Starting phenix.real_space_refine on Fri Feb 16 15:40:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tu4_10587/02_2024/6tu4_10587_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tu4_10587/02_2024/6tu4_10587.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tu4_10587/02_2024/6tu4_10587_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tu4_10587/02_2024/6tu4_10587_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tu4_10587/02_2024/6tu4_10587_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tu4_10587/02_2024/6tu4_10587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tu4_10587/02_2024/6tu4_10587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tu4_10587/02_2024/6tu4_10587_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tu4_10587/02_2024/6tu4_10587_updated.pdb" } resolution = 2.6 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= 0.010 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: 7 Type Number sf(0) Gaussians Br 5 7.06 5 P 10 5.49 5 Mg 5 5.21 5 S 90 5.16 5 C 9935 2.51 5 N 2570 2.21 5 O 3075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A GLU 260": "OE1" <-> "OE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B ASP 289": "OD1" <-> "OD2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "C GLU 308": "OE1" <-> "OE2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 50": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "D GLU 365": "OE1" <-> "OE2" Residue "D PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 49": "OE1" <-> "OE2" Residue "F GLU 50": "OE1" <-> "OE2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 100": "OE1" <-> "OE2" Residue "F GLU 108": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F GLU 168": "OE1" <-> "OE2" Residue "F TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 242": "OE1" <-> "OE2" Residue "F GLU 260": "OE1" <-> "OE2" Residue "F GLU 365": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15690 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3035 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Conformer: "B" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} bond proxies already assigned to first conformer: 2824 Chain: "B" Number of atoms: 3039 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Conformer: "B" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} bond proxies already assigned to first conformer: 2819 Chain: "C" Number of atoms: 3035 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Conformer: "B" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} bond proxies already assigned to first conformer: 2824 Chain: "D" Number of atoms: 3039 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Conformer: "B" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} bond proxies already assigned to first conformer: 2819 Chain: "F" Number of atoms: 3027 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Conformer: "B" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} bond proxies already assigned to first conformer: 2834 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Time building chain proxies: 14.87, per 1000 atoms: 0.95 Number of scatterers: 15690 At special positions: 0 Unit cell: (99.19, 83.93, 198.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 5 34.99 S 90 16.00 P 10 15.00 Mg 5 11.99 O 3075 8.00 N 2570 7.00 C 9935 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 5.5 seconds 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3642 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 99 helices and 25 sheets defined 41.6% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 80 through 92 Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 138 through 146 Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 183 through 197 removed outlier: 4.287A pdb=" N HIS A 195 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLU A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ARG A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 217 removed outlier: 3.585A pdb=" N GLU A 208 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 230 removed outlier: 3.711A pdb=" N LYS A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 257 removed outlier: 3.790A pdb=" N ARG A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 262 Processing helix chain 'A' and resid 265 through 268 Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 291 through 294 No H-bonds generated for 'chain 'A' and resid 291 through 294' Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 336 through 349 removed outlier: 3.661A pdb=" N SER A 339 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL A 340 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 348 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 360 through 366 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.797A pdb=" N VAL A 371 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 80 through 92 Processing helix chain 'B' and resid 99 through 101 No H-bonds generated for 'chain 'B' and resid 99 through 101' Processing helix chain 'B' and resid 114 through 126 Processing helix chain 'B' and resid 138 through 146 removed outlier: 3.519A pdb=" N LEU B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 175 No H-bonds generated for 'chain 'B' and resid 173 through 175' Processing helix chain 'B' and resid 183 through 197 removed outlier: 4.215A pdb=" N HIS B 195 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLU B 196 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARG B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 217 removed outlier: 3.660A pdb=" N GLU B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 231 Processing helix chain 'B' and resid 253 through 257 removed outlier: 3.759A pdb=" N ARG B 257 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 262 Processing helix chain 'B' and resid 265 through 268 Processing helix chain 'B' and resid 275 through 284 Processing helix chain 'B' and resid 291 through 294 No H-bonds generated for 'chain 'B' and resid 291 through 294' Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 339 through 349 removed outlier: 3.698A pdb=" N SER B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 removed outlier: 3.579A pdb=" N GLN B 354 " --> pdb=" O SER B 351 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN B 355 " --> pdb=" O THR B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 355' Processing helix chain 'B' and resid 360 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.571A pdb=" N VAL B 371 " --> pdb=" O PRO B 368 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS B 374 " --> pdb=" O VAL B 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 80 through 92 Processing helix chain 'C' and resid 114 through 126 Processing helix chain 'C' and resid 138 through 146 Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'C' and resid 183 through 197 removed outlier: 4.296A pdb=" N HIS C 195 " --> pdb=" O MET C 191 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU C 196 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ARG C 197 " --> pdb=" O ILE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 217 removed outlier: 3.732A pdb=" N GLU C 208 " --> pdb=" O SER C 204 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 231 Processing helix chain 'C' and resid 253 through 257 removed outlier: 3.747A pdb=" N ARG C 257 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 262 Processing helix chain 'C' and resid 265 through 268 Processing helix chain 'C' and resid 275 through 284 Processing helix chain 'C' and resid 291 through 295 Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 310 through 321 Processing helix chain 'C' and resid 339 through 349 removed outlier: 3.628A pdb=" N SER C 349 " --> pdb=" O SER C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 355 removed outlier: 4.216A pdb=" N GLN C 355 " --> pdb=" O THR C 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 352 through 355' Processing helix chain 'C' and resid 360 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.699A pdb=" N VAL C 371 " --> pdb=" O PRO C 368 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS C 374 " --> pdb=" O VAL C 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 80 through 92 Processing helix chain 'D' and resid 114 through 126 Processing helix chain 'D' and resid 138 through 146 Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 183 through 197 removed outlier: 4.235A pdb=" N HIS D 195 " --> pdb=" O MET D 191 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLU D 196 " --> pdb=" O LYS D 192 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ARG D 197 " --> pdb=" O ILE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'D' and resid 224 through 230 removed outlier: 3.621A pdb=" N LYS D 229 " --> pdb=" O ASP D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 257 removed outlier: 3.749A pdb=" N ARG D 257 " --> pdb=" O GLU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 262 Processing helix chain 'D' and resid 265 through 268 Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 291 through 295 Processing helix chain 'D' and resid 303 through 306 Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 339 through 349 removed outlier: 3.722A pdb=" N SER D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 353 No H-bonds generated for 'chain 'D' and resid 351 through 353' Processing helix chain 'D' and resid 360 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 3.727A pdb=" N VAL D 371 " --> pdb=" O PRO D 368 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS D 374 " --> pdb=" O VAL D 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 61 Processing helix chain 'F' and resid 63 through 65 No H-bonds generated for 'chain 'F' and resid 63 through 65' Processing helix chain 'F' and resid 80 through 92 Processing helix chain 'F' and resid 114 through 126 Processing helix chain 'F' and resid 138 through 146 Processing helix chain 'F' and resid 173 through 175 No H-bonds generated for 'chain 'F' and resid 173 through 175' Processing helix chain 'F' and resid 183 through 197 removed outlier: 4.244A pdb=" N HIS F 195 " --> pdb=" O MET F 191 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLU F 196 " --> pdb=" O LYS F 192 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ARG F 197 " --> pdb=" O ILE F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 217 removed outlier: 3.542A pdb=" N ILE F 209 " --> pdb=" O ALA F 205 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP F 212 " --> pdb=" O GLU F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 233 removed outlier: 3.796A pdb=" N LYS F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 257 removed outlier: 3.755A pdb=" N ARG F 257 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 262 Processing helix chain 'F' and resid 265 through 268 Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 291 through 294 No H-bonds generated for 'chain 'F' and resid 291 through 294' Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 310 through 321 Processing helix chain 'F' and resid 339 through 349 removed outlier: 3.739A pdb=" N SER F 349 " --> pdb=" O SER F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 374 Proline residue: F 368 - end of helix removed outlier: 5.773A pdb=" N VAL F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N HIS F 372 " --> pdb=" O PRO F 368 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG F 373 " --> pdb=" O SER F 369 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 9 through 13 Processing sheet with id= B, first strand: chain 'A' and resid 35 through 39 Processing sheet with id= C, first strand: chain 'A' and resid 104 through 108 Processing sheet with id= D, first strand: chain 'A' and resid 298 through 301 removed outlier: 6.524A pdb=" N ILE A 152 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N SER A 301 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU A 154 " --> pdb=" O SER A 301 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 239 through 242 Processing sheet with id= F, first strand: chain 'B' and resid 9 through 13 Processing sheet with id= G, first strand: chain 'B' and resid 35 through 39 Processing sheet with id= H, first strand: chain 'B' and resid 104 through 108 Processing sheet with id= I, first strand: chain 'B' and resid 298 through 301 removed outlier: 6.506A pdb=" N ILE B 152 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N SER B 301 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU B 154 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 239 through 242 Processing sheet with id= K, first strand: chain 'C' and resid 9 through 13 Processing sheet with id= L, first strand: chain 'C' and resid 35 through 39 Processing sheet with id= M, first strand: chain 'C' and resid 104 through 108 Processing sheet with id= N, first strand: chain 'C' and resid 298 through 301 removed outlier: 6.510A pdb=" N ILE C 152 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N SER C 301 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU C 154 " --> pdb=" O SER C 301 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 239 through 242 Processing sheet with id= P, first strand: chain 'D' and resid 9 through 13 Processing sheet with id= Q, first strand: chain 'D' and resid 36 through 39 Processing sheet with id= R, first strand: chain 'D' and resid 104 through 108 Processing sheet with id= S, first strand: chain 'D' and resid 298 through 301 removed outlier: 6.498A pdb=" N ILE D 152 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N SER D 301 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU D 154 " --> pdb=" O SER D 301 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 239 through 242 Processing sheet with id= U, first strand: chain 'F' and resid 9 through 13 Processing sheet with id= V, first strand: chain 'F' and resid 35 through 39 Processing sheet with id= W, first strand: chain 'F' and resid 104 through 108 Processing sheet with id= X, first strand: chain 'F' and resid 298 through 301 removed outlier: 6.490A pdb=" N ILE F 152 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N SER F 301 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU F 154 " --> pdb=" O SER F 301 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 239 through 242 511 hydrogen bonds defined for protein. 1329 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: 4.60 Time building geometry restraints manager: 6.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4955 1.35 - 1.49: 4054 1.49 - 1.62: 6831 1.62 - 1.76: 0 1.76 - 1.90: 165 Bond restraints: 16005 Sorted by residual: bond pdb=" C4 9UE A 402 " pdb=" C5 9UE A 402 " ideal model delta sigma weight residual 0.880 1.498 -0.618 2.00e-02 2.50e+03 9.54e+02 bond pdb=" C4 9UE D 402 " pdb=" C5 9UE D 402 " ideal model delta sigma weight residual 0.880 1.497 -0.617 2.00e-02 2.50e+03 9.52e+02 bond pdb=" C4 9UE F 402 " pdb=" C5 9UE F 402 " ideal model delta sigma weight residual 0.880 1.497 -0.617 2.00e-02 2.50e+03 9.52e+02 bond pdb=" C4 9UE C 402 " pdb=" C5 9UE C 402 " ideal model delta sigma weight residual 0.880 1.497 -0.617 2.00e-02 2.50e+03 9.51e+02 bond pdb=" C4 9UE B 402 " pdb=" C5 9UE B 402 " ideal model delta sigma weight residual 0.880 1.496 -0.616 2.00e-02 2.50e+03 9.49e+02 ... (remaining 16000 not shown) Histogram of bond angle deviations from ideal: 98.98 - 106.46: 533 106.46 - 113.95: 9225 113.95 - 121.43: 8391 121.43 - 128.91: 3631 128.91 - 136.40: 118 Bond angle restraints: 21898 Sorted by residual: angle pdb=" C20 9UE A 402 " pdb=" C21 9UE A 402 " pdb=" C28 9UE A 402 " ideal model delta sigma weight residual 73.46 124.92 -51.46 3.00e+00 1.11e-01 2.94e+02 angle pdb=" C20 9UE F 402 " pdb=" C21 9UE F 402 " pdb=" C28 9UE F 402 " ideal model delta sigma weight residual 73.46 124.84 -51.38 3.00e+00 1.11e-01 2.93e+02 angle pdb=" C20 9UE D 402 " pdb=" C21 9UE D 402 " pdb=" C28 9UE D 402 " ideal model delta sigma weight residual 73.46 124.56 -51.10 3.00e+00 1.11e-01 2.90e+02 angle pdb=" C20 9UE C 402 " pdb=" C21 9UE C 402 " pdb=" C28 9UE C 402 " ideal model delta sigma weight residual 73.46 124.33 -50.87 3.00e+00 1.11e-01 2.88e+02 angle pdb=" C20 9UE B 402 " pdb=" C21 9UE B 402 " pdb=" C28 9UE B 402 " ideal model delta sigma weight residual 73.46 124.28 -50.82 3.00e+00 1.11e-01 2.87e+02 ... (remaining 21893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 9587 35.99 - 71.97: 170 71.97 - 107.96: 42 107.96 - 143.95: 23 143.95 - 179.93: 12 Dihedral angle restraints: 9834 sinusoidal: 4054 harmonic: 5780 Sorted by residual: dihedral pdb=" O1B ADP D 403 " pdb=" O3A ADP D 403 " pdb=" PB ADP D 403 " pdb=" PA ADP D 403 " ideal model delta sinusoidal sigma weight residual 300.00 129.09 170.90 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O1B ADP F 403 " pdb=" O3A ADP F 403 " pdb=" PB ADP F 403 " pdb=" PA ADP F 403 " ideal model delta sinusoidal sigma weight residual -60.00 104.19 -164.19 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" O1B ADP B 403 " pdb=" O3A ADP B 403 " pdb=" PB ADP B 403 " pdb=" PA ADP B 403 " ideal model delta sinusoidal sigma weight residual 300.00 137.55 162.45 1 2.00e+01 2.50e-03 4.69e+01 ... (remaining 9831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 2422 0.138 - 0.276: 13 0.276 - 0.414: 9 0.414 - 0.552: 2 0.552 - 0.690: 2 Chirality restraints: 2448 Sorted by residual: chirality pdb=" C6 9UE F 402 " pdb=" N 9UE F 402 " pdb=" C29 9UE F 402 " pdb=" C5 9UE F 402 " both_signs ideal model delta sigma weight residual False -2.65 -1.96 -0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" C6 9UE D 402 " pdb=" N 9UE D 402 " pdb=" C29 9UE D 402 " pdb=" C5 9UE D 402 " both_signs ideal model delta sigma weight residual False -2.65 -2.06 -0.59 2.00e-01 2.50e+01 8.72e+00 chirality pdb=" C6 9UE C 402 " pdb=" N 9UE C 402 " pdb=" C29 9UE C 402 " pdb=" C5 9UE C 402 " both_signs ideal model delta sigma weight residual False -2.65 -2.10 -0.55 2.00e-01 2.50e+01 7.43e+00 ... (remaining 2445 not shown) Planarity restraints: 2805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N 9UE F 402 " 0.021 2.00e-02 2.50e+03 1.71e-02 3.66e+00 pdb=" C6 9UE F 402 " -0.020 2.00e-02 2.50e+03 pdb=" C7 9UE F 402 " 0.017 2.00e-02 2.50e+03 pdb=" C8 9UE F 402 " -0.018 2.00e-02 2.50e+03 pdb=" O2 9UE F 402 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 9UE D 402 " -0.016 2.00e-02 2.50e+03 1.55e-02 3.02e+00 pdb=" C6 9UE D 402 " 0.017 2.00e-02 2.50e+03 pdb=" C7 9UE D 402 " -0.019 2.00e-02 2.50e+03 pdb=" C8 9UE D 402 " 0.017 2.00e-02 2.50e+03 pdb=" O2 9UE D 402 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA F 322 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO F 323 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO F 323 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 323 " -0.024 5.00e-02 4.00e+02 ... (remaining 2802 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 127 2.59 - 3.16: 12103 3.16 - 3.74: 22922 3.74 - 4.32: 36074 4.32 - 4.90: 58504 Nonbonded interactions: 129730 Sorted by model distance: nonbonded pdb="MG MG A 401 " pdb=" O HOH A 513 " model vdw 2.007 2.170 nonbonded pdb="MG MG B 401 " pdb=" O HOH B 514 " model vdw 2.018 2.170 nonbonded pdb="MG MG C 401 " pdb=" O HOH C 515 " model vdw 2.026 2.170 nonbonded pdb="MG MG A 401 " pdb=" O HOH A 520 " model vdw 2.035 2.170 nonbonded pdb="MG MG A 401 " pdb=" O HOH A 514 " model vdw 2.035 2.170 ... (remaining 129725 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 5 through 34 or resid 36 through 47 or resid 49 through 60 \ or resid 62 through 66 or resid 69 through 95 or resid 97 through 101 or resid \ 103 through 119 or resid 122 or resid 124 through 128 or resid 130 through 147 o \ r resid 149 through 159 or resid 161 through 165 or resid 167 through 203 or res \ id 205 through 222 or resid 224 through 225 or resid 227 through 267 or resid 26 \ 9 or resid 271 through 289 or resid 291 through 368 or resid 371 through 372 or \ resid 374 through 375 or resid 401 through 403)) selection = (chain 'B' and (resid 5 through 34 or resid 36 through 47 or resid 49 through 60 \ or resid 62 through 66 or resid 69 through 95 or resid 97 through 101 or resid \ 103 through 119 or resid 122 or resid 124 through 128 or resid 130 through 147 o \ r resid 149 through 159 or resid 161 through 165 or resid 167 through 203 or res \ id 205 through 222 or resid 224 through 225 or resid 227 through 267 or resid 26 \ 9 or resid 271 through 289 or resid 291 through 368 or resid 371 through 372 or \ resid 374 through 375 or resid 401 through 403)) selection = (chain 'C' and (resid 5 through 34 or resid 36 through 47 or resid 49 through 60 \ or resid 62 through 66 or resid 69 through 95 or resid 97 through 101 or resid \ 103 through 119 or resid 122 or resid 124 through 128 or resid 130 through 147 o \ r resid 149 through 159 or resid 161 through 165 or resid 167 through 203 or res \ id 205 through 222 or resid 224 through 225 or resid 227 through 267 or resid 26 \ 9 or resid 271 through 289 or resid 291 through 368 or resid 371 through 372 or \ resid 374 through 375 or resid 401 through 403)) selection = (chain 'D' and (resid 5 through 34 or resid 36 through 47 or resid 49 through 60 \ or resid 62 through 66 or resid 69 through 95 or resid 97 through 101 or resid \ 103 through 119 or resid 122 or resid 124 through 128 or resid 130 through 147 o \ r resid 149 through 159 or resid 161 through 165 or resid 167 through 203 or res \ id 205 through 222 or resid 224 through 225 or resid 227 through 267 or resid 26 \ 9 or resid 271 through 289 or resid 291 through 368 or resid 371 through 372 or \ resid 374 through 375 or resid 401 through 403)) selection = (chain 'F' and (resid 5 through 34 or resid 36 through 47 or resid 49 through 60 \ or resid 62 through 66 or resid 69 through 95 or resid 97 through 101 or resid \ 103 through 119 or resid 122 or resid 124 through 128 or resid 130 through 147 o \ r resid 149 through 159 or resid 161 through 165 or resid 167 through 203 or res \ id 205 through 222 or resid 224 through 225 or resid 227 through 267 or resid 26 \ 9 or resid 271 through 289 or resid 291 through 368 or resid 371 through 372 or \ resid 374 through 375 or resid 401 through 403)) } 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=0.50 max=1.00 mean=0.96 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 7.900 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 53.850 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 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 : 0.023 0.618 16005 Z= 1.402 Angle : 2.094 51.465 21898 Z= 0.756 Chirality : 0.057 0.690 2448 Planarity : 0.005 0.043 2805 Dihedral : 17.769 179.933 6192 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.10 % Allowed : 4.44 % Favored : 92.46 % 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: 1962 helix: -1.76 (0.15), residues: 805 sheet: -0.09 (0.23), residues: 352 loop : -0.71 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 341 HIS 0.003 0.001 HIS D 276 PHE 0.009 0.001 PHE A 256 TYR 0.010 0.001 TYR A 144 ARG 0.004 0.001 ARG F 336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 190 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.8527 (tt0) cc_final: 0.8303 (tt0) REVERT: A 177 MET cc_start: 0.9222 (mmm) cc_final: 0.9017 (mmt) REVERT: A 287 ASP cc_start: 0.7444 (m-30) cc_final: 0.7223 (m-30) REVERT: A 316 ARG cc_start: 0.7766 (ttt-90) cc_final: 0.7399 (ttp-170) REVERT: A 326 MET cc_start: 0.8839 (mmp) cc_final: 0.8141 (mmp) REVERT: B 122 GLN cc_start: 0.8484 (tt0) cc_final: 0.8270 (tt0) REVERT: C 83 MET cc_start: 0.8764 (tpt) cc_final: 0.8438 (tpt) REVERT: C 122 GLN cc_start: 0.8343 (tt0) cc_final: 0.8100 (tt0) REVERT: C 355 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7643 (tp40) REVERT: D 7 GLN cc_start: 0.8288 (mt0) cc_final: 0.8041 (mt0) REVERT: D 45 MET cc_start: 0.7913 (mmm) cc_final: 0.6772 (mmt) REVERT: D 60 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8743 (tp40) REVERT: D 65 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8389 (pp) REVERT: D 124 MET cc_start: 0.8956 (mmt) cc_final: 0.8110 (mmt) REVERT: D 365 GLU cc_start: 0.7583 (tt0) cc_final: 0.7344 (tt0) REVERT: F 83 MET cc_start: 0.8602 (tpt) cc_final: 0.8376 (tpt) REVERT: F 94 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8109 (mm-30) REVERT: F 228 MET cc_start: 0.8814 (mmm) cc_final: 0.8499 (mmm) REVERT: F 233 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7436 (mt0) REVERT: F 316 ARG cc_start: 0.7971 (ttt-90) cc_final: 0.7725 (ttp-170) REVERT: F 326 MET cc_start: 0.8767 (mmp) cc_final: 0.8415 (mmp) outliers start: 22 outliers final: 12 residues processed: 204 average time/residue: 1.7223 time to fit residues: 379.2355 Evaluate side-chains 166 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 152 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain F residue 233 GLN Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 0.1980 chunk 107 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 281 ASN B 13 ASN B 247 ASN B 281 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS C 247 ASN C 281 ASN D 223 ASN B D 247 ASN D 281 ASN F 13 ASN F 247 ASN F 281 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16005 Z= 0.207 Angle : 1.228 48.078 21898 Z= 0.463 Chirality : 0.049 0.300 2448 Planarity : 0.005 0.039 2805 Dihedral : 19.585 178.198 2406 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.57 % Allowed : 8.18 % Favored : 88.25 % 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: -0.52 (0.18), residues: 1962 helix: -0.61 (0.18), residues: 770 sheet: 0.33 (0.25), residues: 377 loop : -0.19 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 341 HIS 0.003 0.001 HIS F 162 PHE 0.013 0.001 PHE A 256 TYR 0.010 0.001 TYR A 144 ARG 0.002 0.000 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7012 (tp30) REVERT: A 122 GLN cc_start: 0.8530 (tt0) cc_final: 0.8302 (tt0) REVERT: A 177 MET cc_start: 0.9006 (mmm) cc_final: 0.8788 (mmt) REVERT: A 287 ASP cc_start: 0.7443 (m-30) cc_final: 0.7202 (m-30) REVERT: A 316 ARG cc_start: 0.7712 (ttt-90) cc_final: 0.7376 (ttp-170) REVERT: A 324 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8325 (p) REVERT: A 326 MET cc_start: 0.8816 (mmp) cc_final: 0.8153 (mmp) REVERT: B 51 LYS cc_start: 0.8328 (mttt) cc_final: 0.8104 (mttm) REVERT: B 73 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.6959 (tp30) REVERT: B 122 GLN cc_start: 0.8474 (tt0) cc_final: 0.8264 (tt0) REVERT: B 250 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8758 (m) REVERT: C 50 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7183 (tm-30) REVERT: C 65 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8569 (pp) REVERT: C 73 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.6862 (tp30) REVERT: C 83 MET cc_start: 0.8824 (tpt) cc_final: 0.8488 (tpt) REVERT: C 122 GLN cc_start: 0.8363 (tt0) cc_final: 0.8122 (tt0) REVERT: C 355 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7638 (tp40) REVERT: D 7 GLN cc_start: 0.8230 (mt0) cc_final: 0.7986 (mt0) REVERT: D 45 MET cc_start: 0.7910 (mmm) cc_final: 0.6744 (mmt) REVERT: D 60 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8706 (tp40) REVERT: D 65 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8335 (pp) REVERT: D 73 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7074 (tp30) REVERT: D 124 MET cc_start: 0.8935 (mmt) cc_final: 0.8083 (mmt) REVERT: D 365 GLU cc_start: 0.7542 (tt0) cc_final: 0.7292 (tt0) REVERT: F 73 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7165 (tp30) REVERT: F 94 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8191 (mm-30) REVERT: F 228 MET cc_start: 0.8770 (mmm) cc_final: 0.8487 (mmm) REVERT: F 233 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7551 (mt0) REVERT: F 316 ARG cc_start: 0.7945 (ttt-90) cc_final: 0.7738 (ttp-170) outliers start: 30 outliers final: 14 residues processed: 172 average time/residue: 1.7051 time to fit residues: 317.0913 Evaluate side-chains 169 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 233 GLN Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 181 optimal weight: 0.0980 chunk 149 optimal weight: 6.9990 chunk 166 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 135 optimal weight: 0.0030 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16005 Z= 0.146 Angle : 1.188 47.574 21898 Z= 0.437 Chirality : 0.047 0.260 2448 Planarity : 0.004 0.041 2805 Dihedral : 19.138 173.424 2406 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.92 % Allowed : 9.82 % Favored : 87.26 % 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: 0.24 (0.19), residues: 1962 helix: 0.10 (0.19), residues: 765 sheet: 0.61 (0.26), residues: 377 loop : 0.22 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 341 HIS 0.003 0.001 HIS F 162 PHE 0.008 0.001 PHE A 256 TYR 0.010 0.001 TYR A 144 ARG 0.001 0.000 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 156 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7290 (tm-30) cc_final: 0.7008 (tm-30) REVERT: A 73 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7024 (tp30) REVERT: A 122 GLN cc_start: 0.8527 (tt0) cc_final: 0.8281 (tt0) REVERT: A 177 MET cc_start: 0.8961 (mmm) cc_final: 0.8742 (mmt) REVERT: A 287 ASP cc_start: 0.7325 (m-30) cc_final: 0.7105 (m-30) REVERT: A 316 ARG cc_start: 0.7633 (ttt-90) cc_final: 0.7427 (ttp-170) REVERT: A 324 SER cc_start: 0.8421 (OUTLIER) cc_final: 0.8206 (p) REVERT: A 326 MET cc_start: 0.8824 (mmp) cc_final: 0.8029 (mmp) REVERT: B 51 LYS cc_start: 0.8367 (mttt) cc_final: 0.8133 (mttm) REVERT: B 73 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.6952 (tp30) REVERT: B 122 GLN cc_start: 0.8453 (tt0) cc_final: 0.8238 (tt0) REVERT: C 50 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7119 (tm-30) REVERT: C 73 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.6849 (tp30) REVERT: C 83 MET cc_start: 0.8819 (tpt) cc_final: 0.8454 (tpt) REVERT: C 122 GLN cc_start: 0.8344 (tt0) cc_final: 0.8102 (tt0) REVERT: C 324 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8406 (p) REVERT: D 7 GLN cc_start: 0.8228 (mt0) cc_final: 0.8001 (mt0) REVERT: D 45 MET cc_start: 0.7923 (mmm) cc_final: 0.6806 (mmt) REVERT: D 60 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8696 (tp40) REVERT: D 124 MET cc_start: 0.8894 (mmt) cc_final: 0.8015 (mmt) REVERT: F 73 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7158 (tp30) REVERT: F 94 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8131 (mm-30) REVERT: F 228 MET cc_start: 0.8788 (mmm) cc_final: 0.8479 (mmm) REVERT: F 233 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7487 (mt0) outliers start: 18 outliers final: 7 residues processed: 169 average time/residue: 1.6612 time to fit residues: 304.0466 Evaluate side-chains 157 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 233 GLN Chi-restraints excluded: chain F residue 331 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN B 253 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN C 253 ASN C 297 ASN F 102 HIS A Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16005 Z= 0.246 Angle : 1.236 47.952 21898 Z= 0.467 Chirality : 0.050 0.221 2448 Planarity : 0.005 0.038 2805 Dihedral : 19.173 179.564 2397 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.33 % Allowed : 10.23 % Favored : 86.44 % 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: 0.19 (0.19), residues: 1962 helix: 0.00 (0.19), residues: 775 sheet: 0.63 (0.25), residues: 377 loop : 0.24 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 341 HIS 0.003 0.001 HIS B 162 PHE 0.010 0.002 PHE A 256 TYR 0.011 0.001 TYR F 144 ARG 0.003 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7155 (mt-10) REVERT: A 73 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7049 (tp30) REVERT: A 122 GLN cc_start: 0.8542 (tt0) cc_final: 0.8312 (tt0) REVERT: A 177 MET cc_start: 0.8995 (mmm) cc_final: 0.8779 (mmt) REVERT: A 287 ASP cc_start: 0.7451 (m-30) cc_final: 0.7220 (m-30) REVERT: A 316 ARG cc_start: 0.7700 (ttt-90) cc_final: 0.7448 (ttp-170) REVERT: A 324 SER cc_start: 0.8513 (OUTLIER) cc_final: 0.8303 (p) REVERT: A 326 MET cc_start: 0.8843 (mmp) cc_final: 0.8131 (mmp) REVERT: B 51 LYS cc_start: 0.8347 (mttt) cc_final: 0.8102 (mttm) REVERT: B 73 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.6912 (tp30) REVERT: C 50 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7123 (tm-30) REVERT: C 73 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.6855 (tp30) REVERT: C 83 MET cc_start: 0.8819 (tpt) cc_final: 0.8477 (tpt) REVERT: C 122 GLN cc_start: 0.8409 (tt0) cc_final: 0.8199 (tt0) REVERT: C 324 SER cc_start: 0.8709 (OUTLIER) cc_final: 0.8494 (p) REVERT: D 7 GLN cc_start: 0.8242 (mt0) cc_final: 0.8007 (mt0) REVERT: D 45 MET cc_start: 0.7835 (mmm) cc_final: 0.6706 (mmt) REVERT: D 60 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8659 (tp40) REVERT: D 73 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7082 (tp30) REVERT: D 124 MET cc_start: 0.8912 (mmt) cc_final: 0.7992 (mmt) REVERT: F 73 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7161 (tp30) REVERT: F 228 MET cc_start: 0.8754 (mmm) cc_final: 0.8436 (mmm) outliers start: 25 outliers final: 8 residues processed: 163 average time/residue: 1.6317 time to fit residues: 288.7127 Evaluate side-chains 164 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 123 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS A ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16005 Z= 0.344 Angle : 1.285 48.101 21898 Z= 0.498 Chirality : 0.053 0.202 2448 Planarity : 0.006 0.046 2805 Dihedral : 19.170 179.869 2392 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.57 % Allowed : 10.40 % Favored : 86.03 % 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: 0.02 (0.18), residues: 1962 helix: -0.14 (0.18), residues: 770 sheet: 0.51 (0.25), residues: 387 loop : 0.16 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP F 341 HIS 0.004 0.002 HIS B 162 PHE 0.012 0.002 PHE A 256 TYR 0.011 0.002 TYR F 144 ARG 0.004 0.001 ARG D 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7346 (tm-30) cc_final: 0.6993 (tm-30) REVERT: A 58 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7230 (mt-10) REVERT: A 73 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7079 (tp30) REVERT: A 122 GLN cc_start: 0.8554 (tt0) cc_final: 0.8338 (tt0) REVERT: A 177 MET cc_start: 0.9022 (mmm) cc_final: 0.8815 (mmt) REVERT: A 287 ASP cc_start: 0.7501 (m-30) cc_final: 0.7268 (m-30) REVERT: A 316 ARG cc_start: 0.7749 (ttt-90) cc_final: 0.7414 (ttp-170) REVERT: A 324 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8418 (p) REVERT: A 326 MET cc_start: 0.8847 (mmp) cc_final: 0.8082 (mmp) REVERT: B 51 LYS cc_start: 0.8362 (mttt) cc_final: 0.8115 (mttm) REVERT: B 73 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.6938 (tp30) REVERT: C 50 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7100 (tm-30) REVERT: C 73 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.6863 (tp30) REVERT: C 83 MET cc_start: 0.8846 (tpt) cc_final: 0.8528 (tpt) REVERT: C 122 GLN cc_start: 0.8375 (tt0) cc_final: 0.8161 (tt0) REVERT: C 324 SER cc_start: 0.8796 (OUTLIER) cc_final: 0.8563 (p) REVERT: D 7 GLN cc_start: 0.8288 (mt0) cc_final: 0.8041 (mt0) REVERT: D 60 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8638 (tp40) REVERT: D 65 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8254 (pp) REVERT: D 73 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7089 (tp30) REVERT: D 124 MET cc_start: 0.8913 (mmt) cc_final: 0.8158 (mmt) REVERT: F 73 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7210 (tp30) REVERT: F 228 MET cc_start: 0.8722 (mmm) cc_final: 0.8410 (mmm) outliers start: 28 outliers final: 14 residues processed: 164 average time/residue: 1.6943 time to fit residues: 301.2097 Evaluate side-chains 169 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 146 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16005 Z= 0.290 Angle : 1.257 48.048 21898 Z= 0.480 Chirality : 0.051 0.210 2448 Planarity : 0.005 0.038 2805 Dihedral : 18.981 179.523 2392 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.27 % Allowed : 11.05 % Favored : 85.68 % 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: 0.11 (0.18), residues: 1962 helix: -0.08 (0.18), residues: 775 sheet: 0.63 (0.26), residues: 377 loop : 0.19 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP D 341 HIS 0.004 0.001 HIS B 162 PHE 0.010 0.002 PHE A 32 TYR 0.009 0.001 TYR F 144 ARG 0.003 0.001 ARG D 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 147 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7395 (tm-30) cc_final: 0.7040 (tm-30) REVERT: A 58 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7208 (mt-10) REVERT: A 73 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7075 (tp30) REVERT: A 122 GLN cc_start: 0.8542 (tt0) cc_final: 0.8323 (tt0) REVERT: A 177 MET cc_start: 0.9009 (mmm) cc_final: 0.8807 (mmt) REVERT: A 287 ASP cc_start: 0.7448 (m-30) cc_final: 0.7242 (m-30) REVERT: A 316 ARG cc_start: 0.7732 (ttt-90) cc_final: 0.7494 (ttp-170) REVERT: A 324 SER cc_start: 0.8611 (OUTLIER) cc_final: 0.8372 (p) REVERT: A 326 MET cc_start: 0.8848 (mmp) cc_final: 0.8073 (mmp) REVERT: B 51 LYS cc_start: 0.8381 (mttt) cc_final: 0.8132 (mttm) REVERT: B 73 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.6938 (tp30) REVERT: C 50 GLU cc_start: 0.7414 (tm-30) cc_final: 0.7021 (tm-30) REVERT: C 73 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.6849 (tp30) REVERT: C 83 MET cc_start: 0.8835 (tpt) cc_final: 0.8516 (tpt) REVERT: C 122 GLN cc_start: 0.8369 (tt0) cc_final: 0.8153 (tt0) REVERT: C 324 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8550 (p) REVERT: D 7 GLN cc_start: 0.8283 (mt0) cc_final: 0.8038 (mt0) REVERT: D 60 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8627 (tp40) REVERT: D 65 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8237 (pp) REVERT: D 73 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7073 (tp30) REVERT: D 124 MET cc_start: 0.8908 (mmt) cc_final: 0.8137 (mmt) REVERT: D 133 MET cc_start: 0.8575 (ttp) cc_final: 0.8327 (ttt) REVERT: F 73 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7211 (tp30) REVERT: F 228 MET cc_start: 0.8735 (mmm) cc_final: 0.8421 (mmm) outliers start: 23 outliers final: 11 residues processed: 161 average time/residue: 1.7613 time to fit residues: 307.0756 Evaluate side-chains 166 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16005 Z= 0.263 Angle : 1.250 47.979 21898 Z= 0.476 Chirality : 0.050 0.215 2448 Planarity : 0.005 0.038 2805 Dihedral : 18.772 179.332 2392 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.33 % Allowed : 11.05 % Favored : 85.62 % 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: 0.19 (0.19), residues: 1962 helix: -0.01 (0.18), residues: 775 sheet: 0.64 (0.26), residues: 377 loop : 0.25 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP D 341 HIS 0.004 0.001 HIS F 162 PHE 0.010 0.002 PHE A 256 TYR 0.009 0.001 TYR F 144 ARG 0.003 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7027 (tm-30) REVERT: A 73 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7072 (tp30) REVERT: A 122 GLN cc_start: 0.8538 (tt0) cc_final: 0.8319 (tt0) REVERT: A 177 MET cc_start: 0.9005 (mmm) cc_final: 0.8768 (mmt) REVERT: A 287 ASP cc_start: 0.7461 (m-30) cc_final: 0.7257 (m-30) REVERT: A 316 ARG cc_start: 0.7722 (ttt-90) cc_final: 0.7411 (ttp-170) REVERT: A 324 SER cc_start: 0.8614 (OUTLIER) cc_final: 0.8373 (p) REVERT: A 326 MET cc_start: 0.8850 (mmp) cc_final: 0.8078 (mmp) REVERT: B 51 LYS cc_start: 0.8354 (mttt) cc_final: 0.8116 (mttm) REVERT: B 73 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.6939 (tp30) REVERT: C 50 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7062 (tm-30) REVERT: C 65 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8336 (pp) REVERT: C 73 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.6847 (tp30) REVERT: C 83 MET cc_start: 0.8845 (tpt) cc_final: 0.8522 (tpt) REVERT: C 122 GLN cc_start: 0.8403 (tt0) cc_final: 0.8176 (tt0) REVERT: C 324 SER cc_start: 0.8752 (OUTLIER) cc_final: 0.8527 (p) REVERT: D 7 GLN cc_start: 0.8280 (mt0) cc_final: 0.8027 (mt0) REVERT: D 60 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8612 (tp40) REVERT: D 65 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8267 (pp) REVERT: D 73 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7070 (tp30) REVERT: D 124 MET cc_start: 0.8907 (mmt) cc_final: 0.8083 (mmt) REVERT: F 73 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7195 (tp30) REVERT: F 228 MET cc_start: 0.8718 (mmm) cc_final: 0.8395 (mmm) outliers start: 24 outliers final: 14 residues processed: 161 average time/residue: 1.6527 time to fit residues: 288.5077 Evaluate side-chains 169 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 146 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 162 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16005 Z= 0.192 Angle : 1.217 47.794 21898 Z= 0.454 Chirality : 0.048 0.227 2448 Planarity : 0.004 0.038 2805 Dihedral : 18.475 178.485 2392 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.16 % Allowed : 11.28 % Favored : 85.56 % 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: 0.57 (0.19), residues: 1962 helix: 0.41 (0.19), residues: 745 sheet: 0.70 (0.26), residues: 377 loop : 0.42 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 341 HIS 0.004 0.001 HIS F 162 PHE 0.011 0.001 PHE A 256 TYR 0.009 0.001 TYR A 144 ARG 0.002 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 144 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7070 (tm-30) REVERT: A 73 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7061 (tp30) REVERT: A 122 GLN cc_start: 0.8533 (tt0) cc_final: 0.8304 (tt0) REVERT: A 177 MET cc_start: 0.8995 (mmm) cc_final: 0.8763 (mmt) REVERT: A 287 ASP cc_start: 0.7424 (m-30) cc_final: 0.7199 (m-30) REVERT: A 316 ARG cc_start: 0.7636 (ttt-90) cc_final: 0.7383 (ttp-170) REVERT: A 326 MET cc_start: 0.8854 (mmp) cc_final: 0.8085 (mmp) REVERT: B 51 LYS cc_start: 0.8356 (mttt) cc_final: 0.8126 (mttm) REVERT: B 73 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.6937 (tp30) REVERT: C 50 GLU cc_start: 0.7411 (tm-30) cc_final: 0.7008 (tm-30) REVERT: C 65 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8358 (pp) REVERT: C 73 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.6828 (tp30) REVERT: C 83 MET cc_start: 0.8818 (tpt) cc_final: 0.8470 (tpt) REVERT: C 122 GLN cc_start: 0.8347 (tt0) cc_final: 0.8132 (tt0) REVERT: D 7 GLN cc_start: 0.8240 (mt0) cc_final: 0.7999 (mt0) REVERT: D 60 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8617 (tp40) REVERT: D 65 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8224 (pp) REVERT: D 73 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7079 (tp30) REVERT: D 124 MET cc_start: 0.8896 (mmt) cc_final: 0.8007 (mmt) REVERT: F 73 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7174 (tp30) REVERT: F 228 MET cc_start: 0.8734 (mmm) cc_final: 0.8408 (mmm) outliers start: 21 outliers final: 11 residues processed: 157 average time/residue: 1.7040 time to fit residues: 290.3085 Evaluate side-chains 160 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 331 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 100 optimal weight: 0.3980 chunk 72 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16005 Z= 0.209 Angle : 1.228 47.879 21898 Z= 0.461 Chirality : 0.049 0.228 2448 Planarity : 0.004 0.037 2805 Dihedral : 18.440 178.425 2392 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.16 % Allowed : 11.34 % Favored : 85.51 % 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: 0.46 (0.19), residues: 1962 helix: 0.23 (0.19), residues: 775 sheet: 0.72 (0.26), residues: 377 loop : 0.42 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 341 HIS 0.004 0.001 HIS F 162 PHE 0.010 0.001 PHE A 256 TYR 0.010 0.001 TYR A 144 ARG 0.002 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 142 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7065 (tm-30) REVERT: A 73 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7069 (tp30) REVERT: A 122 GLN cc_start: 0.8532 (tt0) cc_final: 0.8307 (tt0) REVERT: A 177 MET cc_start: 0.8992 (mmm) cc_final: 0.8759 (mmt) REVERT: A 287 ASP cc_start: 0.7437 (m-30) cc_final: 0.7212 (m-30) REVERT: A 316 ARG cc_start: 0.7629 (ttt-90) cc_final: 0.7380 (ttp-170) REVERT: A 326 MET cc_start: 0.8858 (mmp) cc_final: 0.8099 (mmp) REVERT: B 51 LYS cc_start: 0.8369 (mttt) cc_final: 0.8139 (mttm) REVERT: B 73 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.6937 (tp30) REVERT: C 50 GLU cc_start: 0.7414 (tm-30) cc_final: 0.7005 (tm-30) REVERT: C 65 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8358 (pp) REVERT: C 73 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.6839 (tp30) REVERT: C 83 MET cc_start: 0.8819 (tpt) cc_final: 0.8467 (tpt) REVERT: C 122 GLN cc_start: 0.8351 (tt0) cc_final: 0.8138 (tt0) REVERT: D 7 GLN cc_start: 0.8244 (mt0) cc_final: 0.8002 (mt0) REVERT: D 60 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8617 (tp40) REVERT: D 65 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8224 (pp) REVERT: D 73 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7086 (tp30) REVERT: D 124 MET cc_start: 0.8898 (mmt) cc_final: 0.7995 (mmt) REVERT: F 73 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7177 (tp30) REVERT: F 228 MET cc_start: 0.8724 (mmm) cc_final: 0.8392 (mmm) outliers start: 20 outliers final: 12 residues processed: 154 average time/residue: 1.7191 time to fit residues: 286.5802 Evaluate side-chains 161 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 122 optimal weight: 0.0770 chunk 184 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16005 Z= 0.156 Angle : 1.198 47.679 21898 Z= 0.441 Chirality : 0.047 0.233 2448 Planarity : 0.004 0.038 2805 Dihedral : 18.093 174.845 2392 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.86 % Allowed : 11.57 % Favored : 85.56 % 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: 0.90 (0.19), residues: 1962 helix: 0.73 (0.19), residues: 735 sheet: 0.80 (0.26), residues: 377 loop : 0.60 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 341 HIS 0.004 0.001 HIS F 162 PHE 0.010 0.001 PHE A 256 TYR 0.010 0.001 TYR A 144 ARG 0.001 0.000 ARG C 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7062 (tm-30) REVERT: A 73 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7056 (tp30) REVERT: A 122 GLN cc_start: 0.8527 (tt0) cc_final: 0.8264 (tt0) REVERT: A 177 MET cc_start: 0.8975 (mmm) cc_final: 0.8757 (mmt) REVERT: A 287 ASP cc_start: 0.7356 (m-30) cc_final: 0.7130 (m-30) REVERT: A 316 ARG cc_start: 0.7612 (ttt-90) cc_final: 0.7365 (ttp-170) REVERT: A 326 MET cc_start: 0.8862 (mmp) cc_final: 0.8141 (mmp) REVERT: B 51 LYS cc_start: 0.8371 (mttt) cc_final: 0.8133 (mttm) REVERT: C 50 GLU cc_start: 0.7410 (tm-30) cc_final: 0.7003 (tm-30) REVERT: C 65 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8361 (pp) REVERT: C 73 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.6830 (tp30) REVERT: C 83 MET cc_start: 0.8822 (tpt) cc_final: 0.8480 (tpt) REVERT: C 122 GLN cc_start: 0.8346 (tt0) cc_final: 0.8108 (tt0) REVERT: C 326 MET cc_start: 0.8648 (mmp) cc_final: 0.8430 (mmp) REVERT: D 7 GLN cc_start: 0.8210 (mt0) cc_final: 0.7978 (mt0) REVERT: D 60 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8614 (tp40) REVERT: D 65 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8188 (pp) REVERT: D 73 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7075 (tp30) REVERT: D 124 MET cc_start: 0.8883 (mmt) cc_final: 0.8000 (mmt) REVERT: F 73 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7164 (tp30) REVERT: F 228 MET cc_start: 0.8726 (mmm) cc_final: 0.8401 (mmm) outliers start: 15 outliers final: 8 residues processed: 155 average time/residue: 1.7307 time to fit residues: 291.8586 Evaluate side-chains 154 residues out of total 1479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 331 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 135 optimal weight: 0.2980 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** 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 = 0.3139 r_free = 0.3139 target = 0.105405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.081661 restraints weight = 111868.346| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 3.85 r_work: 0.2549 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2519 r_free = 0.2519 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2516 r_free = 0.2516 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16005 Z= 0.237 Angle : 1.240 47.922 21898 Z= 0.468 Chirality : 0.050 0.226 2448 Planarity : 0.005 0.036 2805 Dihedral : 18.274 178.252 2392 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.04 % Allowed : 11.98 % Favored : 84.98 % 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: 0.54 (0.19), residues: 1962 helix: 0.27 (0.19), residues: 775 sheet: 0.77 (0.26), residues: 377 loop : 0.49 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 341 HIS 0.004 0.001 HIS F 162 PHE 0.010 0.001 PHE A 32 TYR 0.009 0.001 TYR F 144 ARG 0.003 0.000 ARG C 178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5519.34 seconds wall clock time: 100 minutes 5.17 seconds (6005.17 seconds total)