Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 16:01:58 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eib_31145/12_2021/7eib_31145.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eib_31145/12_2021/7eib_31145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eib_31145/12_2021/7eib_31145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eib_31145/12_2021/7eib_31145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eib_31145/12_2021/7eib_31145.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eib_31145/12_2021/7eib_31145.pdb" } resolution = 3.0 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model 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 ARG 38": "NH1" <-> "NH2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 137": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 151": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "D PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 14": "OE1" <-> "OE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B GLU 357": "OE1" <-> "OE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "E GLU 42": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 7204 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2419 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Chain: "D" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 5} Chain: "B" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1880 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 2478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2478 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 91 Chain: "E" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 4.28, per 1000 atoms: 0.59 Number of scatterers: 7204 At special positions: 0 Unit cell: (91.8, 82.08, 125.28, 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 37 16.00 O 1286 8.00 N 1253 7.00 C 4628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 189 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo 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: 3.07 Conformation dependent library (CDL) restraints added in 1.2 seconds 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1762 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 9 sheets defined 48.9% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 30 through 64 removed outlier: 3.592A pdb=" N ASP A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Proline residue: A 41 - end of helix Processing helix chain 'A' and resid 70 through 89 removed outlier: 3.505A pdb=" N TYR A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.829A pdb=" N TRP A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 141 removed outlier: 3.795A pdb=" N ASN A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 149 through 168 removed outlier: 3.670A pdb=" N GLN A 153 " --> pdb=" O GLN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 175 Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.672A pdb=" N PHE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 239 removed outlier: 4.013A pdb=" N THR A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 278 removed outlier: 3.757A pdb=" N VAL A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Proline residue: A 265 - end of helix Processing helix chain 'A' and resid 283 through 302 removed outlier: 3.717A pdb=" N GLN A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 removed outlier: 3.982A pdb=" N SER A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 316 through 325 Processing helix chain 'B' and resid 6 through 33 removed outlier: 3.842A pdb=" N GLN B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 29 " --> pdb=" O LYS B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 57 Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.596A pdb=" N ASN B 216 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP B 217 " --> pdb=" O CYS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 246 removed outlier: 3.903A pdb=" N GLN B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 250 removed outlier: 3.661A pdb=" N ARG B 250 " --> pdb=" O ARG B 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 250' Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 298 through 320 removed outlier: 3.893A pdb=" N SER B 319 " --> pdb=" O ILE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 358 Processing helix chain 'C' and resid 4 through 26 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'E' and resid 12 through 24 removed outlier: 3.562A pdb=" N GLU E 17 " --> pdb=" O ARG E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 180 Processing sheet with id=AA2, first strand: chain 'B' and resid 184 through 191 removed outlier: 6.197A pdb=" N LEU B 34 " --> pdb=" O HIS B 197 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N PHE B 199 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU B 36 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N VAL B 201 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N LEU B 38 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE B 222 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU B 39 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ASP B 226 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE B 221 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE B 257 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE B 223 " --> pdb=" O PHE B 257 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN B 259 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL B 225 " --> pdb=" O ASN B 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 51 Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.571A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.902A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 153 removed outlier: 3.749A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.739A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.917A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.849A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1170 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: 2.37 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1165 1.31 - 1.44: 2056 1.44 - 1.57: 4097 1.57 - 1.69: 0 1.69 - 1.82: 48 Bond restraints: 7366 Sorted by residual: bond pdb=" CA PRO D 4 " pdb=" C PRO D 4 " ideal model delta sigma weight residual 1.520 1.458 0.062 1.24e-02 6.50e+03 2.48e+01 bond pdb=" N CYS B 332 " pdb=" CA CYS B 332 " ideal model delta sigma weight residual 1.454 1.402 0.052 1.23e-02 6.61e+03 1.78e+01 bond pdb=" C PRO D 8 " pdb=" O PRO D 8 " ideal model delta sigma weight residual 1.238 1.186 0.052 1.36e-02 5.41e+03 1.44e+01 bond pdb=" C PHE D 6 " pdb=" O PHE D 6 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.28e-02 6.10e+03 1.42e+01 bond pdb=" CA SER D 7 " pdb=" CB SER D 7 " ideal model delta sigma weight residual 1.533 1.477 0.056 1.49e-02 4.50e+03 1.40e+01 ... (remaining 7361 not shown) Histogram of bond angle deviations from ideal: 98.79 - 106.67: 181 106.67 - 114.56: 4285 114.56 - 122.45: 4610 122.45 - 130.34: 903 130.34 - 138.22: 42 Bond angle restraints: 10021 Sorted by residual: angle pdb=" C PRO D 3 " pdb=" N PRO D 4 " pdb=" CA PRO D 4 " ideal model delta sigma weight residual 120.14 109.58 10.56 1.06e+00 8.90e-01 9.92e+01 angle pdb=" CA PRO B 295 " pdb=" N PRO B 295 " pdb=" CD PRO B 295 " ideal model delta sigma weight residual 112.00 100.07 11.93 1.40e+00 5.10e-01 7.26e+01 angle pdb=" N VAL B 334 " pdb=" CA VAL B 334 " pdb=" C VAL B 334 " ideal model delta sigma weight residual 110.62 115.36 -4.74 1.02e+00 9.61e-01 2.16e+01 angle pdb=" CA PRO D 8 " pdb=" C PRO D 8 " pdb=" O PRO D 8 " ideal model delta sigma weight residual 120.03 113.31 6.72 1.45e+00 4.76e-01 2.14e+01 angle pdb=" C VAL B 334 " pdb=" CA VAL B 334 " pdb=" CB VAL B 334 " ideal model delta sigma weight residual 112.14 106.19 5.95 1.35e+00 5.49e-01 1.94e+01 ... (remaining 10016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 3991 16.96 - 33.92: 287 33.92 - 50.88: 34 50.88 - 67.84: 15 67.84 - 84.80: 7 Dihedral angle restraints: 4334 sinusoidal: 1628 harmonic: 2706 Sorted by residual: dihedral pdb=" CA ILE A 97 " pdb=" C ILE A 97 " pdb=" N TRP A 98 " pdb=" CA TRP A 98 " ideal model delta harmonic sigma weight residual 180.00 150.12 29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA LEU A 326 " pdb=" C LEU A 326 " pdb=" N TYR A 327 " pdb=" CA TYR A 327 " ideal model delta harmonic sigma weight residual 180.00 150.71 29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA ASN C 295 " pdb=" C ASN C 295 " pdb=" N VAL C 296 " pdb=" CA VAL C 296 " ideal model delta harmonic sigma weight residual -180.00 -152.46 -27.54 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 4331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 930 0.063 - 0.125: 196 0.125 - 0.188: 23 0.188 - 0.251: 2 0.251 - 0.313: 1 Chirality restraints: 1152 Sorted by residual: chirality pdb=" CA PRO D 8 " pdb=" N PRO D 8 " pdb=" C PRO D 8 " pdb=" CB PRO D 8 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA PHE D 9 " pdb=" N PHE D 9 " pdb=" C PHE D 9 " pdb=" CB PHE D 9 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB VAL A 128 " pdb=" CA VAL A 128 " pdb=" CG1 VAL A 128 " pdb=" CG2 VAL A 128 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 1149 not shown) Planarity restraints: 1276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 326 " 0.059 2.00e-02 2.50e+03 1.17e-01 1.36e+02 pdb=" C LEU A 326 " -0.202 2.00e-02 2.50e+03 pdb=" O LEU A 326 " 0.077 2.00e-02 2.50e+03 pdb=" N TYR A 327 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 206 " 0.024 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" C LEU A 206 " -0.081 2.00e-02 2.50e+03 pdb=" O LEU A 206 " 0.030 2.00e-02 2.50e+03 pdb=" N ASN A 207 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 208 " -0.022 2.00e-02 2.50e+03 4.39e-02 1.92e+01 pdb=" C ILE A 208 " 0.076 2.00e-02 2.50e+03 pdb=" O ILE A 208 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU A 209 " -0.026 2.00e-02 2.50e+03 ... (remaining 1273 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 2122 2.82 - 3.34: 7243 3.34 - 3.86: 12557 3.86 - 4.38: 14516 4.38 - 4.90: 24893 Nonbonded interactions: 61331 Sorted by model distance: nonbonded pdb=" OD2 ASP A 134 " pdb=" OH TYR B 358 " model vdw 2.306 2.440 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.306 2.440 nonbonded pdb=" NH2 ARG B 208 " pdb=" OD1 ASP B 239 " model vdw 2.309 2.520 nonbonded pdb=" NH1 ARG C 251 " pdb=" OE1 GLU C 260 " model vdw 2.316 2.520 nonbonded pdb=" NH1 ARG A 176 " pdb=" O GLY D 5 " model vdw 2.333 2.520 ... (remaining 61326 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 37 5.16 5 C 4628 2.51 5 N 1253 2.21 5 O 1286 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 Write .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: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.250 Check model and map are aligned: 0.100 Convert atoms to be neutral: 0.060 Process input model: 22.320 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.760 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 37.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 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 : 0.005 0.071 7366 Z= 0.348 Angle : 0.855 13.224 10021 Z= 0.530 Chirality : 0.051 0.313 1152 Planarity : 0.010 0.117 1276 Dihedral : 12.654 84.801 2569 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 0.27 % 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: -0.34 (0.26), residues: 914 helix: -0.34 (0.22), residues: 412 sheet: 0.23 (0.35), residues: 195 loop : -0.05 (0.38), residues: 307 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 205 time to evaluate : 0.839 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 207 average time/residue: 0.9654 time to fit residues: 212.5064 Evaluate side-chains 172 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 0.830 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.1426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 GLN B 246 ASN B 359 ASN C 110 ASN C 119 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 7366 Z= 0.300 Angle : 0.649 7.452 10021 Z= 0.349 Chirality : 0.046 0.201 1152 Planarity : 0.005 0.074 1276 Dihedral : 5.679 30.525 1000 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer Outliers : 2.42 % 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: 1.14 (0.28), residues: 914 helix: 1.42 (0.25), residues: 408 sheet: 0.36 (0.36), residues: 182 loop : 0.31 (0.37), residues: 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 178 time to evaluate : 0.836 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 181 average time/residue: 1.0349 time to fit residues: 198.6560 Evaluate side-chains 169 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 0.836 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 3 residues processed: 7 average time/residue: 0.5958 time to fit residues: 5.6777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 102 ASN ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 259 ASN B 359 ASN C 230 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 7366 Z= 0.224 Angle : 0.571 5.355 10021 Z= 0.308 Chirality : 0.043 0.161 1152 Planarity : 0.005 0.076 1276 Dihedral : 5.202 27.440 1000 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer Outliers : 2.69 % 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: 1.27 (0.28), residues: 914 helix: 1.72 (0.26), residues: 414 sheet: 0.19 (0.36), residues: 183 loop : 0.22 (0.38), residues: 317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 0.864 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 169 average time/residue: 1.0854 time to fit residues: 194.3286 Evaluate side-chains 170 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 157 time to evaluate : 0.831 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 6 residues processed: 8 average time/residue: 0.1112 time to fit residues: 2.5474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 ASN B 246 ASN B 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 7366 Z= 0.289 Angle : 0.581 6.195 10021 Z= 0.312 Chirality : 0.043 0.166 1152 Planarity : 0.005 0.073 1276 Dihedral : 5.069 27.873 1000 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 3.76 % 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: 1.27 (0.29), residues: 914 helix: 1.89 (0.26), residues: 406 sheet: -0.17 (0.35), residues: 197 loop : 0.28 (0.39), residues: 311 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 168 time to evaluate : 0.804 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 176 average time/residue: 1.0391 time to fit residues: 193.9247 Evaluate side-chains 179 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 162 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 6 residues processed: 13 average time/residue: 0.1709 time to fit residues: 4.1154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN B 246 ASN B 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 7366 Z= 0.263 Angle : 0.567 6.490 10021 Z= 0.305 Chirality : 0.043 0.156 1152 Planarity : 0.005 0.077 1276 Dihedral : 4.970 29.624 1000 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer Outliers : 3.49 % 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: 1.12 (0.28), residues: 914 helix: 1.84 (0.26), residues: 412 sheet: -0.33 (0.35), residues: 185 loop : 0.09 (0.37), residues: 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 0.782 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 167 average time/residue: 1.0919 time to fit residues: 193.1042 Evaluate side-chains 176 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 160 time to evaluate : 0.751 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 6 residues processed: 13 average time/residue: 0.2072 time to fit residues: 4.4354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 GLN B 28 GLN B 216 ASN B 246 ASN B 259 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 7366 Z= 0.264 Angle : 0.557 6.070 10021 Z= 0.298 Chirality : 0.043 0.164 1152 Planarity : 0.005 0.076 1276 Dihedral : 4.897 29.824 1000 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 3.49 % 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: 1.10 (0.28), residues: 914 helix: 1.90 (0.26), residues: 412 sheet: -0.44 (0.35), residues: 188 loop : 0.04 (0.37), residues: 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 161 time to evaluate : 0.826 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 18 residues processed: 172 average time/residue: 1.1161 time to fit residues: 203.3451 Evaluate side-chains 172 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 12 residues processed: 9 average time/residue: 0.1006 time to fit residues: 2.6537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 73 optimal weight: 0.0370 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 7366 Z= 0.238 Angle : 0.556 6.470 10021 Z= 0.295 Chirality : 0.042 0.218 1152 Planarity : 0.005 0.082 1276 Dihedral : 4.815 29.436 1000 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 3.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.29), residues: 914 helix: 1.95 (0.26), residues: 412 sheet: -0.45 (0.35), residues: 185 loop : 0.02 (0.37), residues: 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 161 time to evaluate : 0.742 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 17 residues processed: 172 average time/residue: 1.1066 time to fit residues: 201.7524 Evaluate side-chains 170 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 0.887 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 8 average time/residue: 0.3779 time to fit residues: 4.9617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 chunk 78 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 7366 Z= 0.245 Angle : 0.566 6.637 10021 Z= 0.303 Chirality : 0.043 0.180 1152 Planarity : 0.006 0.085 1276 Dihedral : 4.786 29.511 1000 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 2.96 % 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: 1.21 (0.28), residues: 914 helix: 2.01 (0.26), residues: 413 sheet: -0.28 (0.37), residues: 171 loop : -0.06 (0.36), residues: 330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 157 time to evaluate : 0.855 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 168 average time/residue: 1.1204 time to fit residues: 199.5754 Evaluate side-chains 174 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 0.799 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 8 residues processed: 9 average time/residue: 0.1083 time to fit residues: 2.6039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 0.3980 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 52 optimal weight: 30.0000 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 7366 Z= 0.286 Angle : 0.588 6.992 10021 Z= 0.314 Chirality : 0.043 0.176 1152 Planarity : 0.006 0.089 1276 Dihedral : 4.822 30.165 1000 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 2.69 % 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: 1.18 (0.28), residues: 914 helix: 1.99 (0.26), residues: 413 sheet: -0.25 (0.37), residues: 174 loop : -0.09 (0.36), residues: 327 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 161 time to evaluate : 0.827 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 168 average time/residue: 1.1420 time to fit residues: 202.9666 Evaluate side-chains 172 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 158 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 7 residues processed: 8 average time/residue: 0.1271 time to fit residues: 2.7158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.9980 chunk 59 optimal weight: 0.3980 chunk 89 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 GLN A 153 GLN ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 7366 Z= 0.231 Angle : 0.563 7.330 10021 Z= 0.302 Chirality : 0.043 0.161 1152 Planarity : 0.005 0.091 1276 Dihedral : 4.726 28.914 1000 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 1.61 % 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: 1.22 (0.29), residues: 914 helix: 2.09 (0.26), residues: 413 sheet: -0.35 (0.36), residues: 181 loop : -0.09 (0.37), residues: 320 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 163 time to evaluate : 0.796 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 169 average time/residue: 1.1667 time to fit residues: 208.1807 Evaluate side-chains 177 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 167 time to evaluate : 0.825 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 4 average time/residue: 0.0916 time to fit residues: 1.7655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.142621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.123399 restraints weight = 9969.136| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.09 r_work: 0.3532 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work: 0.3502 rms_B_bonded: 1.93 restraints_weight: 0.1250 r_work: 0.3485 rms_B_bonded: 2.05 restraints_weight: 0.0625 r_work: 0.3467 rms_B_bonded: 2.22 restraints_weight: 0.0312 r_work: 0.3447 rms_B_bonded: 2.44 restraints_weight: 0.0156 r_work: 0.3425 rms_B_bonded: 2.71 restraints_weight: 0.0078 r_work: 0.3399 rms_B_bonded: 3.04 restraints_weight: 0.0039 r_work: 0.3371 rms_B_bonded: 3.44 restraints_weight: 0.0020 r_work: 0.3339 rms_B_bonded: 3.91 restraints_weight: 0.0010 r_work: 0.3303 rms_B_bonded: 4.46 restraints_weight: 0.0005 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 7366 Z= 0.260 Angle : 0.581 7.567 10021 Z= 0.309 Chirality : 0.043 0.167 1152 Planarity : 0.006 0.089 1276 Dihedral : 4.768 29.208 1000 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 1.48 % 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: 1.18 (0.29), residues: 914 helix: 2.05 (0.26), residues: 413 sheet: -0.34 (0.36), residues: 183 loop : -0.11 (0.37), residues: 318 =============================================================================== Job complete usr+sys time: 3204.90 seconds wall clock time: 57 minutes 23.41 seconds (3443.41 seconds total)