Starting phenix.real_space_refine on Sat Feb 17 03:02:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w53_32313/02_2024/7w53_32313.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w53_32313/02_2024/7w53_32313.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/7w53_32313/02_2024/7w53_32313.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w53_32313/02_2024/7w53_32313.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w53_32313/02_2024/7w53_32313.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w53_32313/02_2024/7w53_32313.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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 62 5.16 5 C 5521 2.51 5 N 1524 2.21 5 O 1603 1.98 5 H 8644 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A ARG 247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 135": "OE1" <-> "OE2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E GLU 153": "OE1" <-> "OE2" Residue "E TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 191": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R GLU 117": "OE1" <-> "OE2" Residue "R ARG 159": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 223": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 292": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 362": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R GLU 365": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17354 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 3443 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 3 Chain: "B" Number of atoms: 5109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5109 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 136 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 1, 'TRANS': 6} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3504 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 885 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 4277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 4277 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 9, 'TRANS': 254} Chain breaks: 3 Time building chain proxies: 8.81, per 1000 atoms: 0.51 Number of scatterers: 17354 At special positions: 0 Unit cell: (117.72, 133.92, 102.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 O 1603 8.00 N 1524 7.00 C 5521 6.00 H 8644 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 134 " - pdb=" SG CYS R 219 " distance=2.04 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: 14.29 Conformation dependent library (CDL) restraints added in 1.9 seconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2068 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 38.7% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.968A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 removed outlier: 3.952A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 218 " --> pdb=" O PHE A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 248 through 252 removed outlier: 4.232A pdb=" N THR A 251 " --> pdb=" O TRP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.572A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 9 through 31 Processing helix chain 'B' and resid 34 through 40 Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 52 through 55 removed outlier: 4.089A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.682A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 60 through 86 Processing helix chain 'R' and resid 87 through 90 Processing helix chain 'R' and resid 95 through 112 removed outlier: 4.117A pdb=" N LEU R 99 " --> pdb=" O THR R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 120 Processing helix chain 'R' and resid 131 through 165 Processing helix chain 'R' and resid 165 through 173 Processing helix chain 'R' and resid 174 through 198 removed outlier: 4.104A pdb=" N ARG R 180 " --> pdb=" O ALA R 176 " (cutoff:3.500A) Proline residue: R 195 - end of helix Processing helix chain 'R' and resid 227 through 263 removed outlier: 3.641A pdb=" N VAL R 231 " --> pdb=" O LEU R 227 " (cutoff:3.500A) Proline residue: R 243 - end of helix Processing helix chain 'R' and resid 290 through 323 Proline residue: R 312 - end of helix removed outlier: 3.704A pdb=" N ARG R 317 " --> pdb=" O PHE R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 327 through 357 Proline residue: R 353 - end of helix Processing helix chain 'R' and resid 360 through 365 removed outlier: 4.162A pdb=" N GLU R 365 " --> pdb=" O SER R 361 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.236A pdb=" N LEU A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE A 199 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.519A pdb=" N ILE B 343 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR B 55 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 341 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS B 322 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.512A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.312A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 158 removed outlier: 3.524A pdb=" N CYS B 153 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLN B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 162 " --> pdb=" O TRP B 174 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.506A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.767A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B 264 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.701A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 5.875A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 removed outlier: 5.875A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.281A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 200 through 202 453 hydrogen bonds defined for protein. 1266 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: 6.17 Time building geometry restraints manager: 14.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 8613 1.02 - 1.22: 45 1.22 - 1.42: 3769 1.42 - 1.63: 5010 1.63 - 1.83: 93 Bond restraints: 17530 Sorted by residual: bond pdb=" SG CYS R 219 " pdb=" HG CYS R 219 " ideal model delta sigma weight residual 1.200 1.344 -0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" SG CYS R 134 " pdb=" HG CYS R 134 " ideal model delta sigma weight residual 1.200 1.343 -0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" SG CYS R 241 " pdb=" HG CYS R 241 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" SG CYS B 299 " pdb=" HG CYS B 299 " ideal model delta sigma weight residual 1.200 1.338 -0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" ND2 ASN A 216 " pdb="HD22 ASN A 216 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.63e+01 ... (remaining 17525 not shown) Histogram of bond angle deviations from ideal: 81.15 - 92.03: 1 92.03 - 102.90: 49 102.90 - 113.77: 20735 113.77 - 124.64: 9754 124.64 - 135.51: 973 Bond angle restraints: 31512 Sorted by residual: angle pdb=" N PRO E 236 " pdb=" CA PRO E 236 " pdb=" C PRO E 236 " ideal model delta sigma weight residual 112.36 81.15 31.21 2.06e+00 2.36e-01 2.29e+02 angle pdb=" N TYR E 235 " pdb=" CA TYR E 235 " pdb=" C TYR E 235 " ideal model delta sigma weight residual 108.66 135.51 -26.85 2.16e+00 2.14e-01 1.55e+02 angle pdb=" N ASP B 296 " pdb=" CA ASP B 296 " pdb=" C ASP B 296 " ideal model delta sigma weight residual 110.50 96.45 14.05 1.41e+00 5.03e-01 9.93e+01 angle pdb=" N PHE B 240 " pdb=" CA PHE B 240 " pdb=" C PHE B 240 " ideal model delta sigma weight residual 110.08 102.09 7.99 1.38e+00 5.25e-01 3.36e+01 angle pdb=" N ILE A 184 " pdb=" CA ILE A 184 " pdb=" C ILE A 184 " ideal model delta sigma weight residual 109.34 121.29 -11.95 2.08e+00 2.31e-01 3.30e+01 ... (remaining 31507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 7517 17.86 - 35.72: 495 35.72 - 53.58: 180 53.58 - 71.44: 61 71.44 - 89.31: 9 Dihedral angle restraints: 8262 sinusoidal: 4452 harmonic: 3810 Sorted by residual: dihedral pdb=" C TYR E 235 " pdb=" N TYR E 235 " pdb=" CA TYR E 235 " pdb=" CB TYR E 235 " ideal model delta harmonic sigma weight residual -122.60 -137.26 14.66 0 2.50e+00 1.60e-01 3.44e+01 dihedral pdb=" N TYR E 235 " pdb=" C TYR E 235 " pdb=" CA TYR E 235 " pdb=" CB TYR E 235 " ideal model delta harmonic sigma weight residual 122.80 137.08 -14.28 0 2.50e+00 1.60e-01 3.26e+01 dihedral pdb=" N PRO E 236 " pdb=" C PRO E 236 " pdb=" CA PRO E 236 " pdb=" CB PRO E 236 " ideal model delta harmonic sigma weight residual 115.10 102.07 13.03 0 2.50e+00 1.60e-01 2.72e+01 ... (remaining 8259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.202: 1355 0.202 - 0.404: 4 0.404 - 0.605: 0 0.605 - 0.807: 0 0.807 - 1.009: 1 Chirality restraints: 1360 Sorted by residual: chirality pdb=" CA TYR E 235 " pdb=" N TYR E 235 " pdb=" C TYR E 235 " pdb=" CB TYR E 235 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.54e+01 chirality pdb=" CA PRO E 236 " pdb=" N PRO E 236 " pdb=" C PRO E 236 " pdb=" CB PRO E 236 " both_signs ideal model delta sigma weight residual False 2.72 2.95 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE A 184 " pdb=" N ILE A 184 " pdb=" C ILE A 184 " pdb=" CB ILE A 184 " both_signs ideal model delta sigma weight residual False 2.43 2.21 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1357 not shown) Planarity restraints: 2589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 216 " -0.308 2.00e-02 2.50e+03 3.57e-01 1.91e+03 pdb=" CG ASN A 216 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 216 " 0.300 2.00e-02 2.50e+03 pdb=" ND2 ASN A 216 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN A 216 " 0.529 2.00e-02 2.50e+03 pdb="HD22 ASN A 216 " -0.547 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 259 " -0.250 2.00e-02 2.50e+03 2.64e-01 1.05e+03 pdb=" CG ASN A 259 " 0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN A 259 " 0.245 2.00e-02 2.50e+03 pdb=" ND2 ASN A 259 " -0.005 2.00e-02 2.50e+03 pdb="HD21 ASN A 259 " 0.388 2.00e-02 2.50e+03 pdb="HD22 ASN A 259 " -0.382 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 298 " 0.139 2.00e-02 2.50e+03 1.38e-01 2.86e+02 pdb=" CG ASN B 298 " -0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN B 298 " -0.133 2.00e-02 2.50e+03 pdb=" ND2 ASN B 298 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 298 " -0.195 2.00e-02 2.50e+03 pdb="HD22 ASN B 298 " 0.198 2.00e-02 2.50e+03 ... (remaining 2586 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 316 2.05 - 2.69: 27725 2.69 - 3.33: 52097 3.33 - 3.96: 66630 3.96 - 4.60: 105385 Nonbonded interactions: 252153 Sorted by model distance: nonbonded pdb=" O ILE B 63 " pdb=" HG SER B 321 " model vdw 1.415 1.850 nonbonded pdb=" OE2 GLU E 5 " pdb=" H CYS E 95 " model vdw 1.462 1.850 nonbonded pdb="HH12 ARG A 15 " pdb=" O VAL B 95 " model vdw 1.478 1.850 nonbonded pdb=" OD1 ASN C 9 " pdb="HD22 ASN R 196 " model vdw 1.487 1.850 nonbonded pdb=" O ASP B 71 " pdb=" H ARG B 73 " model vdw 1.510 1.850 ... (remaining 252148 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=0.00 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: 0.490 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: 0.270 Extract box with map and model: 2.870 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 58.210 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 : 0.007 0.053 8886 Z= 0.453 Angle : 0.860 31.205 12029 Z= 0.503 Chirality : 0.055 1.009 1360 Planarity : 0.004 0.051 1528 Dihedral : 12.622 89.306 3210 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.63 % Allowed : 6.33 % Favored : 93.04 % Cbeta Deviations : 0.10 % 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: -0.67 (0.24), residues: 1082 helix: 0.03 (0.24), residues: 377 sheet: -0.54 (0.30), residues: 272 loop : -0.60 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 310 HIS 0.006 0.002 HIS B 96 PHE 0.015 0.002 PHE B 240 TYR 0.027 0.002 TYR E 235 ARG 0.005 0.001 ARG R 292 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 226 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7150 (mt0) REVERT: A 319 SER cc_start: 0.5546 (t) cc_final: 0.5312 (m) REVERT: B 228 THR cc_start: 0.7805 (p) cc_final: 0.7432 (t) REVERT: R 158 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6783 (mm-30) REVERT: R 293 ARG cc_start: 0.6913 (ptt-90) cc_final: 0.6388 (ptm160) outliers start: 6 outliers final: 3 residues processed: 230 average time/residue: 0.6940 time to fit residues: 198.9840 Evaluate side-chains 175 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 172 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain R residue 240 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 216 ASN ** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 HIS R 335 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8886 Z= 0.215 Angle : 0.576 7.698 12029 Z= 0.312 Chirality : 0.040 0.142 1360 Planarity : 0.005 0.099 1528 Dihedral : 6.124 56.647 1216 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.05 % Allowed : 11.08 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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 (0.25), residues: 1082 helix: 1.10 (0.25), residues: 385 sheet: -0.41 (0.31), residues: 263 loop : -0.58 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 87 HIS 0.005 0.001 HIS R 331 PHE 0.012 0.001 PHE R 334 TYR 0.015 0.001 TYR E 235 ARG 0.006 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 190 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.7771 (mm-40) cc_final: 0.7113 (mt0) REVERT: A 258 LEU cc_start: 0.8269 (mt) cc_final: 0.7990 (mt) REVERT: B 21 ASN cc_start: 0.7509 (m-40) cc_final: 0.7152 (m-40) REVERT: G 11 GLN cc_start: 0.7452 (tm-30) cc_final: 0.6876 (tt0) REVERT: R 143 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.6692 (ttp) REVERT: R 293 ARG cc_start: 0.6555 (ptt-90) cc_final: 0.6147 (ptm160) outliers start: 10 outliers final: 8 residues processed: 195 average time/residue: 0.6007 time to fit residues: 152.8155 Evaluate side-chains 179 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 170 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 2 GLN Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 240 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 0.0770 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 261 GLN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN ** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 335 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8886 Z= 0.228 Angle : 0.555 8.076 12029 Z= 0.296 Chirality : 0.040 0.136 1360 Planarity : 0.004 0.069 1528 Dihedral : 5.840 57.925 1216 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.48 % Allowed : 11.92 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.36 (0.25), residues: 1082 helix: 1.60 (0.26), residues: 385 sheet: -0.47 (0.32), residues: 258 loop : -0.43 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 87 HIS 0.007 0.001 HIS R 331 PHE 0.011 0.001 PHE R 334 TYR 0.019 0.002 TYR R 135 ARG 0.003 0.000 ARG E 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 182 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7164 (mt0) REVERT: B 21 ASN cc_start: 0.7580 (m-40) cc_final: 0.6693 (m-40) REVERT: E 41 GLU cc_start: 0.6816 (tp30) cc_final: 0.6601 (tp30) REVERT: G 11 GLN cc_start: 0.7465 (tm-30) cc_final: 0.6811 (tt0) REVERT: R 61 MET cc_start: 0.5766 (tpt) cc_final: 0.5303 (tpp) REVERT: R 143 MET cc_start: 0.7074 (OUTLIER) cc_final: 0.6792 (ttm) REVERT: R 228 TYR cc_start: 0.6160 (OUTLIER) cc_final: 0.5720 (m-80) REVERT: R 293 ARG cc_start: 0.6533 (ptt-90) cc_final: 0.6047 (ptm160) outliers start: 14 outliers final: 8 residues processed: 190 average time/residue: 0.5904 time to fit residues: 146.6699 Evaluate side-chains 174 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 164 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 2 GLN Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 240 PHE Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 261 GLN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 HIS R 335 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8886 Z= 0.312 Angle : 0.587 8.150 12029 Z= 0.314 Chirality : 0.041 0.146 1360 Planarity : 0.004 0.062 1528 Dihedral : 5.926 59.022 1215 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.79 % Allowed : 14.14 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.26 (0.25), residues: 1082 helix: 1.53 (0.25), residues: 385 sheet: -0.56 (0.31), residues: 263 loop : -0.48 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 87 HIS 0.007 0.001 HIS R 331 PHE 0.014 0.002 PHE B 204 TYR 0.021 0.002 TYR E 235 ARG 0.007 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 167 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7354 (mt0) REVERT: A 300 ARG cc_start: 0.7081 (mtm180) cc_final: 0.6753 (mtm110) REVERT: B 24 ARG cc_start: 0.7603 (ttp80) cc_final: 0.7263 (ttp80) REVERT: B 299 CYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7400 (m) REVERT: E 41 GLU cc_start: 0.6824 (tp30) cc_final: 0.6555 (tp30) REVERT: R 64 CYS cc_start: 0.7317 (p) cc_final: 0.6906 (p) REVERT: R 293 ARG cc_start: 0.6607 (ptt-90) cc_final: 0.6049 (ptm160) outliers start: 17 outliers final: 13 residues processed: 177 average time/residue: 0.6021 time to fit residues: 138.5635 Evaluate side-chains 174 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 2 GLN Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain R residue 240 PHE Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 72 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 261 GLN B 300 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 325 GLN R 331 HIS R 335 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8886 Z= 0.242 Angle : 0.554 7.608 12029 Z= 0.294 Chirality : 0.040 0.132 1360 Planarity : 0.004 0.052 1528 Dihedral : 5.695 58.737 1215 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.90 % Allowed : 13.61 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.25), residues: 1082 helix: 1.86 (0.26), residues: 379 sheet: -0.52 (0.32), residues: 253 loop : -0.47 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 87 HIS 0.007 0.001 HIS R 331 PHE 0.011 0.001 PHE B 204 TYR 0.024 0.001 TYR R 135 ARG 0.006 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7353 (mt0) REVERT: A 300 ARG cc_start: 0.7061 (mtm180) cc_final: 0.6702 (mtm110) REVERT: B 128 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8291 (mp) REVERT: B 239 PHE cc_start: 0.9415 (OUTLIER) cc_final: 0.8863 (t80) REVERT: E 41 GLU cc_start: 0.6936 (tp30) cc_final: 0.6710 (tp30) REVERT: E 54 SER cc_start: 0.8616 (OUTLIER) cc_final: 0.8314 (p) REVERT: G 11 GLN cc_start: 0.7464 (tm-30) cc_final: 0.6978 (tt0) REVERT: R 64 CYS cc_start: 0.7232 (p) cc_final: 0.6968 (p) REVERT: R 293 ARG cc_start: 0.6411 (ptt-90) cc_final: 0.5790 (ptm160) outliers start: 18 outliers final: 14 residues processed: 184 average time/residue: 0.6012 time to fit residues: 145.2880 Evaluate side-chains 177 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 160 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 2 GLN Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain R residue 240 PHE Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 325 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 261 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN ** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 HIS R 335 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 8886 Z= 0.366 Angle : 0.604 7.633 12029 Z= 0.325 Chirality : 0.042 0.142 1360 Planarity : 0.005 0.055 1528 Dihedral : 5.937 58.222 1215 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.43 % Allowed : 14.14 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1082 helix: 1.66 (0.25), residues: 379 sheet: -0.70 (0.31), residues: 263 loop : -0.61 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 326 HIS 0.007 0.001 HIS R 331 PHE 0.016 0.002 PHE B 204 TYR 0.021 0.002 TYR R 135 ARG 0.008 0.001 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 162 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7304 (mt0) REVERT: A 300 ARG cc_start: 0.7087 (mtm180) cc_final: 0.6726 (mtm110) REVERT: B 128 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8319 (mp) REVERT: B 239 PHE cc_start: 0.9428 (OUTLIER) cc_final: 0.8970 (t80) REVERT: B 296 ASP cc_start: 0.7187 (OUTLIER) cc_final: 0.6901 (p0) REVERT: E 41 GLU cc_start: 0.6886 (tp30) cc_final: 0.6626 (tp30) REVERT: G 11 GLN cc_start: 0.7422 (tm-30) cc_final: 0.6768 (tt0) REVERT: R 64 CYS cc_start: 0.7178 (p) cc_final: 0.6943 (p) REVERT: R 293 ARG cc_start: 0.6506 (ptt-90) cc_final: 0.5797 (ptm160) outliers start: 23 outliers final: 18 residues processed: 179 average time/residue: 0.5975 time to fit residues: 139.0249 Evaluate side-chains 179 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 2 GLN Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 231 GLN Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain R residue 240 PHE Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 325 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 261 GLN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 325 GLN R 331 HIS R 335 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8886 Z= 0.161 Angle : 0.519 6.602 12029 Z= 0.274 Chirality : 0.039 0.135 1360 Planarity : 0.004 0.057 1528 Dihedral : 5.482 57.385 1215 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.37 % Allowed : 14.77 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.65 (0.26), residues: 1082 helix: 2.18 (0.26), residues: 379 sheet: -0.49 (0.32), residues: 253 loop : -0.47 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 87 HIS 0.006 0.001 HIS R 331 PHE 0.009 0.001 PHE A 189 TYR 0.022 0.001 TYR R 135 ARG 0.009 0.000 ARG E 218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 173 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8410 (mttt) cc_final: 0.7894 (mmtt) REVERT: A 24 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7290 (mt0) REVERT: A 300 ARG cc_start: 0.7109 (mtm180) cc_final: 0.6587 (mtm110) REVERT: B 128 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8261 (mp) REVERT: B 239 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.8859 (t80) REVERT: E 41 GLU cc_start: 0.6904 (tp30) cc_final: 0.6591 (tp30) REVERT: G 11 GLN cc_start: 0.7408 (tm-30) cc_final: 0.6882 (tt0) REVERT: R 64 CYS cc_start: 0.7332 (p) cc_final: 0.7028 (p) REVERT: R 143 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6751 (ttm) REVERT: R 240 PHE cc_start: 0.6874 (OUTLIER) cc_final: 0.6636 (t80) REVERT: R 293 ARG cc_start: 0.6355 (ptt-90) cc_final: 0.5767 (ptm160) outliers start: 13 outliers final: 8 residues processed: 182 average time/residue: 0.5830 time to fit residues: 136.3327 Evaluate side-chains 176 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 164 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 240 PHE Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 325 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN ** R 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 HIS R 335 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8886 Z= 0.404 Angle : 0.616 7.209 12029 Z= 0.332 Chirality : 0.042 0.142 1360 Planarity : 0.005 0.067 1528 Dihedral : 5.888 56.583 1215 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.64 % Allowed : 14.35 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.22 (0.25), residues: 1082 helix: 1.74 (0.26), residues: 380 sheet: -0.67 (0.31), residues: 255 loop : -0.68 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 326 HIS 0.008 0.001 HIS R 331 PHE 0.018 0.002 PHE B 204 TYR 0.020 0.002 TYR E 190 ARG 0.009 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8575 (mttt) cc_final: 0.8121 (mmtt) REVERT: A 20 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7568 (mm-30) REVERT: A 24 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7209 (mt0) REVERT: A 300 ARG cc_start: 0.7157 (mtm180) cc_final: 0.6791 (mtm110) REVERT: B 128 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8317 (mp) REVERT: B 228 THR cc_start: 0.7434 (p) cc_final: 0.7017 (m) REVERT: B 239 PHE cc_start: 0.9417 (OUTLIER) cc_final: 0.8984 (t80) REVERT: E 41 GLU cc_start: 0.6894 (tp30) cc_final: 0.6551 (tp30) REVERT: R 64 CYS cc_start: 0.7258 (p) cc_final: 0.6997 (p) REVERT: R 250 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7507 (mp) REVERT: R 293 ARG cc_start: 0.6632 (ptt-90) cc_final: 0.5792 (ptm-80) outliers start: 25 outliers final: 19 residues processed: 177 average time/residue: 0.5872 time to fit residues: 135.3532 Evaluate side-chains 182 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 231 GLN Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 240 PHE Chi-restraints excluded: chain R residue 250 LEU Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 0.2980 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 42 optimal weight: 0.2980 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 HIS R 335 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8886 Z= 0.156 Angle : 0.521 6.922 12029 Z= 0.273 Chirality : 0.039 0.134 1360 Planarity : 0.004 0.066 1528 Dihedral : 5.372 55.891 1215 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.37 % Allowed : 15.51 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.77 (0.26), residues: 1082 helix: 2.31 (0.26), residues: 379 sheet: -0.46 (0.32), residues: 257 loop : -0.41 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 87 HIS 0.007 0.001 HIS R 331 PHE 0.009 0.001 PHE A 189 TYR 0.016 0.001 TYR R 135 ARG 0.010 0.000 ARG E 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8351 (mttt) cc_final: 0.7847 (mmtt) REVERT: A 24 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7240 (mt0) REVERT: A 300 ARG cc_start: 0.7146 (mtm180) cc_final: 0.6601 (mtm110) REVERT: B 239 PHE cc_start: 0.9353 (OUTLIER) cc_final: 0.8811 (t80) REVERT: B 328 ASP cc_start: 0.8354 (p0) cc_final: 0.8154 (p0) REVERT: E 12 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7111 (tm-30) REVERT: E 41 GLU cc_start: 0.6955 (tp30) cc_final: 0.6596 (tp30) REVERT: G 11 GLN cc_start: 0.7572 (tm-30) cc_final: 0.6864 (tt0) REVERT: R 64 CYS cc_start: 0.7294 (p) cc_final: 0.6976 (p) REVERT: R 143 MET cc_start: 0.7003 (ttt) cc_final: 0.6758 (ttm) REVERT: R 293 ARG cc_start: 0.6532 (ptt-90) cc_final: 0.5905 (ptm160) outliers start: 13 outliers final: 8 residues processed: 177 average time/residue: 0.5914 time to fit residues: 137.0723 Evaluate side-chains 172 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 162 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 HIS R 335 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8886 Z= 0.167 Angle : 0.511 6.207 12029 Z= 0.269 Chirality : 0.039 0.137 1360 Planarity : 0.004 0.066 1528 Dihedral : 5.030 54.293 1213 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.05 % Allowed : 16.24 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.93 (0.26), residues: 1082 helix: 2.46 (0.26), residues: 380 sheet: -0.40 (0.32), residues: 257 loop : -0.30 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 87 HIS 0.009 0.001 HIS R 331 PHE 0.009 0.001 PHE B 204 TYR 0.018 0.001 TYR R 135 ARG 0.011 0.000 ARG E 218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 173 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8386 (mttt) cc_final: 0.7900 (mmtt) REVERT: A 24 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7182 (mt0) REVERT: A 300 ARG cc_start: 0.7097 (mtm180) cc_final: 0.6661 (mtm110) REVERT: B 239 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.8765 (t80) REVERT: E 41 GLU cc_start: 0.6891 (tp30) cc_final: 0.6531 (tp30) REVERT: E 42 LYS cc_start: 0.8639 (mmmm) cc_final: 0.8267 (mmtm) REVERT: G 11 GLN cc_start: 0.7442 (tm-30) cc_final: 0.6898 (tt0) REVERT: R 64 CYS cc_start: 0.7293 (p) cc_final: 0.6921 (p) REVERT: R 143 MET cc_start: 0.7004 (ttt) cc_final: 0.6761 (ttm) REVERT: R 220 MET cc_start: 0.6185 (ttt) cc_final: 0.5812 (ttp) REVERT: R 293 ARG cc_start: 0.6474 (ptt-90) cc_final: 0.5879 (ptm160) outliers start: 10 outliers final: 7 residues processed: 179 average time/residue: 0.6077 time to fit residues: 140.8979 Evaluate side-chains 174 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 166 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 229 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 300 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN ** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 HIS R 335 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.156092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.121173 restraints weight = 34177.412| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.15 r_work: 0.3356 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8886 Z= 0.234 Angle : 0.544 6.105 12029 Z= 0.288 Chirality : 0.040 0.200 1360 Planarity : 0.004 0.070 1528 Dihedral : 5.176 54.152 1213 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.37 % Allowed : 16.46 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.77 (0.26), residues: 1082 helix: 2.30 (0.26), residues: 379 sheet: -0.45 (0.32), residues: 258 loop : -0.40 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 87 HIS 0.009 0.001 HIS R 331 PHE 0.011 0.001 PHE R 306 TYR 0.020 0.001 TYR R 135 ARG 0.011 0.000 ARG E 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5081.67 seconds wall clock time: 90 minutes 31.36 seconds (5431.36 seconds total)