Starting phenix.real_space_refine (version: dev) on Mon Apr 4 15:37:16 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezk_31388/04_2022/7ezk_31388_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezk_31388/04_2022/7ezk_31388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezk_31388/04_2022/7ezk_31388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezk_31388/04_2022/7ezk_31388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezk_31388/04_2022/7ezk_31388_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezk_31388/04_2022/7ezk_31388_updated.pdb" } resolution = 3.1 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= 0.002 sd= 0.033 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "D ARG 150": "NH1" <-> "NH2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "D ARG 345": "NH1" <-> "NH2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 7196 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1871 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2298 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 12, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "G" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 388 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYS:plan-3': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 4.36, per 1000 atoms: 0.61 Number of scatterers: 7196 At special positions: 0 Unit cell: (102.41, 113.905, 101.365, 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 57 16.00 O 1313 8.00 N 1242 7.00 C 4584 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 114 " - pdb=" SG CYS D 196 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.0 seconds 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1752 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 9 sheets defined 44.4% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.726A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 208 through 214 removed outlier: 3.955A pdb=" N ILE A 212 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLN A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 245 removed outlier: 3.974A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 275 through 278 No H-bonds generated for 'chain 'A' and resid 275 through 278' Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 299 through 318 Processing helix chain 'A' and resid 338 through 358 removed outlier: 4.223A pdb=" N GLN A 357 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 358 " --> pdb=" O HIS A 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 5.314A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.516A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 68 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 75 through 104 Proline residue: D 96 - end of helix Proline residue: D 101 - end of helix Processing helix chain 'D' and resid 111 through 144 Processing helix chain 'D' and resid 146 through 151 removed outlier: 4.279A pdb=" N ARG D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 151' Processing helix chain 'D' and resid 155 through 172 Processing helix chain 'D' and resid 174 through 179 Processing helix chain 'D' and resid 203 through 217 Processing helix chain 'D' and resid 219 through 245 Processing helix chain 'D' and resid 302 through 338 Proline residue: D 328 - end of helix Processing helix chain 'D' and resid 340 through 347 Processing helix chain 'D' and resid 350 through 370 removed outlier: 4.281A pdb=" N SER D 363 " --> pdb=" O SER D 359 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS D 364 " --> pdb=" O TYR D 360 " (cutoff:3.500A) Proline residue: D 367 - end of helix Processing helix chain 'D' and resid 375 through 381 removed outlier: 4.503A pdb=" N GLY D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 23 removed outlier: 3.669A pdb=" N LYS G 20 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 45 Processing sheet with id= A, first strand: chain 'A' and resid 326 through 330 removed outlier: 7.175A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.870A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.012A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.832A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.865A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.855A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.369A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.815A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 180 through 186 371 hydrogen bonds defined for protein. 1053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1832 1.33 - 1.46: 2104 1.46 - 1.60: 3323 1.60 - 1.73: 1 1.73 - 1.86: 84 Bond restraints: 7344 Sorted by residual: bond pdb=" CZ ARG A 347 " pdb=" NH2 ARG A 347 " ideal model delta sigma weight residual 1.330 1.300 0.030 1.30e-02 5.92e+03 5.21e+00 bond pdb=" CZ ARG A 31 " pdb=" NH1 ARG A 31 " ideal model delta sigma weight residual 1.323 1.354 -0.031 1.40e-02 5.10e+03 4.85e+00 bond pdb=" C SER B 31 " pdb=" N GLN B 32 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.38e-02 5.25e+03 4.23e+00 bond pdb=" CA ASN B 237 " pdb=" CB ASN B 237 " ideal model delta sigma weight residual 1.530 1.566 -0.035 1.75e-02 3.27e+03 4.06e+00 bond pdb=" CG ASN A 216 " pdb=" ND2 ASN A 216 " ideal model delta sigma weight residual 1.328 1.369 -0.041 2.10e-02 2.27e+03 3.87e+00 ... (remaining 7339 not shown) Histogram of bond angle deviations from ideal: 97.35 - 104.88: 118 104.88 - 112.40: 3568 112.40 - 119.92: 2917 119.92 - 127.45: 3278 127.45 - 134.97: 81 Bond angle restraints: 9962 Sorted by residual: angle pdb=" N ARG D 310 " pdb=" CA ARG D 310 " pdb=" C ARG D 310 " ideal model delta sigma weight residual 111.36 107.77 3.59 1.09e+00 8.42e-01 1.08e+01 angle pdb=" NE ARG B 48 " pdb=" CZ ARG B 48 " pdb=" NH1 ARG B 48 " ideal model delta sigma weight residual 121.50 118.68 2.82 1.00e+00 1.00e+00 7.93e+00 angle pdb=" N LEU D 217 " pdb=" CA LEU D 217 " pdb=" C LEU D 217 " ideal model delta sigma weight residual 112.94 109.06 3.88 1.41e+00 5.03e-01 7.58e+00 angle pdb=" NE ARG A 303 " pdb=" CZ ARG A 303 " pdb=" NH2 ARG A 303 " ideal model delta sigma weight residual 119.20 121.68 -2.48 9.00e-01 1.23e+00 7.58e+00 angle pdb=" N ARG B 68 " pdb=" CA ARG B 68 " pdb=" C ARG B 68 " ideal model delta sigma weight residual 113.18 109.59 3.59 1.33e+00 5.65e-01 7.30e+00 ... (remaining 9957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.26: 4306 33.26 - 66.51: 60 66.51 - 99.77: 9 99.77 - 133.02: 0 133.02 - 166.27: 1 Dihedral angle restraints: 4376 sinusoidal: 1683 harmonic: 2693 Sorted by residual: dihedral pdb=" CZ TYS P 2 " pdb=" OH TYS P 2 " pdb=" S TYS P 2 " pdb=" O3 TYS P 2 " ideal model delta sinusoidal sigma weight residual 75.04 -91.23 166.27 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" CA ASP A 217 " pdb=" C ASP A 217 " pdb=" N VAL A 218 " pdb=" CA VAL A 218 " ideal model delta harmonic sigma weight residual 180.00 150.64 29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA TYR B 289 " pdb=" C TYR B 289 " pdb=" N ASP B 290 " pdb=" CA ASP B 290 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 4373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 698 0.053 - 0.105: 350 0.105 - 0.157: 83 0.157 - 0.210: 8 0.210 - 0.262: 4 Chirality restraints: 1143 Sorted by residual: chirality pdb=" CG LEU D 214 " pdb=" CB LEU D 214 " pdb=" CD1 LEU D 214 " pdb=" CD2 LEU D 214 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB ILE A 184 " pdb=" CA ILE A 184 " pdb=" CG1 ILE A 184 " pdb=" CG2 ILE A 184 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB VAL D 151 " pdb=" CA VAL D 151 " pdb=" CG1 VAL D 151 " pdb=" CG2 VAL D 151 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1140 not shown) Planarity restraints: 1261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 300 " 0.064 9.50e-02 1.11e+02 4.95e-02 2.07e+01 pdb=" NE ARG A 300 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 300 " 0.077 2.00e-02 2.50e+03 pdb=" NH1 ARG A 300 " -0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG A 300 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 367 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C PRO D 367 " -0.066 2.00e-02 2.50e+03 pdb=" O PRO D 367 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE D 368 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 214 " -0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C LEU D 214 " 0.065 2.00e-02 2.50e+03 pdb=" O LEU D 214 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU D 215 " -0.022 2.00e-02 2.50e+03 ... (remaining 1258 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 696 2.74 - 3.28: 7532 3.28 - 3.82: 12140 3.82 - 4.36: 15027 4.36 - 4.90: 25332 Nonbonded interactions: 60727 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.206 2.440 nonbonded pdb=" OD1 ASN D 98 " pdb=" OH TYR D 360 " model vdw 2.286 2.440 nonbonded pdb=" NZ LYS D 115 " pdb=" O PRO D 177 " model vdw 2.308 2.520 nonbonded pdb=" NH2 ARG A 205 " pdb=" OE1 GLU A 207 " model vdw 2.312 2.520 nonbonded pdb=" NH1 ARG D 197 " pdb=" O1 TYS P 2 " model vdw 2.337 2.520 ... (remaining 60722 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 57 5.16 5 C 4584 2.51 5 N 1242 2.21 5 O 1313 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: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.730 Check model and map are aligned: 0.100 Convert atoms to be neutral: 0.070 Process input model: 22.170 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 : 0.010 0.061 7344 Z= 0.672 Angle : 1.017 8.623 9962 Z= 0.612 Chirality : 0.061 0.262 1143 Planarity : 0.010 0.082 1261 Dihedral : 13.642 166.274 2621 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 0.26 % 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: -1.02 (0.27), residues: 905 helix: -0.92 (0.22), residues: 399 sheet: 0.04 (0.38), residues: 191 loop : -0.47 (0.37), residues: 315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 225 time to evaluate : 0.740 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 225 average time/residue: 0.1920 time to fit residues: 57.0864 Evaluate side-chains 190 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.792 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 2.9990 chunk 67 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 88 ASN B 268 ASN B 295 ASN D 98 ASN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 7344 Z= 0.277 Angle : 0.588 5.711 9962 Z= 0.310 Chirality : 0.044 0.149 1143 Planarity : 0.005 0.086 1261 Dihedral : 7.296 147.241 998 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.29), residues: 905 helix: 1.02 (0.26), residues: 397 sheet: -0.19 (0.36), residues: 194 loop : 0.34 (0.40), residues: 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 223 time to evaluate : 0.879 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 227 average time/residue: 0.2122 time to fit residues: 62.4693 Evaluate side-chains 219 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 206 time to evaluate : 0.825 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0718 time to fit residues: 2.8402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 22 optimal weight: 0.0030 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 72 optimal weight: 0.0470 chunk 27 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 overall best weight: 0.4688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 7344 Z= 0.189 Angle : 0.529 6.809 9962 Z= 0.278 Chirality : 0.042 0.163 1143 Planarity : 0.004 0.066 1261 Dihedral : 6.733 139.711 998 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 2.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.29), residues: 905 helix: 1.52 (0.27), residues: 389 sheet: -0.40 (0.35), residues: 198 loop : 0.42 (0.40), residues: 318 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 215 time to evaluate : 1.140 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 219 average time/residue: 0.2649 time to fit residues: 74.9787 Evaluate side-chains 212 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 206 time to evaluate : 0.933 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0908 time to fit residues: 2.2215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 230 ASN B 268 ASN D 98 ASN D 131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 7344 Z= 0.266 Angle : 0.565 7.113 9962 Z= 0.291 Chirality : 0.044 0.157 1143 Planarity : 0.004 0.075 1261 Dihedral : 6.402 125.496 998 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.29), residues: 905 helix: 1.55 (0.27), residues: 389 sheet: -0.63 (0.34), residues: 196 loop : 0.35 (0.39), residues: 320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 205 time to evaluate : 0.812 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 212 average time/residue: 0.2052 time to fit residues: 57.0239 Evaluate side-chains 214 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 200 time to evaluate : 0.817 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0710 time to fit residues: 2.9309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.0020 chunk 77 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 7344 Z= 0.213 Angle : 0.540 7.577 9962 Z= 0.279 Chirality : 0.043 0.167 1143 Planarity : 0.004 0.065 1261 Dihedral : 6.064 114.045 998 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.29), residues: 905 helix: 1.70 (0.27), residues: 387 sheet: -0.80 (0.33), residues: 188 loop : 0.19 (0.37), residues: 330 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 207 time to evaluate : 0.776 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 214 average time/residue: 0.1997 time to fit residues: 56.0575 Evaluate side-chains 204 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 196 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0753 time to fit residues: 2.1678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 7344 Z= 0.217 Angle : 0.541 9.311 9962 Z= 0.277 Chirality : 0.042 0.168 1143 Planarity : 0.004 0.059 1261 Dihedral : 5.870 106.836 998 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.29), residues: 905 helix: 1.69 (0.27), residues: 389 sheet: -0.73 (0.33), residues: 190 loop : 0.26 (0.37), residues: 326 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 198 time to evaluate : 0.821 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 200 average time/residue: 0.2088 time to fit residues: 54.5186 Evaluate side-chains 203 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 193 time to evaluate : 0.850 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0757 time to fit residues: 2.5173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.0040 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 0.2980 chunk 85 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 7344 Z= 0.191 Angle : 0.543 8.697 9962 Z= 0.281 Chirality : 0.042 0.154 1143 Planarity : 0.004 0.056 1261 Dihedral : 5.688 99.476 998 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.29), residues: 905 helix: 1.73 (0.27), residues: 390 sheet: -0.70 (0.33), residues: 202 loop : 0.43 (0.38), residues: 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 190 time to evaluate : 0.878 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 192 average time/residue: 0.2021 time to fit residues: 51.4750 Evaluate side-chains 193 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 189 time to evaluate : 0.826 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0835 time to fit residues: 1.8217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 58 optimal weight: 0.0060 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 7344 Z= 0.207 Angle : 0.550 9.098 9962 Z= 0.282 Chirality : 0.042 0.143 1143 Planarity : 0.004 0.055 1261 Dihedral : 5.546 93.044 998 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 1.56 % 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: 1.06 (0.29), residues: 905 helix: 1.83 (0.27), residues: 389 sheet: -0.69 (0.33), residues: 206 loop : 0.45 (0.39), residues: 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 188 time to evaluate : 0.873 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 193 average time/residue: 0.2187 time to fit residues: 54.7637 Evaluate side-chains 190 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 180 time to evaluate : 0.853 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0805 time to fit residues: 2.6161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 7344 Z= 0.291 Angle : 0.590 9.474 9962 Z= 0.303 Chirality : 0.044 0.158 1143 Planarity : 0.004 0.055 1261 Dihedral : 5.627 91.208 998 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.29), residues: 905 helix: 1.62 (0.27), residues: 395 sheet: -0.84 (0.33), residues: 197 loop : 0.27 (0.38), residues: 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 197 time to evaluate : 0.800 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 202 average time/residue: 0.2163 time to fit residues: 56.5719 Evaluate side-chains 202 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 195 time to evaluate : 0.797 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0755 time to fit residues: 2.0439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.0070 chunk 81 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 65 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7344 Z= 0.195 Angle : 0.567 9.339 9962 Z= 0.291 Chirality : 0.042 0.158 1143 Planarity : 0.004 0.054 1261 Dihedral : 5.417 84.878 998 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.29), residues: 905 helix: 1.70 (0.27), residues: 397 sheet: -0.72 (0.33), residues: 202 loop : 0.19 (0.39), residues: 306 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 0.725 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 190 average time/residue: 0.1961 time to fit residues: 48.9187 Evaluate side-chains 182 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.728 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.142457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.121406 restraints weight = 9548.249| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.18 r_work: 0.3514 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.3483 rms_B_bonded: 1.99 restraints_weight: 0.1250 r_work: 0.3466 rms_B_bonded: 2.08 restraints_weight: 0.0625 r_work: 0.3449 rms_B_bonded: 2.22 restraints_weight: 0.0312 r_work: 0.3430 rms_B_bonded: 2.39 restraints_weight: 0.0156 r_work: 0.3409 rms_B_bonded: 2.61 restraints_weight: 0.0078 r_work: 0.3386 rms_B_bonded: 2.87 restraints_weight: 0.0039 r_work: 0.3361 rms_B_bonded: 3.18 restraints_weight: 0.0020 r_work: 0.3333 rms_B_bonded: 3.54 restraints_weight: 0.0010 r_work: 0.3302 rms_B_bonded: 3.95 restraints_weight: 0.0005 r_work: 0.3268 rms_B_bonded: 4.44 restraints_weight: 0.0002 r_work: 0.3230 rms_B_bonded: 5.00 restraints_weight: 0.0001 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7344 Z= 0.232 Angle : 0.591 9.345 9962 Z= 0.303 Chirality : 0.043 0.167 1143 Planarity : 0.004 0.054 1261 Dihedral : 5.421 82.390 998 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.29), residues: 905 helix: 1.64 (0.27), residues: 397 sheet: -0.77 (0.32), residues: 202 loop : 0.18 (0.38), residues: 306 =============================================================================== Job complete usr+sys time: 1882.88 seconds wall clock time: 34 minutes 43.97 seconds (2083.97 seconds total)