Starting phenix.real_space_refine (version: dev) on Sat Feb 18 04:57:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eib_31145/02_2023/7eib_31145.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eib_31145/02_2023/7eib_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_31145/02_2023/7eib_31145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eib_31145/02_2023/7eib_31145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eib_31145/02_2023/7eib_31145.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eib_31145/02_2023/7eib_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 Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 4.57, per 1000 atoms: 0.63 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 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: 2.99 Conformation dependent library (CDL) restraints added in 1.1 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: 0.37 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: 2.07 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: 1.19 - 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 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: 0.520 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: 2.480 Check model and map are aligned: 0.110 Process input model: 22.950 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 0.789 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 207 average time/residue: 1.1164 time to fit residues: 244.0123 Evaluate side-chains 172 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 0.793 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.1242 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.5980 chunk 70 optimal weight: 0.8980 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: 0.8380 ------------------------------------------------------------------------------- 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** A 308 ASN 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 7366 Z= 0.268 Angle : 0.633 7.192 10021 Z= 0.340 Chirality : 0.045 0.197 1152 Planarity : 0.005 0.043 1276 Dihedral : 5.622 30.455 1000 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer Outliers : 2.28 % 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: 1.41 (0.25), residues: 410 sheet: 0.33 (0.36), residues: 191 loop : 0.31 (0.38), residues: 313 *********************** 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: 17 poor density : 179 time to evaluate : 0.934 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 182 average time/residue: 1.2123 time to fit residues: 232.8151 Evaluate side-chains 170 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 161 time to evaluate : 0.846 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 3 residues processed: 7 average time/residue: 0.6392 time to fit residues: 6.0533 ------------------------------------------------------------------------------- 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: 4.9990 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** A 308 ASN B 246 ASN B 259 ASN B 359 ASN C 230 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 7366 Z= 0.323 Angle : 0.612 5.653 10021 Z= 0.329 Chirality : 0.045 0.189 1152 Planarity : 0.005 0.045 1276 Dihedral : 5.320 28.085 1000 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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: 1.21 (0.28), residues: 914 helix: 1.68 (0.25), residues: 408 sheet: 0.07 (0.36), residues: 183 loop : 0.27 (0.37), residues: 323 *********************** 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 195 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 0.769 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 180 average time/residue: 1.2572 time to fit residues: 238.2071 Evaluate side-chains 170 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 0.852 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 6 residues processed: 8 average time/residue: 0.2466 time to fit residues: 3.6225 ------------------------------------------------------------------------------- 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: 0.0670 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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** A 308 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 7366 Z= 0.237 Angle : 0.572 6.991 10021 Z= 0.305 Chirality : 0.043 0.210 1152 Planarity : 0.005 0.041 1276 Dihedral : 5.059 27.225 1000 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 4.03 % 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: 1.19 (0.28), residues: 914 helix: 1.79 (0.26), residues: 412 sheet: -0.06 (0.37), residues: 171 loop : 0.10 (0.36), residues: 331 *********************** 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 195 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 165 time to evaluate : 0.768 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 174 average time/residue: 1.2263 time to fit residues: 225.0024 Evaluate side-chains 179 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 161 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 7 residues processed: 13 average time/residue: 0.2553 time to fit residues: 5.3177 ------------------------------------------------------------------------------- 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: 0.8980 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 308 ASN ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 GLN ** 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: 0.7508 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 7366 Z= 0.305 Angle : 0.575 5.597 10021 Z= 0.309 Chirality : 0.044 0.167 1152 Planarity : 0.005 0.070 1276 Dihedral : 5.060 30.423 1000 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 4.03 % 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: 1.19 (0.28), residues: 914 helix: 1.85 (0.26), residues: 406 sheet: -0.17 (0.37), residues: 172 loop : 0.14 (0.36), residues: 336 *********************** 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 191 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 161 time to evaluate : 1.004 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 173 average time/residue: 1.2418 time to fit residues: 226.0731 Evaluate side-chains 173 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 7 residues processed: 11 average time/residue: 0.0941 time to fit residues: 2.8001 ------------------------------------------------------------------------------- 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: 0.6980 chunk 87 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.0040 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 ** 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 308 ASN A 329 GLN ** B 28 GLN ** 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: 0.7481 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 7366 Z= 0.216 Angle : 0.536 5.444 10021 Z= 0.286 Chirality : 0.042 0.167 1152 Planarity : 0.004 0.058 1276 Dihedral : 4.855 29.314 1000 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 3.36 % 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: 1.17 (0.28), residues: 914 helix: 1.91 (0.26), residues: 412 sheet: -0.27 (0.37), residues: 171 loop : 0.04 (0.36), residues: 331 *********************** 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 185 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 0.914 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 171 average time/residue: 1.2502 time to fit residues: 225.2517 Evaluate side-chains 167 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 0.866 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 7 average time/residue: 0.1093 time to fit residues: 2.3728 ------------------------------------------------------------------------------- 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: 0.9990 chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 0.0470 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.7882 ------------------------------------------------------------------------------- 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 ** 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 28 GLN ** 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: 0.7491 moved from start: 0.3206 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= 0.255 Angle : 0.554 5.434 10021 Z= 0.296 Chirality : 0.042 0.177 1152 Planarity : 0.004 0.055 1276 Dihedral : 4.823 29.720 1000 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 3.36 % 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: 1.92 (0.26), residues: 413 sheet: -0.41 (0.38), residues: 166 loop : -0.01 (0.36), residues: 335 *********************** 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 181 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 0.950 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 21 residues processed: 166 average time/residue: 1.2708 time to fit residues: 222.0040 Evaluate side-chains 167 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 146 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 12 residues processed: 11 average time/residue: 0.2566 time to fit residues: 4.6647 ------------------------------------------------------------------------------- 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: 0.2980 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.0570 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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** B 28 GLN B 246 ASN B 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 7366 Z= 0.204 Angle : 0.547 5.505 10021 Z= 0.292 Chirality : 0.042 0.217 1152 Planarity : 0.004 0.052 1276 Dihedral : 4.708 29.108 1000 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.42 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: 1.18 (0.28), residues: 914 helix: 1.97 (0.26), residues: 413 sheet: -0.28 (0.38), residues: 167 loop : -0.05 (0.36), residues: 334 *********************** 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 177 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 0.862 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 167 average time/residue: 1.3128 time to fit residues: 230.6735 Evaluate side-chains 172 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 157 time to evaluate : 0.933 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 7 average time/residue: 0.1021 time to fit residues: 2.2379 ------------------------------------------------------------------------------- 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: 0.6980 chunk 83 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 0.0570 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 overall best weight: 0.8100 ------------------------------------------------------------------------------- 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: 0.7489 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 7366 Z= 0.266 Angle : 0.574 5.467 10021 Z= 0.307 Chirality : 0.043 0.182 1152 Planarity : 0.004 0.052 1276 Dihedral : 4.761 29.916 1000 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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: 1.13 (0.28), residues: 914 helix: 1.94 (0.26), residues: 413 sheet: -0.33 (0.38), residues: 167 loop : -0.08 (0.36), residues: 334 *********************** 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 : 0.770 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 173 average time/residue: 1.2396 time to fit residues: 226.0309 Evaluate side-chains 170 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 4 average time/residue: 0.1317 time to fit residues: 2.0822 ------------------------------------------------------------------------------- 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: 0.8980 chunk 59 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 71 optimal weight: 0.0040 chunk 7 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 0.0980 chunk 21 optimal weight: 0.1980 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 C 88 ASN C 91 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7366 Z= 0.183 Angle : 0.537 5.508 10021 Z= 0.289 Chirality : 0.041 0.165 1152 Planarity : 0.005 0.113 1276 Dihedral : 4.640 28.561 1000 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 2.28 % 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: 1.23 (0.29), residues: 914 helix: 2.05 (0.26), residues: 413 sheet: -0.38 (0.38), residues: 169 loop : -0.01 (0.36), residues: 332 ********************** 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: 17 poor density : 158 time to evaluate : 0.867 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 168 average time/residue: 1.2171 time to fit residues: 215.6071 Evaluate side-chains 165 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 0.823 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 4 average time/residue: 0.4193 time to fit residues: 3.0856 ------------------------------------------------------------------------------- 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: 0.6980 chunk 19 optimal weight: 0.8980 chunk 71 optimal weight: 0.0470 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 C 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.141424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.122586 restraints weight = 9605.772| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.09 r_work: 0.3366 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 7366 Z= 0.225 Angle : 0.570 7.000 10021 Z= 0.304 Chirality : 0.042 0.162 1152 Planarity : 0.004 0.049 1276 Dihedral : 4.604 29.440 1000 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 1.88 % 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 (0.29), residues: 914 helix: 2.05 (0.26), residues: 413 sheet: -0.40 (0.39), residues: 167 loop : -0.04 (0.36), residues: 334 =============================================================================== Job complete usr+sys time: 3654.83 seconds wall clock time: 65 minutes 42.70 seconds (3942.70 seconds total)