Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 8 13:52:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/07_2023/5bkk_9407_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/07_2023/5bkk_9407.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/07_2023/5bkk_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_9407/07_2023/5bkk_9407_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/07_2023/5bkk_9407_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/07_2023/5bkk_9407.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/07_2023/5bkk_9407.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/07_2023/5bkk_9407_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/07_2023/5bkk_9407_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 18 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: 24 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: 8.14, per 1000 atoms: 0.48 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: 6.97 Conformation dependent library (CDL) restraints added in 2.7 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: 1.64 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: 5.31 Time building geometry restraints manager: 7.43 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: 10092 32.80 - 65.61: 245 65.61 - 98.41: 30 98.41 - 131.22: 0 131.22 - 164.02: 1 Dihedral angle restraints: 10368 sinusoidal: 4216 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 10365 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: 0.570 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: 4.560 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 44.670 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.100 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:3.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.950 ------------------------------------------------------------------------------- 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 : 14.722 164.021 6416 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 % 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 *********************** 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 : 1.903 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 454 average time/residue: 0.3569 time to fit residues: 226.3924 Evaluate side-chains 344 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 2.014 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7300 ------------------------------------------------------------------------------- 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: 2.9990 chunk 89 optimal weight: 0.0570 chunk 54 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 85 optimal weight: 0.2980 chunk 166 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.0702 ------------------------------------------------------------------------------- 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: 0.7983 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 17067 Z= 0.212 Angle : 0.494 8.170 23073 Z= 0.260 Chirality : 0.046 0.216 2687 Planarity : 0.004 0.061 2993 Dihedral : 6.557 135.313 2418 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 2.24 % 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: -3.50 (0.15), residues: 2140 helix: -2.29 (0.13), residues: 982 sheet: -1.66 (0.26), residues: 312 loop : -2.40 (0.19), residues: 846 *********************** 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 406 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 365 time to evaluate : 1.922 Fit side-chains outliers start: 41 outliers final: 25 residues processed: 383 average time/residue: 0.3325 time to fit residues: 182.9270 Evaluate side-chains 353 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 328 time to evaluate : 1.918 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1581 time to fit residues: 10.1557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 208 optimal weight: 7.9990 chunk 171 optimal weight: 3.9990 chunk 191 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 154 optimal weight: 0.3980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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: 0.8040 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 17067 Z= 0.342 Angle : 0.535 7.721 23073 Z= 0.279 Chirality : 0.047 0.145 2687 Planarity : 0.004 0.055 2993 Dihedral : 6.376 135.308 2418 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 1.09 % 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: -2.74 (0.16), residues: 2140 helix: -1.57 (0.14), residues: 1008 sheet: -1.49 (0.27), residues: 312 loop : -2.05 (0.20), residues: 820 *********************** 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 362 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 342 time to evaluate : 1.827 Fit side-chains outliers start: 20 outliers final: 13 residues processed: 352 average time/residue: 0.3358 time to fit residues: 168.7944 Evaluate side-chains 330 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 317 time to evaluate : 1.772 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1513 time to fit residues: 6.4606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 chunk 193 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 55 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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: 0.7985 moved from start: 0.2129 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= 0.145 Angle : 0.452 7.195 23073 Z= 0.233 Chirality : 0.045 0.281 2687 Planarity : 0.003 0.049 2993 Dihedral : 5.780 128.150 2418 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer Outliers : 1.42 % 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: -2.08 (0.17), residues: 2140 helix: -0.93 (0.15), residues: 1006 sheet: -1.26 (0.27), residues: 308 loop : -1.82 (0.21), residues: 826 *********************** 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 357 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 331 time to evaluate : 1.809 Fit side-chains outliers start: 26 outliers final: 19 residues processed: 338 average time/residue: 0.3218 time to fit residues: 156.2145 Evaluate side-chains 329 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 310 time to evaluate : 1.943 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1692 time to fit residues: 8.5536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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: 0.8053 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.068 17067 Z= 0.375 Angle : 0.540 7.597 23073 Z= 0.281 Chirality : 0.048 0.166 2687 Planarity : 0.004 0.051 2993 Dihedral : 5.995 132.933 2418 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer Outliers : 1.53 % 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: -2.00 (0.17), residues: 2140 helix: -0.81 (0.15), residues: 1012 sheet: -1.27 (0.27), residues: 312 loop : -1.84 (0.20), residues: 816 *********************** 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 355 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 327 time to evaluate : 1.871 Fit side-chains outliers start: 28 outliers final: 15 residues processed: 342 average time/residue: 0.3406 time to fit residues: 168.5605 Evaluate side-chains 312 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 297 time to evaluate : 1.957 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1926 time to fit residues: 7.6920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 0.0070 chunk 50 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 170 optimal weight: 0.0170 chunk 94 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.4236 ------------------------------------------------------------------------------- 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: 0.7982 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 17067 Z= 0.137 Angle : 0.455 6.975 23073 Z= 0.235 Chirality : 0.044 0.142 2687 Planarity : 0.003 0.048 2993 Dihedral : 5.581 123.852 2418 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 1.42 % 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: -1.49 (0.18), residues: 2140 helix: -0.40 (0.16), residues: 1008 sheet: -0.99 (0.28), residues: 304 loop : -1.57 (0.21), residues: 828 *********************** 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 359 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 333 time to evaluate : 1.916 Fit side-chains outliers start: 26 outliers final: 17 residues processed: 342 average time/residue: 0.3291 time to fit residues: 163.2959 Evaluate side-chains 325 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 308 time to evaluate : 1.951 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1769 time to fit residues: 8.0742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 149 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 204 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 124 optimal weight: 0.0570 chunk 94 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN C 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2500 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= 0.148 Angle : 0.461 7.628 23073 Z= 0.236 Chirality : 0.045 0.302 2687 Planarity : 0.003 0.047 2993 Dihedral : 5.446 121.563 2418 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 0.93 % 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: -1.23 (0.18), residues: 2140 helix: -0.19 (0.16), residues: 1008 sheet: -0.83 (0.29), residues: 304 loop : -1.46 (0.21), residues: 828 *********************** 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 343 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 326 time to evaluate : 1.970 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 331 average time/residue: 0.3482 time to fit residues: 166.1195 Evaluate side-chains 328 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 316 time to evaluate : 1.969 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1790 time to fit residues: 6.5786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 129 optimal weight: 0.3980 chunk 139 optimal weight: 0.9980 chunk 101 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 185 optimal weight: 3.9990 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** E 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.060 17067 Z= 0.160 Angle : 0.462 7.830 23073 Z= 0.234 Chirality : 0.045 0.144 2687 Planarity : 0.003 0.043 2993 Dihedral : 5.366 118.430 2418 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 0.93 % 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: -1.04 (0.18), residues: 2140 helix: -0.04 (0.16), residues: 1004 sheet: -0.74 (0.29), residues: 304 loop : -1.36 (0.22), residues: 832 *********************** 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 342 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 325 time to evaluate : 1.821 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 332 average time/residue: 0.3365 time to fit residues: 160.8122 Evaluate side-chains 323 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 314 time to evaluate : 1.870 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1577 time to fit residues: 5.3457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 0.4980 chunk 178 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 189 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.2621 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= 0.165 Angle : 0.471 8.344 23073 Z= 0.238 Chirality : 0.045 0.147 2687 Planarity : 0.003 0.043 2993 Dihedral : 5.309 116.350 2418 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 0.49 % 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: 0.10 (0.17), residues: 992 sheet: -0.71 (0.29), residues: 304 loop : -1.30 (0.22), residues: 844 *********************** 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 326 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 317 time to evaluate : 2.084 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 318 average time/residue: 0.3417 time to fit residues: 156.8298 Evaluate side-chains 319 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 312 time to evaluate : 2.066 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1625 time to fit residues: 4.9338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 211 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 17067 Z= 0.237 Angle : 0.494 8.277 23073 Z= 0.253 Chirality : 0.046 0.190 2687 Planarity : 0.003 0.044 2993 Dihedral : 5.408 118.351 2418 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.38 % 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: -1.00 (0.18), residues: 2140 helix: 0.01 (0.16), residues: 1008 sheet: -0.76 (0.29), residues: 304 loop : -1.33 (0.22), residues: 828 ********************** 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 321 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 314 time to evaluate : 1.924 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 316 average time/residue: 0.3410 time to fit residues: 154.5768 Evaluate side-chains 314 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 309 time to evaluate : 1.989 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1645 time to fit residues: 4.2782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 155 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 172 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 147 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.137642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.110169 restraints weight = 21065.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.112846 restraints weight = 12822.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.114833 restraints weight = 9208.428| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2704 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= 0.169 Angle : 0.473 8.000 23073 Z= 0.241 Chirality : 0.045 0.175 2687 Planarity : 0.003 0.045 2993 Dihedral : 5.295 114.981 2418 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.18), residues: 2140 helix: 0.20 (0.17), residues: 994 sheet: -0.70 (0.29), residues: 304 loop : -1.28 (0.22), residues: 842 =============================================================================== Job complete usr+sys time: 3663.34 seconds wall clock time: 67 minutes 9.25 seconds (4029.25 seconds total)