Starting phenix.real_space_refine on Fri Jul 19 07:53:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzg_38795/07_2024/8xzg_38795.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzg_38795/07_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_38795/07_2024/8xzg_38795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzg_38795/07_2024/8xzg_38795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzg_38795/07_2024/8xzg_38795.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzg_38795/07_2024/8xzg_38795.cif" } 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 2.58 Conformation dependent library (CDL) restraints added in 1.2 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... Secondary structure from input PDB file: 29 helices and 9 sheets defined 44.8% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.941A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.524A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.114A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.509A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.019A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.703A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.899A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'G' and resid 6 through 22 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.717A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 27 through 53 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 65 through 81 removed outlier: 3.841A pdb=" N THR R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 90 removed outlier: 3.517A pdb=" N TYR R 90 " --> pdb=" O ALA R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 132 removed outlier: 4.168A pdb=" N SER R 106 " --> pdb=" O CYS R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 144 removed outlier: 3.859A pdb=" N ARG R 141 " --> pdb=" O ASN R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 161 Processing helix chain 'R' and resid 162 through 165 Processing helix chain 'R' and resid 190 through 192 No H-bonds generated for 'chain 'R' and resid 190 through 192' Processing helix chain 'R' and resid 193 through 210 removed outlier: 3.522A pdb=" N TRP R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 232 Processing helix chain 'R' and resid 240 through 275 removed outlier: 4.072A pdb=" N ARG R 245 " --> pdb=" O ARG R 241 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU R 246 " --> pdb=" O LYS R 242 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU R 247 " --> pdb=" O ARG R 243 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE R 257 " --> pdb=" O LEU R 253 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET R 262 " --> pdb=" O ALA R 258 " (cutoff:3.500A) Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 283 through 298 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) Processing helix chain 'R' and resid 300 through 305 Processing helix chain 'R' and resid 305 through 310 Processing helix chain 'R' and resid 313 through 327 removed outlier: 3.739A pdb=" N ARG R 317 " --> pdb=" O ASP R 313 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY R 327 " --> pdb=" O MET R 323 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 190 removed outlier: 3.819A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) 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) Processing sheet with id=AA2, 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=AA3, first strand: chain 'B' and resid 58 through 61 removed outlier: 6.844A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (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) Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 114 removed outlier: 5.969A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 190 removed outlier: 6.543A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 231 removed outlier: 3.865A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.691A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 168 through 172 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) 331 hydrogen bonds defined for protein. 957 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: 2.09 Time building geometry restraints manager: 2.88 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: 433 2.72 - 3.26: 6935 3.26 - 3.81: 10928 3.81 - 4.35: 13336 4.35 - 4.90: 23771 Nonbonded interactions: 55403 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 55398 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 22.220 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.960 ------------------------------------------------------------------------------- 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= 0.514 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 : 0.711 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: 0.2452 time to fit residues: 37.2106 Evaluate side-chains 91 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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: 0.2980 chunk 68 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 B 183 HIS G 24 ASN L 7 HIS ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 ASN R 289 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7319 Z= 0.195 Angle : 0.537 6.073 9912 Z= 0.283 Chirality : 0.042 0.147 1135 Planarity : 0.004 0.044 1247 Dihedral : 5.126 52.349 999 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.20 % Allowed : 14.40 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.27), residues: 900 helix: 0.70 (0.27), residues: 396 sheet: -2.55 (0.31), residues: 179 loop : -1.92 (0.31), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 95 HIS 0.005 0.001 HIS B 91 PHE 0.025 0.002 PHE R 39 TYR 0.012 0.001 TYR R 35 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 106 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 0.725 Fit side-chains REVERT: B 17 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7668 (tm-30) REVERT: B 118 ASP cc_start: 0.7523 (t0) cc_final: 0.7309 (t0) REVERT: B 129 ARG cc_start: 0.7028 (tpt90) cc_final: 0.6140 (mtp-110) REVERT: B 200 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7989 (m) REVERT: B 214 ARG cc_start: 0.7291 (mtt180) cc_final: 0.6928 (mmt180) REVERT: B 226 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7823 (mt-10) REVERT: B 234 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8447 (m-80) REVERT: B 258 ASP cc_start: 0.6103 (t70) cc_final: 0.5549 (t70) REVERT: R 323 MET cc_start: 0.6624 (mmm) cc_final: 0.5878 (mtt) outliers start: 17 outliers final: 12 residues processed: 102 average time/residue: 0.2263 time to fit residues: 29.9767 Evaluate side-chains 91 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 336 LEU Chi-restraints excluded: chain G residue 25 ILE 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: 5.9990 chunk 68 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 80 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN R 46 ASN R 231 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1708 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= 0.196 Angle : 0.488 5.378 9912 Z= 0.255 Chirality : 0.040 0.138 1135 Planarity : 0.004 0.039 1247 Dihedral : 4.463 48.689 994 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.11 % Allowed : 15.82 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.28), residues: 900 helix: 1.04 (0.27), residues: 407 sheet: -2.42 (0.32), residues: 182 loop : -1.55 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 95 HIS 0.003 0.001 HIS B 183 PHE 0.019 0.001 PHE R 39 TYR 0.008 0.001 TYR R 221 ARG 0.005 0.000 ARG G 62 *********************** 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 115 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 91 time to evaluate : 0.780 Fit side-chains REVERT: A 306 GLN cc_start: 0.7520 (tp40) cc_final: 0.7299 (tp40) REVERT: B 118 ASP cc_start: 0.7520 (t0) cc_final: 0.7239 (t0) REVERT: B 129 ARG cc_start: 0.6994 (tpt90) cc_final: 0.6165 (mtp-110) REVERT: B 152 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8026 (tt) REVERT: B 200 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7835 (m) REVERT: B 214 ARG cc_start: 0.7302 (mtt180) cc_final: 0.6958 (mmt180) REVERT: B 226 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7832 (mt-10) REVERT: B 234 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8425 (m-80) REVERT: B 258 ASP cc_start: 0.6174 (t70) cc_final: 0.5583 (t70) REVERT: R 323 MET cc_start: 0.6554 (mmm) cc_final: 0.5813 (mtt) outliers start: 24 outliers final: 15 residues processed: 110 average time/residue: 0.2484 time to fit residues: 35.3508 Evaluate side-chains 101 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 61 MET 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 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE 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: 3.9990 chunk 42 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 0.0770 chunk 54 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7319 Z= 0.235 Angle : 0.499 5.238 9912 Z= 0.261 Chirality : 0.041 0.152 1135 Planarity : 0.004 0.042 1247 Dihedral : 4.326 47.589 994 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.63 % Allowed : 17.90 % Favored : 78.47 % 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: -0.71 (0.28), residues: 900 helix: 1.16 (0.27), residues: 408 sheet: -2.30 (0.33), residues: 182 loop : -1.41 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS B 183 PHE 0.019 0.001 PHE B 199 TYR 0.009 0.001 TYR B 105 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 114 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 86 time to evaluate : 0.910 Fit side-chains REVERT: B 118 ASP cc_start: 0.7450 (t0) cc_final: 0.7228 (t0) REVERT: B 129 ARG cc_start: 0.7063 (tpt90) cc_final: 0.6266 (mtp-110) REVERT: B 152 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8070 (tt) REVERT: B 200 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7858 (m) REVERT: B 214 ARG cc_start: 0.7330 (mtt180) cc_final: 0.6992 (mmt180) REVERT: B 226 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7820 (mt-10) REVERT: B 234 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: R 126 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7218 (t70) REVERT: R 323 MET cc_start: 0.6547 (mmm) cc_final: 0.5764 (mtt) outliers start: 28 outliers final: 20 residues processed: 106 average time/residue: 0.2099 time to fit residues: 29.1818 Evaluate side-chains 109 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 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 217 MET 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 246 ASP Chi-restraints excluded: chain B residue 263 THR 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 81 THR Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 207 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 60 optimal weight: 0.0370 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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: 0.7258 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7319 Z= 0.153 Angle : 0.457 6.269 9912 Z= 0.236 Chirality : 0.040 0.141 1135 Planarity : 0.003 0.037 1247 Dihedral : 3.739 19.137 992 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.24 % Allowed : 19.33 % Favored : 77.43 % 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: -0.41 (0.29), residues: 900 helix: 1.37 (0.27), residues: 408 sheet: -1.96 (0.34), residues: 182 loop : -1.33 (0.34), residues: 310 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 0.014 0.001 PHE R 39 TYR 0.007 0.001 TYR R 35 ARG 0.005 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 118 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 0.751 Fit side-chains REVERT: B 17 GLN cc_start: 0.8109 (tm-30) cc_final: 0.7548 (tm-30) REVERT: B 118 ASP cc_start: 0.7482 (t0) cc_final: 0.7279 (t0) REVERT: B 129 ARG cc_start: 0.6938 (tpt90) cc_final: 0.6185 (mtp-110) REVERT: B 152 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8005 (tt) REVERT: B 163 ASP cc_start: 0.7198 (t0) cc_final: 0.6918 (t0) REVERT: B 200 VAL cc_start: 0.7998 (OUTLIER) cc_final: 0.7703 (m) REVERT: B 214 ARG cc_start: 0.7300 (mtt180) cc_final: 0.6978 (mmt180) REVERT: B 217 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6957 (mtm) REVERT: B 226 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7777 (mt-10) REVERT: B 234 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8381 (m-80) REVERT: B 258 ASP cc_start: 0.6195 (t70) cc_final: 0.5563 (t70) REVERT: R 91 ARG cc_start: 0.4015 (OUTLIER) cc_final: 0.3562 (ptp-170) REVERT: R 120 LEU cc_start: 0.5057 (OUTLIER) cc_final: 0.4781 (tt) REVERT: R 309 TYR cc_start: 0.7976 (m-80) cc_final: 0.7715 (m-80) REVERT: R 323 MET cc_start: 0.6496 (mmm) cc_final: 0.5655 (mtt) outliers start: 25 outliers final: 14 residues processed: 110 average time/residue: 0.2128 time to fit residues: 30.9057 Evaluate side-chains 105 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 201 SER 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 275 SER 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 87 THR Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 120 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 83 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7319 Z= 0.170 Angle : 0.457 6.415 9912 Z= 0.235 Chirality : 0.040 0.140 1135 Planarity : 0.003 0.038 1247 Dihedral : 3.696 18.485 992 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.11 % Allowed : 21.01 % Favored : 75.88 % 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 (0.29), residues: 900 helix: 1.45 (0.27), residues: 409 sheet: -1.87 (0.36), residues: 174 loop : -1.21 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS L 7 PHE 0.013 0.001 PHE R 39 TYR 0.007 0.001 TYR B 59 ARG 0.005 0.000 ARG B 52 *********************** 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 116 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 0.794 Fit side-chains REVERT: B 17 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7559 (tm-30) REVERT: B 118 ASP cc_start: 0.7501 (t0) cc_final: 0.7285 (t0) REVERT: B 129 ARG cc_start: 0.6932 (tpt90) cc_final: 0.6209 (mtp-110) REVERT: B 152 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8007 (tt) REVERT: B 163 ASP cc_start: 0.7207 (t0) cc_final: 0.7004 (t0) REVERT: B 197 ARG cc_start: 0.7107 (ttp-110) cc_final: 0.6865 (ttp-110) REVERT: B 200 VAL cc_start: 0.8023 (OUTLIER) cc_final: 0.7712 (m) REVERT: B 214 ARG cc_start: 0.7322 (mtt180) cc_final: 0.7036 (mmt180) REVERT: B 217 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.6935 (mtm) REVERT: B 226 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7776 (mt-10) REVERT: B 234 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8293 (m-80) REVERT: R 91 ARG cc_start: 0.4032 (OUTLIER) cc_final: 0.3596 (ptp-170) REVERT: R 309 TYR cc_start: 0.7943 (m-80) cc_final: 0.7648 (m-80) REVERT: R 323 MET cc_start: 0.6462 (mmm) cc_final: 0.5579 (mtt) outliers start: 24 outliers final: 13 residues processed: 111 average time/residue: 0.2123 time to fit residues: 30.8551 Evaluate side-chains 109 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 201 SER 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 263 THR 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 109 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.0870 chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 0.0670 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 0.8298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2331 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= 0.163 Angle : 0.449 6.107 9912 Z= 0.232 Chirality : 0.040 0.138 1135 Planarity : 0.003 0.038 1247 Dihedral : 3.619 17.650 992 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.37 % Allowed : 21.27 % 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: -0.07 (0.29), residues: 900 helix: 1.55 (0.27), residues: 409 sheet: -1.64 (0.35), residues: 182 loop : -1.11 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 261 HIS 0.003 0.001 HIS L 7 PHE 0.012 0.001 PHE R 39 TYR 0.008 0.001 TYR B 59 ARG 0.006 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 116 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 90 time to evaluate : 0.784 Fit side-chains REVERT: B 17 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7605 (tm-30) REVERT: B 129 ARG cc_start: 0.6931 (tpt90) cc_final: 0.6221 (mtp-110) REVERT: B 152 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8033 (tt) REVERT: B 200 VAL cc_start: 0.8048 (OUTLIER) cc_final: 0.7717 (m) REVERT: B 214 ARG cc_start: 0.7314 (mtt180) cc_final: 0.6995 (mmt180) REVERT: B 217 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6896 (mtm) REVERT: B 226 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7749 (mt-10) REVERT: B 234 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8274 (m-80) REVERT: R 91 ARG cc_start: 0.4058 (OUTLIER) cc_final: 0.3633 (ptp-170) REVERT: R 120 LEU cc_start: 0.5051 (OUTLIER) cc_final: 0.4733 (tt) REVERT: R 187 MET cc_start: 0.4430 (mmm) cc_final: 0.3932 (ttm) REVERT: R 242 LYS cc_start: 0.8162 (mmtt) cc_final: 0.6933 (mtmt) REVERT: R 323 MET cc_start: 0.6601 (mmm) cc_final: 0.5632 (mtt) outliers start: 26 outliers final: 18 residues processed: 109 average time/residue: 0.2298 time to fit residues: 32.5819 Evaluate side-chains 110 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 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 201 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 8 optimal weight: 0.0670 chunk 68 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 overall best weight: 1.1520 ------------------------------------------------------------------------------- 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: 0.7280 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7319 Z= 0.204 Angle : 0.472 6.734 9912 Z= 0.244 Chirality : 0.040 0.138 1135 Planarity : 0.003 0.038 1247 Dihedral : 3.702 19.197 992 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.76 % Allowed : 21.01 % Favored : 75.23 % 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: -0.06 (0.29), residues: 900 helix: 1.60 (0.27), residues: 404 sheet: -1.56 (0.34), residues: 187 loop : -1.17 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 261 HIS 0.003 0.001 HIS L 7 PHE 0.012 0.001 PHE R 78 TYR 0.012 0.001 TYR B 59 ARG 0.006 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 126 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 97 time to evaluate : 0.779 Fit side-chains REVERT: B 17 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7637 (tm-30) REVERT: B 129 ARG cc_start: 0.6927 (tpt90) cc_final: 0.6234 (mtp-110) REVERT: B 152 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8001 (tt) REVERT: B 200 VAL cc_start: 0.8090 (OUTLIER) cc_final: 0.7745 (m) REVERT: B 214 ARG cc_start: 0.7316 (mtt180) cc_final: 0.6996 (mmt180) REVERT: B 217 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6835 (mtm) REVERT: B 226 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7669 (mt-10) REVERT: B 234 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8196 (m-80) REVERT: G 58 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7302 (tm-30) REVERT: R 91 ARG cc_start: 0.3973 (OUTLIER) cc_final: 0.3555 (ptp-170) REVERT: R 120 LEU cc_start: 0.5103 (OUTLIER) cc_final: 0.4748 (tt) REVERT: R 187 MET cc_start: 0.4439 (mmm) cc_final: 0.3968 (ttm) REVERT: R 242 LYS cc_start: 0.8152 (mmtt) cc_final: 0.6922 (mtmt) REVERT: R 323 MET cc_start: 0.6616 (mmm) cc_final: 0.5632 (mtt) outliers start: 29 outliers final: 21 residues processed: 116 average time/residue: 0.2170 time to fit residues: 33.0298 Evaluate side-chains 121 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 38 LEU 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 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 201 SER 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 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 109 ILE Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 207 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 0.0870 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 175 GLN B 230 ASN B 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7319 Z= 0.285 Angle : 0.519 7.570 9912 Z= 0.271 Chirality : 0.042 0.138 1135 Planarity : 0.004 0.041 1247 Dihedral : 3.951 20.780 992 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.63 % Allowed : 22.05 % Favored : 74.32 % 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: -0.18 (0.29), residues: 900 helix: 1.51 (0.27), residues: 404 sheet: -1.61 (0.35), residues: 185 loop : -1.25 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 261 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.001 PHE R 78 TYR 0.014 0.001 TYR B 59 ARG 0.006 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 120 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 0.764 Fit side-chains REVERT: B 17 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7606 (tm-30) REVERT: B 129 ARG cc_start: 0.6937 (tpt90) cc_final: 0.6137 (mtp-110) REVERT: B 152 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8087 (tt) REVERT: B 200 VAL cc_start: 0.8107 (OUTLIER) cc_final: 0.7826 (m) REVERT: B 214 ARG cc_start: 0.7330 (mtt180) cc_final: 0.7017 (mmt180) REVERT: B 217 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6892 (mtm) REVERT: B 226 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7725 (mt-10) REVERT: B 234 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8175 (m-80) REVERT: R 91 ARG cc_start: 0.4068 (OUTLIER) cc_final: 0.3664 (ptp-170) REVERT: R 120 LEU cc_start: 0.5163 (OUTLIER) cc_final: 0.4801 (tt) REVERT: R 187 MET cc_start: 0.4404 (mmm) cc_final: 0.3943 (ttm) REVERT: R 242 LYS cc_start: 0.8187 (mmtt) cc_final: 0.6966 (mtmt) REVERT: R 323 MET cc_start: 0.6509 (mmm) cc_final: 0.5637 (mtt) outliers start: 28 outliers final: 19 residues processed: 110 average time/residue: 0.2198 time to fit residues: 31.5750 Evaluate side-chains 117 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 92 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 61 MET 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 201 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR 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 109 ILE Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 207 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.0060 chunk 59 optimal weight: 8.9990 chunk 89 optimal weight: 0.2980 chunk 82 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 overall best weight: 1.2200 ------------------------------------------------------------------------------- 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: 0.7297 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7319 Z= 0.214 Angle : 0.489 6.453 9912 Z= 0.255 Chirality : 0.040 0.139 1135 Planarity : 0.003 0.039 1247 Dihedral : 3.836 20.035 992 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.37 % Allowed : 22.44 % Favored : 74.19 % 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: -0.05 (0.29), residues: 900 helix: 1.64 (0.27), residues: 400 sheet: -1.52 (0.36), residues: 179 loop : -1.22 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 261 HIS 0.003 0.001 HIS L 7 PHE 0.011 0.001 PHE R 78 TYR 0.014 0.001 TYR B 59 ARG 0.005 0.000 ARG G 62 ********************** 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 118 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 92 time to evaluate : 0.760 Fit side-chains REVERT: B 17 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7592 (tm-30) REVERT: B 129 ARG cc_start: 0.6917 (tpt90) cc_final: 0.6134 (mtp-110) REVERT: B 152 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8040 (tt) REVERT: B 200 VAL cc_start: 0.8128 (OUTLIER) cc_final: 0.7837 (m) REVERT: B 214 ARG cc_start: 0.7321 (mtt180) cc_final: 0.7003 (mmt180) REVERT: B 217 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.6875 (mtm) REVERT: B 226 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7707 (mt-10) REVERT: B 234 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8266 (m-80) REVERT: R 91 ARG cc_start: 0.4007 (OUTLIER) cc_final: 0.3503 (ptp-170) REVERT: R 120 LEU cc_start: 0.5124 (OUTLIER) cc_final: 0.4764 (tt) REVERT: R 187 MET cc_start: 0.4335 (mmm) cc_final: 0.3914 (ttm) REVERT: R 242 LYS cc_start: 0.8171 (mmtt) cc_final: 0.6972 (mtmt) REVERT: R 323 MET cc_start: 0.6634 (mmm) cc_final: 0.5710 (mtt) outliers start: 26 outliers final: 20 residues processed: 108 average time/residue: 0.2187 time to fit residues: 30.7247 Evaluate side-chains 117 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 61 MET 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 201 SER 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 263 THR 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 80 VAL 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 120 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 207 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.184510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134657 restraints weight = 7504.699| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.44 r_work: 0.3348 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7319 Z= 0.197 Angle : 0.478 6.462 9912 Z= 0.249 Chirality : 0.040 0.140 1135 Planarity : 0.003 0.038 1247 Dihedral : 3.768 19.171 992 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.76 % Allowed : 22.18 % Favored : 74.06 % 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 (0.29), residues: 900 helix: 1.69 (0.27), residues: 399 sheet: -1.50 (0.36), residues: 179 loop : -1.16 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 261 HIS 0.003 0.001 HIS L 7 PHE 0.011 0.001 PHE R 39 TYR 0.014 0.001 TYR B 59 ARG 0.006 0.000 ARG G 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1694.58 seconds wall clock time: 31 minutes 7.56 seconds (1867.56 seconds total)