Starting phenix.real_space_refine on Sat Apr 6 05:30:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzg_38795/04_2024/8xzg_38795_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzg_38795/04_2024/8xzg_38795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzg_38795/04_2024/8xzg_38795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzg_38795/04_2024/8xzg_38795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzg_38795/04_2024/8xzg_38795_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzg_38795/04_2024/8xzg_38795_updated.pdb" } resolution = 3.2 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= 0.013 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: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 4572 2.51 5 N 1222 2.21 5 O 1317 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 43": "OE1" <-> "OE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 231": "OD1" <-> "OD2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ASP 328": "OD1" <-> "OD2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ASP 5": "OD1" <-> "OD2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "G ASP 48": "OD1" <-> "OD2" Residue "L ARG 2": "NH1" <-> "NH2" Residue "L PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 62": "NH1" <-> "NH2" Residue "R PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 75": "OD1" <-> "OD2" Residue "R PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 174": "OE1" <-> "OE2" Residue "R TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 184": "OD1" <-> "OD2" Residue "R TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 194": "OE1" <-> "OE2" Residue "R PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 282": "OD1" <-> "OD2" Residue "R PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7172 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1737 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2528 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "L" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 107 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 3, 'TRANS': 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2356 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 288} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 4.37, per 1000 atoms: 0.61 Number of scatterers: 7172 At special positions: 0 Unit cell: (78.078, 120.666, 118.638, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 61 16.00 O 1317 8.00 N 1222 7.00 C 4572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.02 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: 2.68 Conformation dependent library (CDL) restraints added in 1.4 seconds 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1734 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 8 sheets defined 40.5% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 7 through 29 Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 215 removed outlier: 5.268A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 231 removed outlier: 4.005A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 231' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.619A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 21 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 27 through 52 Proline residue: R 32 - end of helix removed outlier: 3.942A pdb=" N GLY R 47 " --> pdb=" O THR R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 89 removed outlier: 3.841A pdb=" N THR R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LEU R 82 " --> pdb=" O PHE R 78 " (cutoff:3.500A) Proline residue: R 83 - end of helix Processing helix chain 'R' and resid 101 through 131 removed outlier: 4.168A pdb=" N SER R 106 " --> pdb=" O CYS R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 143 Processing helix chain 'R' and resid 149 through 162 removed outlier: 3.860A pdb=" N MET R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 209 removed outlier: 6.038A pdb=" N TRP R 195 " --> pdb=" O SER R 192 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU R 198 " --> pdb=" O TRP R 195 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL R 203 " --> pdb=" O GLY R 200 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER R 205 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 231 Processing helix chain 'R' and resid 240 through 274 removed outlier: 4.426A pdb=" N ARG R 244 " --> pdb=" O ARG R 241 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ARG R 245 " --> pdb=" O LYS R 242 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU R 246 " --> pdb=" O ARG R 243 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU R 247 " --> pdb=" O ARG R 244 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER R 248 " --> pdb=" O ARG R 245 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL R 252 " --> pdb=" O ILE R 249 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR R 256 " --> pdb=" O LEU R 253 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE R 257 " --> pdb=" O VAL R 254 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N TRP R 261 " --> pdb=" O ALA R 258 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N MET R 262 " --> pdb=" O LEU R 259 " (cutoff:3.500A) Proline residue: R 263 - end of helix removed outlier: 3.557A pdb=" N THR R 269 " --> pdb=" O LEU R 266 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY R 274 " --> pdb=" O TYR R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 299 Proline residue: R 292 - end of helix removed outlier: 4.224A pdb=" N CYS R 296 " --> pdb=" O PRO R 292 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER R 298 " --> pdb=" O CYS R 294 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TYR R 299 " --> pdb=" O THR R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 304 No H-bonds generated for 'chain 'R' and resid 301 through 304' Processing helix chain 'R' and resid 306 through 309 No H-bonds generated for 'chain 'R' and resid 306 through 309' Processing helix chain 'R' and resid 314 through 326 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.512A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.690A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.844A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TRP B 82 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 111 through 114 removed outlier: 3.506A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 178 through 180 Processing sheet with id= F, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.963A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.607A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'R' and resid 168 through 173 removed outlier: 3.533A pdb=" N THR R 169 " --> pdb=" O TYR R 182 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR R 182 " --> pdb=" O THR R 169 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU R 173 " --> pdb=" O LYS R 178 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS R 178 " --> pdb=" O LEU R 173 " (cutoff:3.500A) 298 hydrogen bonds defined for protein. 786 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: 1.85 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2259 1.34 - 1.45: 1178 1.45 - 1.57: 3794 1.57 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 7319 Sorted by residual: bond pdb=" N PCA L 1 " pdb=" CD PCA L 1 " ideal model delta sigma weight residual 1.345 1.463 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" N TRP R 279 " pdb=" CA TRP R 279 " ideal model delta sigma weight residual 1.453 1.487 -0.034 9.20e-03 1.18e+04 1.37e+01 bond pdb=" N ILE R 290 " pdb=" CA ILE R 290 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.09e-02 8.42e+03 1.23e+01 bond pdb=" N VAL R 79 " pdb=" CA VAL R 79 " ideal model delta sigma weight residual 1.458 1.496 -0.037 1.22e-02 6.72e+03 9.37e+00 bond pdb=" N VAL R 80 " pdb=" CA VAL R 80 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.12e+00 ... (remaining 7314 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.41: 155 106.41 - 113.38: 4023 113.38 - 120.35: 2940 120.35 - 127.32: 2721 127.32 - 134.30: 73 Bond angle restraints: 9912 Sorted by residual: angle pdb=" N HIS R 231 " pdb=" CA HIS R 231 " pdb=" C HIS R 231 " ideal model delta sigma weight residual 111.36 117.00 -5.64 1.09e+00 8.42e-01 2.68e+01 angle pdb=" N THR R 99 " pdb=" CA THR R 99 " pdb=" C THR R 99 " ideal model delta sigma weight residual 111.71 105.87 5.84 1.15e+00 7.56e-01 2.58e+01 angle pdb=" O ILE R 31 " pdb=" C ILE R 31 " pdb=" N PRO R 32 " ideal model delta sigma weight residual 120.42 123.50 -3.08 6.40e-01 2.44e+00 2.31e+01 angle pdb=" N LYS R 242 " pdb=" CA LYS R 242 " pdb=" C LYS R 242 " ideal model delta sigma weight residual 113.17 107.68 5.49 1.26e+00 6.30e-01 1.90e+01 angle pdb=" C TRP R 279 " pdb=" N PRO R 280 " pdb=" CA PRO R 280 " ideal model delta sigma weight residual 119.84 124.99 -5.15 1.25e+00 6.40e-01 1.70e+01 ... (remaining 9907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 3844 17.18 - 34.36: 419 34.36 - 51.53: 69 51.53 - 68.71: 7 68.71 - 85.89: 4 Dihedral angle restraints: 4343 sinusoidal: 1669 harmonic: 2674 Sorted by residual: dihedral pdb=" CA PHE B 199 " pdb=" C PHE B 199 " pdb=" N VAL B 200 " pdb=" CA VAL B 200 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA PHE B 241 " pdb=" C PHE B 241 " pdb=" N ALA B 242 " pdb=" CA ALA B 242 " ideal model delta harmonic sigma weight residual 180.00 156.67 23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 161.96 18.04 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 4340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 834 0.054 - 0.108: 226 0.108 - 0.162: 62 0.162 - 0.216: 12 0.216 - 0.270: 1 Chirality restraints: 1135 Sorted by residual: chirality pdb=" CA HIS R 231 " pdb=" N HIS R 231 " pdb=" C HIS R 231 " pdb=" CB HIS R 231 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA LEU R 71 " pdb=" N LEU R 71 " pdb=" C LEU R 71 " pdb=" CB LEU R 71 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA LEU R 120 " pdb=" N LEU R 120 " pdb=" C LEU R 120 " pdb=" CB LEU R 120 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 1132 not shown) Planarity restraints: 1247 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY R 230 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C GLY R 230 " -0.056 2.00e-02 2.50e+03 pdb=" O GLY R 230 " 0.021 2.00e-02 2.50e+03 pdb=" N HIS R 231 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 60 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C ALA B 60 " 0.048 2.00e-02 2.50e+03 pdb=" O ALA B 60 " -0.018 2.00e-02 2.50e+03 pdb=" N MET B 61 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 83 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.18e+00 pdb=" C ASP B 83 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP B 83 " 0.013 2.00e-02 2.50e+03 pdb=" N SER B 84 " 0.012 2.00e-02 2.50e+03 ... (remaining 1244 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 432 2.72 - 3.26: 6977 3.26 - 3.81: 10946 3.81 - 4.35: 13397 4.35 - 4.90: 23783 Nonbonded interactions: 55535 Sorted by model distance: nonbonded pdb=" ND2 ASN R 46 " pdb=" OD2 ASP R 75 " model vdw 2.173 2.520 nonbonded pdb=" O THR R 295 " pdb=" CE1 TYR R 299 " model vdw 2.209 3.340 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.229 2.440 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.234 2.440 nonbonded pdb=" NH2 ARG B 49 " pdb=" O PHE G 61 " model vdw 2.279 2.520 ... (remaining 55530 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.910 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 23.110 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 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 : 0.008 0.118 7319 Z= 0.526 Angle : 0.881 10.115 9912 Z= 0.580 Chirality : 0.055 0.270 1135 Planarity : 0.005 0.047 1247 Dihedral : 14.038 85.891 2606 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.11 % Favored : 93.78 % Rotamer: Outliers : 1.56 % Allowed : 9.08 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.25), residues: 900 helix: -0.45 (0.25), residues: 382 sheet: -3.04 (0.29), residues: 169 loop : -2.59 (0.28), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.017 0.002 PHE G 61 TYR 0.009 0.001 TYR B 124 ARG 0.004 0.000 ARG R 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 0.802 Fit side-chains REVERT: A 35 LYS cc_start: 0.7726 (mttt) cc_final: 0.7488 (mttp) REVERT: A 251 ASP cc_start: 0.8791 (t70) cc_final: 0.8575 (t0) REVERT: A 260 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.8104 (t) REVERT: B 118 ASP cc_start: 0.7505 (t0) cc_final: 0.7245 (t0) REVERT: B 129 ARG cc_start: 0.7139 (tpt90) cc_final: 0.6346 (mtp-110) REVERT: B 214 ARG cc_start: 0.7224 (mtt180) cc_final: 0.6712 (mmt180) REVERT: B 226 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7847 (mt-10) REVERT: R 31 ILE cc_start: 0.4786 (OUTLIER) cc_final: 0.4547 (mm) REVERT: R 323 MET cc_start: 0.6677 (mmm) cc_final: 0.5828 (mtt) outliers start: 12 outliers final: 3 residues processed: 120 average time/residue: 0.2561 time to fit residues: 38.7145 Evaluate side-chains 91 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 253 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS B 91 HIS B 155 ASN B 176 GLN G 24 ASN L 7 HIS ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 289 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7319 Z= 0.184 Angle : 0.528 6.470 9912 Z= 0.277 Chirality : 0.042 0.147 1135 Planarity : 0.004 0.043 1247 Dihedral : 5.266 58.128 999 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.08 % Allowed : 13.75 % Favored : 84.18 % 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: -1.71 (0.27), residues: 900 helix: 0.39 (0.27), residues: 383 sheet: -2.49 (0.31), residues: 178 loop : -2.04 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 95 HIS 0.005 0.001 HIS L 7 PHE 0.025 0.001 PHE R 39 TYR 0.013 0.001 TYR A 230 ARG 0.006 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.660 Fit side-chains REVERT: A 24 ARG cc_start: 0.6943 (ttp80) cc_final: 0.6665 (ttp-110) REVERT: B 17 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7670 (tm-30) REVERT: B 118 ASP cc_start: 0.7485 (t0) cc_final: 0.7256 (t0) REVERT: B 129 ARG cc_start: 0.7057 (tpt90) cc_final: 0.6145 (mtp-110) REVERT: B 200 VAL cc_start: 0.7813 (OUTLIER) cc_final: 0.7547 (m) REVERT: B 214 ARG cc_start: 0.7302 (mtt180) cc_final: 0.6944 (mmt180) REVERT: B 226 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7825 (mt-10) REVERT: B 234 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8505 (m-80) REVERT: B 258 ASP cc_start: 0.6056 (t70) cc_final: 0.5512 (t70) REVERT: R 323 MET cc_start: 0.6615 (mmm) cc_final: 0.5774 (mtt) outliers start: 16 outliers final: 12 residues processed: 110 average time/residue: 0.2234 time to fit residues: 32.0196 Evaluate side-chains 99 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 253 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 0.0470 chunk 80 optimal weight: 0.8980 overall best weight: 1.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 46 ASN ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7319 Z= 0.298 Angle : 0.539 6.696 9912 Z= 0.282 Chirality : 0.042 0.144 1135 Planarity : 0.004 0.046 1247 Dihedral : 5.074 57.492 994 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.24 % Allowed : 16.86 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.48 (0.27), residues: 900 helix: 0.42 (0.27), residues: 389 sheet: -2.45 (0.31), residues: 182 loop : -1.67 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS B 91 PHE 0.021 0.002 PHE B 199 TYR 0.011 0.001 TYR R 221 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 0.697 Fit side-chains REVERT: A 24 ARG cc_start: 0.7003 (ttp80) cc_final: 0.6727 (ttp-110) REVERT: A 251 ASP cc_start: 0.8646 (t70) cc_final: 0.8444 (t0) REVERT: B 118 ASP cc_start: 0.7552 (t0) cc_final: 0.7314 (t0) REVERT: B 129 ARG cc_start: 0.7069 (tpt90) cc_final: 0.6239 (mtp-110) REVERT: B 152 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8081 (tt) REVERT: B 200 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7809 (m) REVERT: B 214 ARG cc_start: 0.7333 (mtt180) cc_final: 0.7001 (mmt180) REVERT: B 226 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7829 (mt-10) REVERT: B 234 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8332 (m-80) REVERT: R 242 LYS cc_start: 0.8241 (mmtt) cc_final: 0.6850 (mtmt) REVERT: R 323 MET cc_start: 0.6631 (mmm) cc_final: 0.5852 (mtt) outliers start: 25 outliers final: 14 residues processed: 115 average time/residue: 0.2361 time to fit residues: 35.3001 Evaluate side-chains 108 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 253 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 0.0270 chunk 23 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7319 Z= 0.160 Angle : 0.466 6.266 9912 Z= 0.241 Chirality : 0.040 0.141 1135 Planarity : 0.004 0.037 1247 Dihedral : 4.511 55.397 994 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.98 % Allowed : 18.68 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.28), residues: 900 helix: 0.72 (0.27), residues: 387 sheet: -2.06 (0.33), residues: 182 loop : -1.42 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS R 231 PHE 0.016 0.001 PHE R 39 TYR 0.009 0.001 TYR R 221 ARG 0.005 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 0.831 Fit side-chains REVERT: A 24 ARG cc_start: 0.6946 (ttp80) cc_final: 0.6660 (ttp-110) REVERT: B 118 ASP cc_start: 0.7452 (t0) cc_final: 0.7240 (t0) REVERT: B 129 ARG cc_start: 0.6962 (tpt90) cc_final: 0.6153 (mtp-110) REVERT: B 152 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8002 (tt) REVERT: B 163 ASP cc_start: 0.7321 (t0) cc_final: 0.7034 (t0) REVERT: B 200 VAL cc_start: 0.7764 (OUTLIER) cc_final: 0.7438 (m) REVERT: B 214 ARG cc_start: 0.7347 (mtt180) cc_final: 0.7005 (mmt180) REVERT: B 226 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7819 (mt-10) REVERT: B 234 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8441 (m-80) REVERT: B 258 ASP cc_start: 0.6157 (t70) cc_final: 0.5552 (t70) REVERT: R 242 LYS cc_start: 0.8302 (mmtt) cc_final: 0.6961 (mtmt) REVERT: R 323 MET cc_start: 0.6500 (mmm) cc_final: 0.5724 (mtt) outliers start: 23 outliers final: 16 residues processed: 101 average time/residue: 0.2464 time to fit residues: 32.3253 Evaluate side-chains 103 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 316 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7319 Z= 0.312 Angle : 0.529 8.755 9912 Z= 0.274 Chirality : 0.042 0.140 1135 Planarity : 0.004 0.044 1247 Dihedral : 4.573 53.911 994 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.76 % Allowed : 19.46 % Favored : 76.78 % 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: -1.10 (0.28), residues: 900 helix: 0.61 (0.27), residues: 394 sheet: -2.02 (0.32), residues: 188 loop : -1.47 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS B 91 PHE 0.026 0.002 PHE B 199 TYR 0.010 0.001 TYR B 105 ARG 0.007 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 83 time to evaluate : 0.775 Fit side-chains REVERT: A 24 ARG cc_start: 0.6976 (ttp80) cc_final: 0.6706 (ttp-110) REVERT: A 277 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8417 (ttmt) REVERT: B 129 ARG cc_start: 0.7082 (tpt90) cc_final: 0.6251 (mtp-110) REVERT: B 152 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8098 (tt) REVERT: B 200 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7740 (m) REVERT: B 214 ARG cc_start: 0.7355 (mtt180) cc_final: 0.7030 (mmt180) REVERT: B 226 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7841 (mt-10) REVERT: B 234 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.8278 (m-80) REVERT: R 91 ARG cc_start: 0.4363 (OUTLIER) cc_final: 0.3823 (ptp-170) REVERT: R 187 MET cc_start: 0.4608 (mmm) cc_final: 0.4229 (ttm) REVERT: R 242 LYS cc_start: 0.8327 (mmtt) cc_final: 0.6956 (mtmt) REVERT: R 253 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6777 (mt) REVERT: R 323 MET cc_start: 0.6575 (mmm) cc_final: 0.5784 (mtt) outliers start: 29 outliers final: 19 residues processed: 103 average time/residue: 0.2540 time to fit residues: 33.6508 Evaluate side-chains 108 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 316 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 0.0020 chunk 83 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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: 0.7274 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7319 Z= 0.146 Angle : 0.454 7.420 9912 Z= 0.235 Chirality : 0.040 0.163 1135 Planarity : 0.003 0.038 1247 Dihedral : 4.192 50.490 994 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.46 % Allowed : 21.79 % Favored : 75.75 % 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: -0.78 (0.28), residues: 900 helix: 0.86 (0.28), residues: 390 sheet: -1.77 (0.34), residues: 180 loop : -1.34 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS L 7 PHE 0.015 0.001 PHE B 199 TYR 0.008 0.001 TYR B 264 ARG 0.004 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 0.847 Fit side-chains REVERT: A 24 ARG cc_start: 0.6937 (ttp80) cc_final: 0.6659 (ttp-110) REVERT: A 277 LYS cc_start: 0.8662 (mtpt) cc_final: 0.8416 (ttmt) REVERT: B 17 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7563 (tm-30) REVERT: B 129 ARG cc_start: 0.6939 (tpt90) cc_final: 0.6175 (mtp-110) REVERT: B 152 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8036 (tt) REVERT: B 200 VAL cc_start: 0.7791 (OUTLIER) cc_final: 0.7453 (m) REVERT: B 214 ARG cc_start: 0.7311 (mtt180) cc_final: 0.6959 (mmt180) REVERT: B 226 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7835 (mt-10) REVERT: B 234 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.8425 (m-80) REVERT: B 258 ASP cc_start: 0.6135 (t70) cc_final: 0.5518 (t70) REVERT: R 91 ARG cc_start: 0.4070 (OUTLIER) cc_final: 0.3622 (ptp-170) REVERT: R 187 MET cc_start: 0.4548 (mmm) cc_final: 0.4184 (ttm) REVERT: R 242 LYS cc_start: 0.8306 (mmtt) cc_final: 0.6945 (mtmt) REVERT: R 253 LEU cc_start: 0.7031 (mp) cc_final: 0.6662 (mt) REVERT: R 309 TYR cc_start: 0.8168 (m-80) cc_final: 0.7866 (m-80) REVERT: R 316 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7404 (t80) REVERT: R 323 MET cc_start: 0.6504 (mmm) cc_final: 0.5674 (mtt) outliers start: 19 outliers final: 13 residues processed: 105 average time/residue: 0.2458 time to fit residues: 33.1572 Evaluate side-chains 104 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 316 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 73 optimal weight: 9.9990 chunk 48 optimal weight: 0.0980 chunk 86 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7319 Z= 0.158 Angle : 0.473 10.938 9912 Z= 0.239 Chirality : 0.039 0.161 1135 Planarity : 0.003 0.037 1247 Dihedral : 3.737 23.974 992 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.76 % Allowed : 20.88 % Favored : 75.36 % 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: -0.56 (0.28), residues: 900 helix: 0.98 (0.28), residues: 390 sheet: -1.50 (0.34), residues: 189 loop : -1.23 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.003 0.001 HIS L 7 PHE 0.015 0.001 PHE B 199 TYR 0.007 0.001 TYR B 264 ARG 0.004 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 86 time to evaluate : 0.956 Fit side-chains REVERT: A 24 ARG cc_start: 0.6937 (ttp80) cc_final: 0.6655 (ttp-110) REVERT: A 277 LYS cc_start: 0.8670 (mtpt) cc_final: 0.8429 (ttmt) REVERT: B 17 GLN cc_start: 0.8139 (tm-30) cc_final: 0.7581 (tm-30) REVERT: B 129 ARG cc_start: 0.6937 (tpt90) cc_final: 0.6205 (mtp-110) REVERT: B 152 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8025 (tt) REVERT: B 200 VAL cc_start: 0.7766 (OUTLIER) cc_final: 0.7422 (m) REVERT: B 214 ARG cc_start: 0.7288 (mtt180) cc_final: 0.6958 (mmt180) REVERT: B 226 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7809 (mt-10) REVERT: B 234 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8362 (m-80) REVERT: B 258 ASP cc_start: 0.6091 (t70) cc_final: 0.5473 (t70) REVERT: R 91 ARG cc_start: 0.4147 (OUTLIER) cc_final: 0.3717 (ptp-170) REVERT: R 120 LEU cc_start: 0.5016 (OUTLIER) cc_final: 0.4624 (tt) REVERT: R 187 MET cc_start: 0.4469 (mmm) cc_final: 0.4124 (ttm) REVERT: R 242 LYS cc_start: 0.8191 (mmtt) cc_final: 0.6863 (mtmt) REVERT: R 249 ILE cc_start: 0.6932 (OUTLIER) cc_final: 0.6675 (tp) REVERT: R 316 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.7445 (t80) REVERT: R 323 MET cc_start: 0.6469 (mmm) cc_final: 0.5538 (mtt) outliers start: 29 outliers final: 18 residues processed: 105 average time/residue: 0.2461 time to fit residues: 33.3414 Evaluate side-chains 111 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 86 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 316 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 55 optimal weight: 0.0770 chunk 59 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 8 optimal weight: 0.1980 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 0.1980 overall best weight: 0.2938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7319 Z= 0.119 Angle : 0.435 6.306 9912 Z= 0.224 Chirality : 0.039 0.151 1135 Planarity : 0.003 0.037 1247 Dihedral : 3.517 21.966 992 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.59 % Allowed : 22.05 % Favored : 75.36 % 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: -0.43 (0.28), residues: 900 helix: 1.08 (0.27), residues: 394 sheet: -1.42 (0.36), residues: 177 loop : -1.20 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.000 HIS L 7 PHE 0.011 0.001 PHE R 39 TYR 0.005 0.001 TYR R 35 ARG 0.004 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 0.846 Fit side-chains REVERT: A 24 ARG cc_start: 0.6905 (ttp80) cc_final: 0.6627 (ttp-110) REVERT: A 277 LYS cc_start: 0.8643 (mtpt) cc_final: 0.8410 (ttpt) REVERT: B 17 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7588 (tm-30) REVERT: B 111 TYR cc_start: 0.8409 (m-80) cc_final: 0.8201 (m-80) REVERT: B 129 ARG cc_start: 0.6867 (tpt90) cc_final: 0.6189 (mtp-110) REVERT: B 146 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7421 (mp) REVERT: B 152 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8028 (tt) REVERT: B 200 VAL cc_start: 0.7761 (OUTLIER) cc_final: 0.7495 (m) REVERT: B 214 ARG cc_start: 0.7371 (mtt180) cc_final: 0.6918 (mmt180) REVERT: B 226 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7795 (mt-10) REVERT: B 258 ASP cc_start: 0.6063 (t70) cc_final: 0.5431 (t70) REVERT: R 91 ARG cc_start: 0.3911 (OUTLIER) cc_final: 0.3513 (ptp-170) REVERT: R 120 LEU cc_start: 0.4998 (OUTLIER) cc_final: 0.4625 (tt) REVERT: R 187 MET cc_start: 0.4282 (mmm) cc_final: 0.3961 (ttm) REVERT: R 242 LYS cc_start: 0.8200 (mmtt) cc_final: 0.6884 (mtmt) REVERT: R 249 ILE cc_start: 0.6778 (OUTLIER) cc_final: 0.6552 (tp) REVERT: R 323 MET cc_start: 0.6443 (mmm) cc_final: 0.5482 (mtt) outliers start: 20 outliers final: 11 residues processed: 102 average time/residue: 0.2367 time to fit residues: 31.1047 Evaluate side-chains 104 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 249 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.0670 chunk 83 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 0.0070 chunk 24 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7319 Z= 0.140 Angle : 0.465 11.878 9912 Z= 0.234 Chirality : 0.039 0.154 1135 Planarity : 0.003 0.038 1247 Dihedral : 3.520 22.211 992 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.46 % Allowed : 22.18 % Favored : 75.36 % 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: -0.28 (0.29), residues: 900 helix: 1.26 (0.28), residues: 387 sheet: -1.28 (0.35), residues: 187 loop : -1.19 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 211 HIS 0.003 0.000 HIS L 7 PHE 0.016 0.001 PHE B 234 TYR 0.009 0.001 TYR B 59 ARG 0.003 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 0.830 Fit side-chains REVERT: A 24 ARG cc_start: 0.6996 (ttp80) cc_final: 0.6758 (ttp-110) REVERT: A 277 LYS cc_start: 0.8633 (mtpt) cc_final: 0.8407 (ttpt) REVERT: B 17 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7608 (tm-30) REVERT: B 129 ARG cc_start: 0.6851 (tpt90) cc_final: 0.6159 (mtp-110) REVERT: B 146 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7443 (mp) REVERT: B 152 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8026 (tt) REVERT: B 214 ARG cc_start: 0.7366 (mtt180) cc_final: 0.6948 (mmt180) REVERT: B 226 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7767 (mt-10) REVERT: B 258 ASP cc_start: 0.6008 (t70) cc_final: 0.5401 (t70) REVERT: G 58 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7297 (tm-30) REVERT: R 91 ARG cc_start: 0.3896 (OUTLIER) cc_final: 0.3525 (ptp-170) REVERT: R 120 LEU cc_start: 0.4876 (OUTLIER) cc_final: 0.4478 (tt) REVERT: R 187 MET cc_start: 0.4257 (mmm) cc_final: 0.3962 (ttm) REVERT: R 242 LYS cc_start: 0.8162 (mmtt) cc_final: 0.6869 (mtmt) REVERT: R 249 ILE cc_start: 0.6740 (OUTLIER) cc_final: 0.6518 (tp) REVERT: R 323 MET cc_start: 0.6498 (mmm) cc_final: 0.5519 (mtt) outliers start: 19 outliers final: 13 residues processed: 101 average time/residue: 0.2286 time to fit residues: 29.8833 Evaluate side-chains 105 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 249 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 89 optimal weight: 0.0040 chunk 82 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 230 ASN ** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7319 Z= 0.211 Angle : 0.472 7.374 9912 Z= 0.244 Chirality : 0.040 0.158 1135 Planarity : 0.003 0.041 1247 Dihedral : 3.710 23.289 992 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.46 % Allowed : 21.92 % Favored : 75.62 % 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: -0.31 (0.28), residues: 900 helix: 1.23 (0.27), residues: 389 sheet: -1.27 (0.35), residues: 187 loop : -1.23 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS L 7 PHE 0.020 0.001 PHE B 234 TYR 0.008 0.001 TYR R 221 ARG 0.004 0.000 ARG B 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 0.828 Fit side-chains REVERT: A 24 ARG cc_start: 0.7019 (ttp80) cc_final: 0.6782 (ttp-110) REVERT: A 277 LYS cc_start: 0.8638 (mtpt) cc_final: 0.8398 (ttpt) REVERT: B 17 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7621 (tm-30) REVERT: B 129 ARG cc_start: 0.6879 (tpt90) cc_final: 0.6179 (mtp-110) REVERT: B 152 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8035 (tt) REVERT: B 214 ARG cc_start: 0.7395 (mtt180) cc_final: 0.6973 (mmt180) REVERT: B 226 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7762 (mt-10) REVERT: G 58 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7231 (tm-30) REVERT: R 91 ARG cc_start: 0.4013 (OUTLIER) cc_final: 0.3565 (ptp-170) REVERT: R 120 LEU cc_start: 0.5024 (OUTLIER) cc_final: 0.4653 (tt) REVERT: R 187 MET cc_start: 0.4199 (mmm) cc_final: 0.3896 (ttm) REVERT: R 242 LYS cc_start: 0.8170 (mmtt) cc_final: 0.6866 (mtmt) REVERT: R 249 ILE cc_start: 0.6951 (OUTLIER) cc_final: 0.6689 (tp) REVERT: R 323 MET cc_start: 0.6514 (mmm) cc_final: 0.5583 (mtt) outliers start: 19 outliers final: 14 residues processed: 101 average time/residue: 0.2457 time to fit residues: 31.9183 Evaluate side-chains 106 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 249 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 71 optimal weight: 8.9990 chunk 29 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 0.0040 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 175 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 = 0.4147 r_free = 0.4147 target = 0.188231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138978 restraints weight = 7479.415| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.32 r_work: 0.3403 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7319 Z= 0.145 Angle : 0.459 10.089 9912 Z= 0.234 Chirality : 0.039 0.153 1135 Planarity : 0.003 0.038 1247 Dihedral : 3.584 22.796 992 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.33 % Allowed : 22.31 % Favored : 75.36 % 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: -0.21 (0.29), residues: 900 helix: 1.32 (0.28), residues: 387 sheet: -1.24 (0.36), residues: 177 loop : -1.17 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.002 0.000 HIS L 7 PHE 0.019 0.001 PHE B 234 TYR 0.006 0.001 TYR B 264 ARG 0.003 0.000 ARG G 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1923.82 seconds wall clock time: 35 minutes 57.90 seconds (2157.90 seconds total)