.8365 (pm20) cc_final: 0.7934 (mp0) REVERT: D 328 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7766 (mm-30) REVERT: E 73 MET cc_start: 0.8280 (mtm) cc_final: 0.8013 (mtm) REVERT: E 84 ILE cc_start: 0.8992 (mm) cc_final: 0.8583 (mt) REVERT: E 101 ARG cc_start: 0.7964 (ttp-170) cc_final: 0.7641 (ttp80) REVERT: E 241 ARG cc_start: 0.6755 (mtt180) cc_final: 0.6366 (mtt-85) REVERT: F 125 GLU cc_start: 0.8770 (tp30) cc_final: 0.8457 (tp30) REVERT: F 300 ASP cc_start: 0.7294 (m-30) cc_final: 0.7048 (t70) REVERT: F 323 LYS cc_start: 0.8887 (mttt) cc_final: 0.8629 (mtpp) REVERT: H 203 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6548 (tp30) REVERT: H 239 MET cc_start: 0.8582 (mtt) cc_final: 0.8207 (mtt) outliers start: 41 outliers final: 35 residues processed: 343 average time/residue: 0.3098 time to fit residues: 153.7585 Evaluate side-chains 352 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 315 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 282 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 168 optimal weight: 0.0980 chunk 17 optimal weight: 0.6980 chunk 129 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17067 Z= 0.159 Angle : 0.475 9.750 23073 Z= 0.238 Chirality : 0.045 0.239 2687 Planarity : 0.003 0.047 2993 Dihedral : 6.049 105.931 2426 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.07 % Allowed : 19.91 % Favored : 78.01 % 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: -0.77 (0.18), residues: 2140 helix: 0.24 (0.17), residues: 990 sheet: -0.60 (0.29), residues: 304 loop : -1.28 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 52 HIS 0.008 0.001 HIS G 39 PHE 0.016 0.001 PHE G 75 TYR 0.026 0.001 TYR F 333 ARG 0.007 0.000 ARG F 241 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 324 time to evaluate : 1.677 Fit side-chains REVERT: A 114 LYS cc_start: 0.8004 (mmtp) cc_final: 0.7469 (mmmt) REVERT: B 210 GLU cc_start: 0.7777 (tt0) cc_final: 0.7528 (tt0) REVERT: C 71 LEU cc_start: 0.7891 (tp) cc_final: 0.7496 (mp) REVERT: D 215 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8426 (pm20) REVERT: D 239 MET cc_start: 0.8048 (mtt) cc_final: 0.7800 (mtt) REVERT: D 266 GLU cc_start: 0.8370 (pm20) cc_final: 0.7944 (mp0) REVERT: D 328 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7739 (mm-30) REVERT: E 73 MET cc_start: 0.8259 (mtm) cc_final: 0.7992 (mtm) REVERT: E 84 ILE cc_start: 0.8987 (mm) cc_final: 0.8574 (mt) REVERT: E 101 ARG cc_start: 0.7955 (ttp-170) cc_final: 0.7631 (ttp80) REVERT: E 241 ARG cc_start: 0.6759 (mtt180) cc_final: 0.6369 (mtt-85) REVERT: F 125 GLU cc_start: 0.8751 (tp30) cc_final: 0.8284 (tp30) REVERT: F 291 VAL cc_start: 0.8661 (OUTLIER) cc_final: 0.8396 (p) REVERT: F 300 ASP cc_start: 0.7278 (m-30) cc_final: 0.7057 (t70) REVERT: F 323 LYS cc_start: 0.8889 (mttt) cc_final: 0.8613 (mtpp) REVERT: G 28 LEU cc_start: 0.8616 (mm) cc_final: 0.8247 (tp) REVERT: H 203 GLU cc_start: 0.6874 (mm-30) cc_final: 0.6533 (tp30) REVERT: H 239 MET cc_start: 0.8581 (mtt) cc_final: 0.8182 (mtt) outliers start: 38 outliers final: 33 residues processed: 341 average time/residue: 0.3128 time to fit residues: 154.3803 Evaluate side-chains 355 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 320 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain H residue 266 GLU Chi-restraints excluded: chain H residue 282 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 172 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.161816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.134042 restraints weight = 20070.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.138184 restraints weight = 10106.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.140741 restraints weight = 6530.791| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17067 Z= 0.220 Angle : 0.493 8.798 23073 Z= 0.248 Chirality : 0.046 0.217 2687 Planarity : 0.003 0.047 2993 Dihedral : 6.069 104.758 2426 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.07 % Allowed : 19.80 % Favored : 78.12 % 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: -0.79 (0.18), residues: 2140 helix: 0.22 (0.17), residues: 990 sheet: -0.68 (0.29), residues: 304 loop : -1.26 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 52 HIS 0.009 0.001 HIS G 39 PHE 0.018 0.001 PHE G 75 TYR 0.027 0.001 TYR F 333 ARG 0.011 0.000 ARG G 263 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3702.19 seconds wall clock time: 67 minutes 10.44 seconds (4030.44 seconds total)