Starting phenix.real_space_refine (version: dev) on Sat Feb 18 23:39:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3x_27872/02_2023/8e3x_27872.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3x_27872/02_2023/8e3x_27872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3x_27872/02_2023/8e3x_27872.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3x_27872/02_2023/8e3x_27872.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3x_27872/02_2023/8e3x_27872.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3x_27872/02_2023/8e3x_27872.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 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 Process input model Symmetric amino acids flipped Residue "A ARG 265": "NH1" <-> "NH2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "R GLU 138": "OE1" <-> "OE2" Residue "R GLU 247": "OE1" <-> "OE2" Residue "R GLU 262": "OE1" <-> "OE2" Residue "R ARG 288": "NH1" <-> "NH2" Residue "R ARG 350": "NH1" <-> "NH2" Residue "R ARG 353": "NH1" <-> "NH2" Residue "R ARG 379": "NH1" <-> "NH2" Residue "R GLU 380": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8979 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1921 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 221 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "R" Number of atoms: 2841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2841 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 13, 'TRANS': 348} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 79 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 5.59, per 1000 atoms: 0.62 Number of scatterers: 8979 At special positions: 0 Unit cell: (92.96, 94.62, 159.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 61 16.00 O 1668 8.00 N 1558 7.00 C 5692 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 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 Simple disulfide: pdb=" SG CYS R 34 " - pdb=" SG CYS R 63 " distance=2.04 Simple disulfide: pdb=" SG CYS R 54 " - pdb=" SG CYS R 118 " distance=2.03 Simple disulfide: pdb=" SG CYS R 77 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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: 3.42 Conformation dependent library (CDL) restraints added in 1.5 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 41.4% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 Processing helix chain 'A' and resid 52 through 61 removed outlier: 4.009A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.514A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.708A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.542A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 27 Processing helix chain 'R' and resid 25 through 45 removed outlier: 3.620A pdb=" N GLN R 31 " --> pdb=" O PHE R 27 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET R 33 " --> pdb=" O LYS R 29 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N CYS R 34 " --> pdb=" O GLU R 30 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU R 35 " --> pdb=" O GLN R 31 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU R 36 " --> pdb=" O ALA R 32 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN R 39 " --> pdb=" O LEU R 35 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET R 45 " --> pdb=" O ALA R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 177 Processing helix chain 'R' and resid 183 through 211 Processing helix chain 'R' and resid 211 through 218 removed outlier: 3.614A pdb=" N SER R 216 " --> pdb=" O ALA R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 257 removed outlier: 3.658A pdb=" N LYS R 227 " --> pdb=" O THR R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 291 Proline residue: R 277 - end of helix Processing helix chain 'R' and resid 302 through 336 removed outlier: 3.779A pdb=" N ILE R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 346 through 363 removed outlier: 3.556A pdb=" N ARG R 350 " --> pdb=" O SER R 346 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU R 357 " --> pdb=" O ARG R 353 " (cutoff:3.500A) Proline residue: R 360 - end of helix Processing helix chain 'R' and resid 366 through 371 removed outlier: 4.506A pdb=" N PHE R 371 " --> pdb=" O THR R 367 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 386 Processing helix chain 'R' and resid 388 through 390 No H-bonds generated for 'chain 'R' and resid 388 through 390' Processing helix chain 'R' and resid 391 through 401 Processing helix chain 'R' and resid 404 through 417 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 7.259A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.172A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.859A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.582A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.509A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.086A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.694A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.708A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 5.431A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1317 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1541 1.32 - 1.45: 2519 1.45 - 1.57: 5015 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 9159 Sorted by residual: bond pdb=" CA SER R 316 " pdb=" CB SER R 316 " ideal model delta sigma weight residual 1.528 1.480 0.048 1.59e-02 3.96e+03 9.20e+00 bond pdb=" C LEU R 251 " pdb=" O LEU R 251 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.19e-02 7.06e+03 9.04e+00 bond pdb=" N LEU R 361 " pdb=" CA LEU R 361 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.31e-02 5.83e+03 7.72e+00 bond pdb=" C LEU R 249 " pdb=" O LEU R 249 " ideal model delta sigma weight residual 1.237 1.207 0.029 1.17e-02 7.31e+03 6.30e+00 bond pdb=" N TYR R 400 " pdb=" CA TYR R 400 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.32e-02 5.74e+03 5.53e+00 ... (remaining 9154 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.87: 129 105.87 - 112.91: 4875 112.91 - 119.95: 3057 119.95 - 127.00: 4240 127.00 - 134.04: 99 Bond angle restraints: 12400 Sorted by residual: angle pdb=" N ASN R 320 " pdb=" CA ASN R 320 " pdb=" C ASN R 320 " ideal model delta sigma weight residual 112.23 105.58 6.65 1.26e+00 6.30e-01 2.79e+01 angle pdb=" N SER R 316 " pdb=" CA SER R 316 " pdb=" C SER R 316 " ideal model delta sigma weight residual 111.36 105.78 5.58 1.09e+00 8.42e-01 2.62e+01 angle pdb=" N ILE R 188 " pdb=" CA ILE R 188 " pdb=" C ILE R 188 " ideal model delta sigma weight residual 110.62 105.82 4.80 1.02e+00 9.61e-01 2.21e+01 angle pdb=" N PHE R 362 " pdb=" CA PHE R 362 " pdb=" C PHE R 362 " ideal model delta sigma weight residual 114.12 107.73 6.39 1.39e+00 5.18e-01 2.11e+01 angle pdb=" N LEU R 244 " pdb=" CA LEU R 244 " pdb=" C LEU R 244 " ideal model delta sigma weight residual 111.36 106.63 4.73 1.09e+00 8.42e-01 1.89e+01 ... (remaining 12395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 4879 16.07 - 32.13: 428 32.13 - 48.20: 92 48.20 - 64.26: 16 64.26 - 80.33: 8 Dihedral angle restraints: 5423 sinusoidal: 2113 harmonic: 3310 Sorted by residual: dihedral pdb=" CB CYS R 77 " pdb=" SG CYS R 77 " pdb=" SG CYS R 134 " pdb=" CB CYS R 134 " ideal model delta sinusoidal sigma weight residual 93.00 150.58 -57.58 1 1.00e+01 1.00e-02 4.45e+01 dihedral pdb=" CB CYS R 34 " pdb=" SG CYS R 34 " pdb=" SG CYS R 63 " pdb=" CB CYS R 63 " ideal model delta sinusoidal sigma weight residual -86.00 -127.56 41.56 1 1.00e+01 1.00e-02 2.42e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -122.59 36.59 1 1.00e+01 1.00e-02 1.89e+01 ... (remaining 5420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1116 0.050 - 0.101: 204 0.101 - 0.151: 46 0.151 - 0.202: 4 0.202 - 0.252: 3 Chirality restraints: 1373 Sorted by residual: chirality pdb=" CA ASN R 186 " pdb=" N ASN R 186 " pdb=" C ASN R 186 " pdb=" CB ASN R 186 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA PHE R 242 " pdb=" N PHE R 242 " pdb=" C PHE R 242 " pdb=" CB PHE R 242 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ASN R 191 " pdb=" N ASN R 191 " pdb=" C ASN R 191 " pdb=" CB ASN R 191 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1370 not shown) Planarity restraints: 1585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY R 315 " 0.013 2.00e-02 2.50e+03 2.75e-02 7.56e+00 pdb=" C GLY R 315 " -0.048 2.00e-02 2.50e+03 pdb=" O GLY R 315 " 0.018 2.00e-02 2.50e+03 pdb=" N SER R 316 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 319 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C VAL R 319 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL R 319 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN R 320 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO B 236 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.025 5.00e-02 4.00e+02 ... (remaining 1582 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1681 2.77 - 3.30: 8600 3.30 - 3.84: 15318 3.84 - 4.37: 17983 4.37 - 4.90: 31029 Nonbonded interactions: 74611 Sorted by model distance: nonbonded pdb=" NH2 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.239 2.520 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.255 2.440 nonbonded pdb=" OE2 GLU B 12 " pdb=" ND2 ASN B 16 " model vdw 2.279 2.520 nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.334 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.344 2.440 ... (remaining 74606 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 5692 2.51 5 N 1558 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.190 Check model and map are aligned: 0.140 Process input model: 26.680 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 : 0.003 0.048 9159 Z= 0.197 Angle : 0.582 9.249 12400 Z= 0.389 Chirality : 0.042 0.252 1373 Planarity : 0.003 0.045 1585 Dihedral : 13.023 80.331 3267 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 0.00 % 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: 1.49 (0.25), residues: 1120 helix: 2.27 (0.25), residues: 434 sheet: 0.92 (0.32), residues: 222 loop : -0.19 (0.28), residues: 464 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.185 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 1.6350 time to fit residues: 253.1059 Evaluate side-chains 105 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.104 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 0.0000 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 54 ASN A 292 ASN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN R 189 HIS R 336 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 9159 Z= 0.155 Angle : 0.478 8.115 12400 Z= 0.255 Chirality : 0.039 0.139 1373 Planarity : 0.004 0.053 1585 Dihedral : 3.523 15.464 1241 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 0.84 % 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: 1.90 (0.25), residues: 1120 helix: 2.78 (0.25), residues: 428 sheet: 1.19 (0.33), residues: 219 loop : -0.13 (0.29), residues: 473 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 1.108 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 110 average time/residue: 1.5037 time to fit residues: 175.5596 Evaluate side-chains 102 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.089 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.4749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 32 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9159 Z= 0.202 Angle : 0.492 8.046 12400 Z= 0.264 Chirality : 0.040 0.222 1373 Planarity : 0.003 0.049 1585 Dihedral : 3.776 17.166 1241 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 1.37 % 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: 1.84 (0.25), residues: 1120 helix: 2.72 (0.25), residues: 434 sheet: 1.10 (0.32), residues: 225 loop : -0.18 (0.29), residues: 461 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 0.997 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 115 average time/residue: 1.5909 time to fit residues: 193.6025 Evaluate side-chains 103 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 1.090 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.2156 time to fit residues: 1.7850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 67 optimal weight: 0.3980 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN N 13 GLN N 77 ASN N 120 GLN R 186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 9159 Z= 0.337 Angle : 0.557 7.797 12400 Z= 0.301 Chirality : 0.043 0.202 1373 Planarity : 0.004 0.054 1585 Dihedral : 4.274 20.334 1241 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 1.90 % 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: 1.44 (0.25), residues: 1120 helix: 2.26 (0.24), residues: 446 sheet: 1.02 (0.33), residues: 226 loop : -0.42 (0.29), residues: 448 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 1.108 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 115 average time/residue: 1.6388 time to fit residues: 199.0052 Evaluate side-chains 111 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 0.962 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 5 average time/residue: 0.4460 time to fit residues: 3.9000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN N 120 GLN R 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9159 Z= 0.200 Angle : 0.493 9.620 12400 Z= 0.264 Chirality : 0.039 0.138 1373 Planarity : 0.004 0.050 1585 Dihedral : 3.993 18.863 1241 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 1.58 % 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: 1.67 (0.25), residues: 1120 helix: 2.61 (0.25), residues: 435 sheet: 0.96 (0.32), residues: 231 loop : -0.31 (0.29), residues: 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 1.169 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 114 average time/residue: 1.5688 time to fit residues: 190.2674 Evaluate side-chains 108 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.1828 time to fit residues: 2.0431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 0.0370 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN N 120 GLN R 186 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9159 Z= 0.169 Angle : 0.476 9.242 12400 Z= 0.256 Chirality : 0.039 0.135 1373 Planarity : 0.003 0.050 1585 Dihedral : 3.837 17.300 1241 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 0.84 % 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: 1.76 (0.25), residues: 1120 helix: 2.78 (0.25), residues: 435 sheet: 0.97 (0.33), residues: 225 loop : -0.32 (0.29), residues: 460 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 1.104 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 113 average time/residue: 1.4719 time to fit residues: 176.4001 Evaluate side-chains 108 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 1.047 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.1650 time to fit residues: 1.8898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 0.0770 chunk 42 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN R 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9159 Z= 0.179 Angle : 0.483 11.090 12400 Z= 0.258 Chirality : 0.039 0.136 1373 Planarity : 0.003 0.052 1585 Dihedral : 3.820 17.413 1241 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 1.27 % 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: 1.79 (0.25), residues: 1120 helix: 2.82 (0.25), residues: 435 sheet: 0.93 (0.33), residues: 225 loop : -0.30 (0.29), residues: 460 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 1.092 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 109 average time/residue: 1.4665 time to fit residues: 169.7111 Evaluate side-chains 109 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 1.141 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.7172 time to fit residues: 4.0045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN R 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 9159 Z= 0.293 Angle : 0.537 10.286 12400 Z= 0.290 Chirality : 0.041 0.146 1373 Planarity : 0.004 0.056 1585 Dihedral : 4.173 20.272 1241 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 1.27 % 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: 1.62 (0.25), residues: 1120 helix: 2.51 (0.24), residues: 442 sheet: 0.96 (0.33), residues: 235 loop : -0.35 (0.29), residues: 443 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 1.045 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 105 average time/residue: 1.5655 time to fit residues: 174.1051 Evaluate side-chains 108 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 1.019 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.1986 time to fit residues: 2.2865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9159 Z= 0.175 Angle : 0.499 12.486 12400 Z= 0.266 Chirality : 0.039 0.136 1373 Planarity : 0.003 0.061 1585 Dihedral : 3.933 18.092 1241 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 0.74 % 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: 1.73 (0.25), residues: 1120 helix: 2.66 (0.25), residues: 441 sheet: 0.96 (0.33), residues: 235 loop : -0.29 (0.29), residues: 444 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 1.006 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 108 average time/residue: 1.5624 time to fit residues: 179.1775 Evaluate side-chains 106 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.7272 time to fit residues: 3.2112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN R 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9159 Z= 0.241 Angle : 0.531 12.794 12400 Z= 0.282 Chirality : 0.040 0.144 1373 Planarity : 0.004 0.063 1585 Dihedral : 4.055 19.157 1241 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 0.84 % 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: 1.67 (0.25), residues: 1120 helix: 2.58 (0.24), residues: 442 sheet: 0.94 (0.33), residues: 235 loop : -0.32 (0.29), residues: 443 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 1.102 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 106 average time/residue: 1.5449 time to fit residues: 173.4421 Evaluate side-chains 107 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 1.102 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.1058 time to fit residues: 1.8199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 36 optimal weight: 0.0570 chunk 90 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 40.0000 chunk 5 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN R 186 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.112835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.070644 restraints weight = 14418.505| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.56 r_work: 0.2797 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9159 Z= 0.194 Angle : 0.503 11.642 12400 Z= 0.269 Chirality : 0.039 0.139 1373 Planarity : 0.003 0.061 1585 Dihedral : 3.935 17.925 1241 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.25), residues: 1120 helix: 2.63 (0.25), residues: 442 sheet: 0.94 (0.33), residues: 235 loop : -0.31 (0.29), residues: 443 =============================================================================== Job complete usr+sys time: 3877.61 seconds wall clock time: 69 minutes 50.15 seconds (4190.15 seconds total)