Starting phenix.real_space_refine on Mon Dec 11 05:51:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/12_2023/5bkk_9407_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/12_2023/5bkk_9407.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/12_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_9407/12_2023/5bkk_9407_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/12_2023/5bkk_9407_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/12_2023/5bkk_9407.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/12_2023/5bkk_9407.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/12_2023/5bkk_9407_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkk_9407/12_2023/5bkk_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 8.88, 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: 6.27 Conformation dependent library (CDL) restraints added in 3.1 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: 3.54 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: 4.93 Time building geometry restraints manager: 6.75 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: 1.180 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: 0.010 Extract box with map and model: 3.930 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 46.250 Find NCS groups from input model: 1.230 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.210 ------------------------------------------------------------------------------- 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 : 1.897 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 454 average time/residue: 0.3525 time to fit residues: 223.4734 Evaluate side-chains 344 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 1.882 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5808 ------------------------------------------------------------------------------- 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: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17067 Z= 0.212 Angle : 0.497 7.902 23073 Z= 0.262 Chirality : 0.046 0.219 2687 Planarity : 0.004 0.062 2993 Dihedral : 7.719 147.814 2426 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.24 % Allowed : 11.13 % Favored : 86.63 % 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: -3.53 (0.15), residues: 2140 helix: -2.33 (0.13), residues: 982 sheet: -1.67 (0.26), residues: 312 loop : -2.41 (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 G 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 402 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 361 time to evaluate : 1.821 Fit side-chains outliers start: 41 outliers final: 26 residues processed: 379 average time/residue: 0.3275 time to fit residues: 177.5509 Evaluate side-chains 357 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 331 time to evaluate : 1.846 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1721 time to fit residues: 10.7032 ------------------------------------------------------------------------------- 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: 9.9990 chunk 59 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 131 optimal weight: 0.9990 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: 0.4980 chunk 65 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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: 0.8036 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17067 Z= 0.334 Angle : 0.531 7.626 23073 Z= 0.277 Chirality : 0.047 0.146 2687 Planarity : 0.004 0.054 2993 Dihedral : 7.410 138.995 2426 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.20 % Allowed : 15.17 % Favored : 83.63 % 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: -2.77 (0.16), residues: 2140 helix: -1.61 (0.14), residues: 1008 sheet: -1.49 (0.27), residues: 312 loop : -2.06 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 46 HIS 0.007 0.001 HIS A 117 PHE 0.011 0.001 PHE G 75 TYR 0.023 0.002 TYR F 333 ARG 0.004 0.000 ARG E 135 *********************** 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 365 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 343 time to evaluate : 2.077 Fit side-chains outliers start: 22 outliers final: 13 residues processed: 354 average time/residue: 0.3459 time to fit residues: 175.0913 Evaluate side-chains 327 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 314 time to evaluate : 1.954 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1545 time to fit residues: 6.6601 ------------------------------------------------------------------------------- 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: 0.7980 chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 193 optimal weight: 0.6980 chunk 204 optimal weight: 0.0050 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 55 optimal weight: 0.0170 overall best weight: 0.4032 ------------------------------------------------------------------------------- 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: 0.7969 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17067 Z= 0.129 Angle : 0.447 7.759 23073 Z= 0.231 Chirality : 0.045 0.275 2687 Planarity : 0.003 0.049 2993 Dihedral : 6.824 125.912 2426 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.20 % Allowed : 16.04 % Favored : 82.76 % 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: -2.06 (0.17), residues: 2140 helix: -0.93 (0.15), residues: 1004 sheet: -1.18 (0.28), residues: 304 loop : -1.82 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 E 237 *********************** 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 364 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 342 time to evaluate : 2.360 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 348 average time/residue: 0.3420 time to fit residues: 171.4803 Evaluate side-chains 331 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 315 time to evaluate : 1.887 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1542 time to fit residues: 7.1820 ------------------------------------------------------------------------------- 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: 4.9990 chunk 116 optimal weight: 0.3980 chunk 2 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- 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** E 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 17067 Z= 0.506 Angle : 0.605 7.827 23073 Z= 0.316 Chirality : 0.051 0.171 2687 Planarity : 0.004 0.053 2993 Dihedral : 7.106 133.402 2426 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.75 % Allowed : 18.28 % Favored : 79.98 % 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: -2.20 (0.17), residues: 2140 helix: -0.96 (0.15), residues: 1004 sheet: -1.28 (0.27), residues: 312 loop : -1.99 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 52 HIS 0.010 0.002 HIS A 117 PHE 0.013 0.002 PHE A 75 TYR 0.024 0.002 TYR F 333 ARG 0.007 0.001 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 366 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 334 time to evaluate : 1.968 Fit side-chains outliers start: 32 outliers final: 22 residues processed: 352 average time/residue: 0.3332 time to fit residues: 168.9112 Evaluate side-chains 323 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 301 time to evaluate : 1.848 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1824 time to fit residues: 9.6946 ------------------------------------------------------------------------------- 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: 0.9990 chunk 184 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 205 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.8007 moved from start: 0.2375 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= 0.182 Angle : 0.470 7.051 23073 Z= 0.243 Chirality : 0.045 0.144 2687 Planarity : 0.003 0.048 2993 Dihedral : 6.706 121.671 2426 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.31 % Allowed : 18.66 % Favored : 80.03 % 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: -1.72 (0.17), residues: 2140 helix: -0.57 (0.16), residues: 1010 sheet: -1.07 (0.28), residues: 304 loop : -1.74 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 52 HIS 0.003 0.001 HIS A 117 PHE 0.012 0.001 PHE G 75 TYR 0.021 0.001 TYR C 333 ARG 0.005 0.000 ARG F 241 *********************** 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 347 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 323 time to evaluate : 2.021 Fit side-chains outliers start: 24 outliers final: 16 residues processed: 332 average time/residue: 0.3307 time to fit residues: 159.3600 Evaluate side-chains 319 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 303 time to evaluate : 1.913 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1587 time to fit residues: 7.3849 ------------------------------------------------------------------------------- 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: 0.6980 chunk 116 optimal weight: 0.0870 chunk 149 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 204 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- 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: 0.7998 moved from start: 0.2457 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= 0.180 Angle : 0.467 7.402 23073 Z= 0.239 Chirality : 0.045 0.141 2687 Planarity : 0.003 0.047 2993 Dihedral : 6.500 118.713 2426 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.09 % Allowed : 19.80 % 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: -1.38 (0.18), residues: 2140 helix: -0.32 (0.16), residues: 1008 sheet: -0.89 (0.29), residues: 304 loop : -1.52 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 46 HIS 0.003 0.001 HIS C 117 PHE 0.012 0.001 PHE G 75 TYR 0.025 0.001 TYR F 333 ARG 0.007 0.000 ARG E 313 *********************** 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 340 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 320 time to evaluate : 1.889 Fit side-chains outliers start: 20 outliers final: 13 residues processed: 326 average time/residue: 0.3240 time to fit residues: 153.5190 Evaluate side-chains 318 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 305 time to evaluate : 1.865 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1562 time to fit residues: 6.3840 ------------------------------------------------------------------------------- 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: 9.9990 chunk 122 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.0970 chunk 129 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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: 0.7982 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17067 Z= 0.155 Angle : 0.466 7.856 23073 Z= 0.237 Chirality : 0.045 0.146 2687 Planarity : 0.003 0.042 2993 Dihedral : 6.339 113.971 2426 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.98 % Allowed : 20.02 % Favored : 79.00 % 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: -1.13 (0.18), residues: 2140 helix: -0.12 (0.16), residues: 1004 sheet: -0.77 (0.29), residues: 304 loop : -1.40 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 52 HIS 0.002 0.000 HIS C 117 PHE 0.017 0.001 PHE G 75 TYR 0.025 0.001 TYR F 333 ARG 0.005 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 345 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 327 time to evaluate : 1.766 Fit side-chains outliers start: 18 outliers final: 15 residues processed: 334 average time/residue: 0.3316 time to fit residues: 159.6148 Evaluate side-chains 321 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 306 time to evaluate : 1.750 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1558 time to fit residues: 6.7580 ------------------------------------------------------------------------------- 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: 2.9990 chunk 178 optimal weight: 0.7980 chunk 190 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 82 optimal weight: 0.2980 chunk 149 optimal weight: 0.0670 chunk 58 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 189 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 17067 Z= 0.150 Angle : 0.473 9.671 23073 Z= 0.239 Chirality : 0.045 0.300 2687 Planarity : 0.003 0.044 2993 Dihedral : 6.205 110.375 2426 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.27 % Allowed : 20.89 % Favored : 78.83 % 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: -0.94 (0.18), residues: 2140 helix: 0.06 (0.17), residues: 992 sheet: -0.71 (0.29), residues: 304 loop : -1.31 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 52 HIS 0.002 0.000 HIS C 117 PHE 0.021 0.001 PHE C 75 TYR 0.025 0.001 TYR F 333 ARG 0.007 0.000 ARG G 263 *********************** 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 324 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 319 time to evaluate : 1.919 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 321 average time/residue: 0.3397 time to fit residues: 158.0588 Evaluate side-chains 312 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 309 time to evaluate : 1.907 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1817 time to fit residues: 3.7594 ------------------------------------------------------------------------------- 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: 0.8980 chunk 122 optimal weight: 0.7980 chunk 95 optimal weight: 0.0870 chunk 139 optimal weight: 0.9980 chunk 211 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 129 optimal weight: 0.0870 chunk 103 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 overall best weight: 0.5336 ------------------------------------------------------------------------------- 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: 0.7963 moved from start: 0.2671 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= 0.142 Angle : 0.470 9.936 23073 Z= 0.236 Chirality : 0.045 0.227 2687 Planarity : 0.003 0.045 2993 Dihedral : 6.089 106.507 2426 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.22 % Allowed : 21.17 % Favored : 78.61 % 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: 0.21 (0.17), residues: 992 sheet: -0.62 (0.29), residues: 304 loop : -1.26 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 52 HIS 0.002 0.000 HIS A 117 PHE 0.019 0.001 PHE C 75 TYR 0.025 0.001 TYR F 333 ARG 0.005 0.000 ARG C 263 ********************** 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 322 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 318 time to evaluate : 1.921 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 320 average time/residue: 0.3433 time to fit residues: 158.6171 Evaluate side-chains 316 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 312 time to evaluate : 2.007 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1474 time to fit residues: 3.8810 ------------------------------------------------------------------------------- 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: 0.9990 chunk 51 optimal weight: 5.9990 chunk 155 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 147 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.138828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.111123 restraints weight = 21021.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.113972 restraints weight = 12763.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.115824 restraints weight = 9086.209| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2717 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 : 0.467 9.077 23073 Z= 0.235 Chirality : 0.045 0.184 2687 Planarity : 0.003 0.045 2993 Dihedral : 5.987 103.424 2426 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.16 % Allowed : 21.49 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.18), residues: 2140 helix: 0.30 (0.17), residues: 990 sheet: -0.56 (0.29), residues: 304 loop : -1.23 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 46 HIS 0.002 0.000 HIS A 117 PHE 0.018 0.001 PHE C 75 TYR 0.025 0.001 TYR F 333 ARG 0.006 0.000 ARG C 263 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3813.55 seconds wall clock time: 69 minutes 54.65 seconds (4194.65 seconds total)