Starting phenix.real_space_refine on Tue Aug 6 13:06:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhb_42268/08_2024/8uhb_42268_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhb_42268/08_2024/8uhb_42268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhb_42268/08_2024/8uhb_42268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhb_42268/08_2024/8uhb_42268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhb_42268/08_2024/8uhb_42268_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhb_42268/08_2024/8uhb_42268_trim.cif" } resolution = 3.35 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= 0.038 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 65 5.16 5 C 5346 2.51 5 N 1453 2.21 5 O 1553 1.98 5 H 8144 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "C PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 240": "OD1" <-> "OD2" Residue "C GLU 392": "OE1" <-> "OE2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N ASP 106": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 16561 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4754 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 11, 'TRANS': 304} Chain breaks: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 5106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5106 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 3890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3890 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Chain: "G" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 884 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 1911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1911 Classifications: {'peptide': 128} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'WV8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.40, per 1000 atoms: 0.45 Number of scatterers: 16561 At special positions: 0 Unit cell: (85.52, 100.486, 136.832, 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 65 16.00 O 1553 8.00 N 1453 7.00 C 5346 6.00 H 8144 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 178 " distance=2.03 Simple disulfide: pdb=" SG CYS A 13 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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: 13.77 Conformation dependent library (CDL) restraints added in 1.8 seconds 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 12 sheets defined 39.9% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 19 through 51 removed outlier: 3.835A pdb=" N ILE A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 76 removed outlier: 3.918A pdb=" N ILE A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 64 " --> pdb=" O TRP A 60 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR A 67 " --> pdb=" O HIS A 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 68 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 69 " --> pdb=" O MET A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.556A pdb=" N SER A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 101 removed outlier: 3.686A pdb=" N LYS A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 126 Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.506A pdb=" N LYS A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 157 Proline residue: A 151 - end of helix Processing helix chain 'A' and resid 169 through 178 removed outlier: 3.954A pdb=" N CYS A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 199 through 228 removed outlier: 4.152A pdb=" N ARG A 212 " --> pdb=" O CYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 278 removed outlier: 4.272A pdb=" N LYS A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Proline residue: A 266 - end of helix removed outlier: 3.725A pdb=" N ASP A 274 " --> pdb=" O CYS A 270 " (cutoff:3.500A) Proline residue: A 275 - end of helix Processing helix chain 'A' and resid 282 through 305 removed outlier: 3.693A pdb=" N ASN A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 308 through 319 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.761A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.677A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 38 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 269 through 279 removed outlier: 3.526A pdb=" N ASP C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 303 Processing helix chain 'C' and resid 334 through 353 removed outlier: 4.249A pdb=" N LYS C 338 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG C 342 " --> pdb=" O LYS C 338 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU C 344 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE C 345 " --> pdb=" O ILE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 391 removed outlier: 3.951A pdb=" N VAL C 375 " --> pdb=" O ASN C 371 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP C 381 " --> pdb=" O ASN C 377 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 383 " --> pdb=" O CYS C 379 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.532A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.673A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.986A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.984A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.617A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.715A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.809A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.471A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=AA9, first strand: chain 'C' and resid 208 through 209 Processing sheet with id=AB1, first strand: chain 'C' and resid 246 through 249 removed outlier: 7.020A pdb=" N VAL C 287 " --> pdb=" O TYR C 360 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N HIS C 362 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU C 289 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.502A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1113 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: 5.76 Time building geometry restraints manager: 14.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8118 1.03 - 1.23: 141 1.23 - 1.43: 3560 1.43 - 1.62: 4828 1.62 - 1.82: 94 Bond restraints: 16741 Sorted by residual: bond pdb=" C8 WV8 A 401 " pdb=" N9 WV8 A 401 " ideal model delta sigma weight residual 1.359 1.326 0.033 2.00e-02 2.50e+03 2.74e+00 bond pdb=" C MET A 77 " pdb=" O MET A 77 " ideal model delta sigma weight residual 1.244 1.231 0.013 1.00e-02 1.00e+04 1.60e+00 bond pdb=" CB TRP B 99 " pdb=" CG TRP B 99 " ideal model delta sigma weight residual 1.498 1.468 0.030 3.10e-02 1.04e+03 9.30e-01 bond pdb=" C VAL A 250 " pdb=" O VAL A 250 " ideal model delta sigma weight residual 1.237 1.226 0.011 1.12e-02 7.97e+03 9.28e-01 bond pdb=" C8 WV8 A 401 " pdb=" O7 WV8 A 401 " ideal model delta sigma weight residual 1.361 1.344 0.017 2.00e-02 2.50e+03 6.90e-01 ... (remaining 16736 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.13: 358 107.13 - 113.89: 19466 113.89 - 120.65: 5811 120.65 - 127.41: 4350 127.41 - 134.17: 88 Bond angle restraints: 30073 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.20 109.67 3.53 9.60e-01 1.09e+00 1.35e+01 angle pdb=" N ILE C 372 " pdb=" CA ILE C 372 " pdb=" C ILE C 372 " ideal model delta sigma weight residual 112.35 107.30 5.05 1.41e+00 5.03e-01 1.28e+01 angle pdb=" N ILE C 235 " pdb=" CA ILE C 235 " pdb=" C ILE C 235 " ideal model delta sigma weight residual 113.07 108.53 4.54 1.37e+00 5.33e-01 1.10e+01 angle pdb=" N ASP C 310 " pdb=" CA ASP C 310 " pdb=" C ASP C 310 " ideal model delta sigma weight residual 114.04 110.13 3.91 1.24e+00 6.50e-01 9.93e+00 angle pdb=" N VAL A 46 " pdb=" CA VAL A 46 " pdb=" C VAL A 46 " ideal model delta sigma weight residual 111.45 108.65 2.80 9.30e-01 1.16e+00 9.06e+00 ... (remaining 30068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 7184 17.66 - 35.32: 599 35.32 - 52.98: 135 52.98 - 70.64: 21 70.64 - 88.30: 9 Dihedral angle restraints: 7948 sinusoidal: 4200 harmonic: 3748 Sorted by residual: dihedral pdb=" CB CYS A 5 " pdb=" SG CYS A 5 " pdb=" SG CYS A 178 " pdb=" CB CYS A 178 " ideal model delta sinusoidal sigma weight residual 93.00 175.02 -82.02 1 1.00e+01 1.00e-02 8.27e+01 dihedral pdb=" CB CYS A 96 " pdb=" SG CYS A 96 " pdb=" SG CYS A 182 " pdb=" CB CYS A 182 " ideal model delta sinusoidal sigma weight residual -86.00 -154.02 68.02 1 1.00e+01 1.00e-02 6.01e+01 dihedral pdb=" CA ILE C 341 " pdb=" C ILE C 341 " pdb=" N ARG C 342 " pdb=" CA ARG C 342 " ideal model delta harmonic sigma weight residual 180.00 155.50 24.50 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 7945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 787 0.032 - 0.064: 371 0.064 - 0.096: 94 0.096 - 0.128: 44 0.128 - 0.160: 8 Chirality restraints: 1304 Sorted by residual: chirality pdb=" CA ILE C 341 " pdb=" N ILE C 341 " pdb=" C ILE C 341 " pdb=" CB ILE C 341 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CB VAL A 46 " pdb=" CA VAL A 46 " pdb=" CG1 VAL A 46 " pdb=" CG2 VAL A 46 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE C 244 " pdb=" N ILE C 244 " pdb=" C ILE C 244 " pdb=" CB ILE C 244 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 1301 not shown) Planarity restraints: 2509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5 WV8 A 401 " 0.048 2.00e-02 2.50e+03 3.77e-02 1.78e+01 pdb=" C8 WV8 A 401 " -0.013 2.00e-02 2.50e+03 pdb=" N10 WV8 A 401 " -0.051 2.00e-02 2.50e+03 pdb=" N9 WV8 A 401 " 0.039 2.00e-02 2.50e+03 pdb=" O7 WV8 A 401 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 234 " 0.020 2.00e-02 2.50e+03 1.16e-02 4.04e+00 pdb=" CG PHE B 234 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 234 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 234 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 234 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 234 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 234 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE B 234 " -0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE B 234 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE B 234 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE B 234 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE B 234 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 281 " 0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 282 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " 0.026 5.00e-02 4.00e+02 ... (remaining 2506 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 262 2.06 - 2.69: 26322 2.69 - 3.33: 47799 3.33 - 3.96: 61919 3.96 - 4.60: 97889 Nonbonded interactions: 234191 Sorted by model distance: nonbonded pdb=" HE2 HIS C 362 " pdb=" OD2 ASP C 378 " model vdw 1.420 2.450 nonbonded pdb=" OD1 ASP C 331 " pdb=" H VAL C 334 " model vdw 1.525 2.450 nonbonded pdb=" OD1 ASP B 228 " pdb=" HH TYR N 117 " model vdw 1.564 2.450 nonbonded pdb=" O ARG B 68 " pdb=" HG SER B 84 " model vdw 1.606 2.450 nonbonded pdb="HH12 ARG N 67 " pdb=" OD2 ASP N 90 " model vdw 1.630 2.450 ... (remaining 234186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.870 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: 0.250 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 54.430 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8597 Z= 0.239 Angle : 0.619 5.054 11643 Z= 0.367 Chirality : 0.041 0.160 1304 Planarity : 0.003 0.048 1482 Dihedral : 14.115 88.305 3086 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: -1.42 (0.26), residues: 1059 helix: 0.13 (0.28), residues: 385 sheet: -1.84 (0.33), residues: 218 loop : -1.30 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.035 0.001 PHE B 234 TYR 0.013 0.001 TYR C 311 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.469 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: 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.5901 time to fit residues: 135.7026 Evaluate side-chains 116 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 81 optimal weight: 0.0870 chunk 31 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 55 HIS B 16 ASN B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8597 Z= 0.177 Angle : 0.563 5.568 11643 Z= 0.307 Chirality : 0.040 0.136 1304 Planarity : 0.004 0.048 1482 Dihedral : 5.484 38.398 1183 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.33 % Allowed : 8.03 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.23 (0.26), residues: 1059 helix: 0.33 (0.27), residues: 400 sheet: -1.65 (0.33), residues: 222 loop : -1.31 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.006 0.001 HIS C 362 PHE 0.018 0.001 PHE C 212 TYR 0.010 0.001 TYR B 59 ARG 0.004 0.000 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 124 time to evaluate : 1.444 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 126 average time/residue: 0.4962 time to fit residues: 83.6505 Evaluate side-chains 114 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 379 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 78 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8597 Z= 0.231 Angle : 0.547 5.977 11643 Z= 0.299 Chirality : 0.040 0.133 1304 Planarity : 0.003 0.041 1482 Dihedral : 5.178 35.564 1183 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.56 % Allowed : 9.25 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.27), residues: 1059 helix: 0.58 (0.27), residues: 400 sheet: -1.38 (0.34), residues: 219 loop : -1.20 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS C 362 PHE 0.016 0.001 PHE C 212 TYR 0.008 0.001 TYR C 358 ARG 0.007 0.001 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 1.839 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 118 average time/residue: 0.5237 time to fit residues: 82.7650 Evaluate side-chains 112 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 107 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8597 Z= 0.193 Angle : 0.527 6.375 11643 Z= 0.285 Chirality : 0.039 0.134 1304 Planarity : 0.003 0.040 1482 Dihedral : 4.991 33.676 1183 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.00 % Allowed : 9.36 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.66 (0.27), residues: 1059 helix: 0.85 (0.27), residues: 397 sheet: -1.19 (0.35), residues: 221 loop : -1.14 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS C 362 PHE 0.016 0.001 PHE C 212 TYR 0.008 0.001 TYR A 200 ARG 0.002 0.000 ARG C 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 1.408 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 119 average time/residue: 0.5112 time to fit residues: 80.5267 Evaluate side-chains 109 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 51 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 8597 Z= 0.429 Angle : 0.617 6.271 11643 Z= 0.342 Chirality : 0.042 0.137 1304 Planarity : 0.004 0.047 1482 Dihedral : 5.119 32.909 1183 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.23 % Allowed : 10.48 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.72 (0.26), residues: 1059 helix: 0.79 (0.26), residues: 403 sheet: -1.19 (0.34), residues: 220 loop : -1.22 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.010 0.001 HIS C 220 PHE 0.027 0.001 PHE C 222 TYR 0.013 0.002 TYR C 311 ARG 0.003 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 1.320 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 108 average time/residue: 0.5224 time to fit residues: 74.7411 Evaluate side-chains 104 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 390 GLN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 0.2980 chunk 97 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8597 Z= 0.160 Angle : 0.528 6.645 11643 Z= 0.284 Chirality : 0.040 0.137 1304 Planarity : 0.003 0.039 1482 Dihedral : 4.904 34.047 1183 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.67 % Allowed : 11.59 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.35 (0.27), residues: 1059 helix: 1.19 (0.27), residues: 397 sheet: -0.96 (0.35), residues: 211 loop : -1.10 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS C 362 PHE 0.026 0.001 PHE C 222 TYR 0.009 0.001 TYR A 200 ARG 0.002 0.000 ARG C 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 1.338 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: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 118 average time/residue: 0.5123 time to fit residues: 81.0150 Evaluate side-chains 109 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8597 Z= 0.172 Angle : 0.526 6.051 11643 Z= 0.283 Chirality : 0.039 0.147 1304 Planarity : 0.003 0.037 1482 Dihedral : 4.729 34.477 1183 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.67 % Allowed : 11.93 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.27), residues: 1059 helix: 1.31 (0.27), residues: 397 sheet: -0.78 (0.35), residues: 206 loop : -1.06 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS C 357 PHE 0.022 0.001 PHE C 222 TYR 0.011 0.001 TYR B 264 ARG 0.002 0.000 ARG C 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 1.369 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 111 average time/residue: 0.4980 time to fit residues: 73.9379 Evaluate side-chains 109 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 91 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8597 Z= 0.265 Angle : 0.556 7.603 11643 Z= 0.300 Chirality : 0.040 0.160 1304 Planarity : 0.003 0.036 1482 Dihedral : 4.765 34.106 1183 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.78 % Allowed : 12.15 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.23 (0.27), residues: 1059 helix: 1.32 (0.27), residues: 398 sheet: -0.91 (0.35), residues: 215 loop : -1.07 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS C 357 PHE 0.018 0.001 PHE C 222 TYR 0.009 0.001 TYR B 264 ARG 0.002 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 1.377 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 105 average time/residue: 0.5095 time to fit residues: 71.9889 Evaluate side-chains 108 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 73 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 0.0980 chunk 61 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8597 Z= 0.154 Angle : 0.536 7.816 11643 Z= 0.283 Chirality : 0.040 0.138 1304 Planarity : 0.003 0.037 1482 Dihedral : 4.653 34.874 1183 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.45 % Allowed : 12.49 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.03 (0.27), residues: 1059 helix: 1.47 (0.27), residues: 398 sheet: -0.57 (0.36), residues: 195 loop : -1.07 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS C 357 PHE 0.019 0.001 PHE C 222 TYR 0.009 0.001 TYR C 318 ARG 0.002 0.000 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 1.338 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 115 average time/residue: 0.5053 time to fit residues: 77.8292 Evaluate side-chains 110 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8597 Z= 0.246 Angle : 0.557 6.761 11643 Z= 0.299 Chirality : 0.040 0.134 1304 Planarity : 0.003 0.037 1482 Dihedral : 4.677 34.521 1183 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.56 % Allowed : 12.60 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.08 (0.27), residues: 1059 helix: 1.41 (0.26), residues: 398 sheet: -0.68 (0.34), residues: 218 loop : -1.04 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS C 357 PHE 0.019 0.001 PHE C 222 TYR 0.009 0.001 TYR B 264 ARG 0.002 0.000 ARG N 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 1.428 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 108 average time/residue: 0.5369 time to fit residues: 77.5363 Evaluate side-chains 109 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 59 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.069226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.053692 restraints weight = 88697.435| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 4.17 r_work: 0.2852 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8597 Z= 0.210 Angle : 0.547 7.513 11643 Z= 0.293 Chirality : 0.040 0.135 1304 Planarity : 0.003 0.037 1482 Dihedral : 4.652 34.715 1183 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.78 % Allowed : 12.93 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.01 (0.27), residues: 1059 helix: 1.48 (0.26), residues: 398 sheet: -0.61 (0.35), residues: 216 loop : -1.03 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS C 357 PHE 0.020 0.001 PHE C 222 TYR 0.013 0.001 TYR B 59 ARG 0.002 0.000 ARG A 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3870.58 seconds wall clock time: 68 minutes 17.04 seconds (4097.04 seconds total)