Starting phenix.real_space_refine on Wed Feb 14 00:45:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioc_35615/02_2024/8ioc_35615.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioc_35615/02_2024/8ioc_35615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioc_35615/02_2024/8ioc_35615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioc_35615/02_2024/8ioc_35615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioc_35615/02_2024/8ioc_35615.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioc_35615/02_2024/8ioc_35615.pdb" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 67 5.16 5 C 5219 2.51 5 N 1422 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8223 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1950 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "R" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2158 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 8, 'TRANS': 263} Chain breaks: 1 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "L" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 107 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.37, per 1000 atoms: 0.65 Number of scatterers: 8223 At special positions: 0 Unit cell: (84.609, 98.532, 128.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 67 16.00 O 1514 8.00 N 1422 7.00 C 5219 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 35 " - pdb=" SG CYS R 276 " distance=2.03 Simple disulfide: pdb=" SG CYS R 268 " - pdb=" SG CYS R 274 " distance=2.02 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 1.4 seconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 10 sheets defined 40.4% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.867A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.802A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.674A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.587A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.558A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.613A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 31 through 35' Processing helix chain 'R' and resid 41 through 65 removed outlier: 4.148A pdb=" N PHE R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 103 removed outlier: 3.702A pdb=" N PHE R 75 " --> pdb=" O SER R 71 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE R 76 " --> pdb=" O PRO R 72 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU R 77 " --> pdb=" O MET R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 148 removed outlier: 3.730A pdb=" N ILE R 113 " --> pdb=" O GLU R 109 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN R 114 " --> pdb=" O ASP R 110 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS R 115 " --> pdb=" O GLN R 111 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE R 119 " --> pdb=" O HIS R 115 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE R 120 " --> pdb=" O MET R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 155 Processing helix chain 'R' and resid 157 through 182 removed outlier: 3.505A pdb=" N TYR R 182 " --> pdb=" O VAL R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 223 removed outlier: 4.473A pdb=" N ILE R 189 " --> pdb=" O SER R 185 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL R 190 " --> pdb=" O LYS R 186 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET R 203 " --> pdb=" O MET R 199 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA R 223 " --> pdb=" O LYS R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 235 through 268 removed outlier: 3.932A pdb=" N PHE R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) Proline residue: R 257 - end of helix Processing helix chain 'R' and resid 271 through 279 removed outlier: 4.120A pdb=" N CYS R 276 " --> pdb=" O PRO R 272 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N TYR R 277 " --> pdb=" O TYR R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 299 removed outlier: 3.889A pdb=" N TYR R 284 " --> pdb=" O HIS R 280 " (cutoff:3.500A) Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 303 through 313 Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.771A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 39 through 45 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.523A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.828A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.422A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.601A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.810A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.817A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.877A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.911A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.030A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.927A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP N 73 " --> pdb=" O THR N 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.695A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1167 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: 2.15 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1413 1.32 - 1.45: 2263 1.45 - 1.57: 4616 1.57 - 1.69: 0 1.69 - 1.82: 97 Bond restraints: 8389 Sorted by residual: bond pdb=" CA ARG L 7 " pdb=" C ARG L 7 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.24e-02 6.50e+03 1.40e+01 bond pdb=" C HIS L 5 " pdb=" O HIS L 5 " ideal model delta sigma weight residual 1.236 1.197 0.039 1.17e-02 7.31e+03 1.08e+01 bond pdb=" N ARG L 7 " pdb=" CA ARG L 7 " ideal model delta sigma weight residual 1.455 1.419 0.036 1.32e-02 5.74e+03 7.51e+00 bond pdb=" CA HIS L 5 " pdb=" CB HIS L 5 " ideal model delta sigma weight residual 1.527 1.493 0.034 1.44e-02 4.82e+03 5.45e+00 bond pdb=" C HIS L 5 " pdb=" N PHE L 6 " ideal model delta sigma weight residual 1.327 1.303 0.024 1.06e-02 8.90e+03 5.04e+00 ... (remaining 8384 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.69: 121 105.69 - 113.23: 4647 113.23 - 120.77: 3905 120.77 - 128.30: 2625 128.30 - 135.84: 62 Bond angle restraints: 11360 Sorted by residual: angle pdb=" C PHE L 6 " pdb=" CA PHE L 6 " pdb=" CB PHE L 6 " ideal model delta sigma weight residual 116.34 110.74 5.60 1.40e+00 5.10e-01 1.60e+01 angle pdb=" N ARG L 7 " pdb=" CA ARG L 7 " pdb=" C ARG L 7 " ideal model delta sigma weight residual 108.74 113.59 -4.85 1.38e+00 5.25e-01 1.23e+01 angle pdb=" N ASN G 24 " pdb=" CA ASN G 24 " pdb=" C ASN G 24 " ideal model delta sigma weight residual 114.56 110.57 3.99 1.27e+00 6.20e-01 9.85e+00 angle pdb=" C LYS N 33 " pdb=" N MET N 34 " pdb=" CA MET N 34 " ideal model delta sigma weight residual 122.59 118.15 4.44 1.57e+00 4.06e-01 8.00e+00 angle pdb=" CB MET R 97 " pdb=" CG MET R 97 " pdb=" SD MET R 97 " ideal model delta sigma weight residual 112.70 104.34 8.36 3.00e+00 1.11e-01 7.77e+00 ... (remaining 11355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 4498 17.49 - 34.97: 413 34.97 - 52.46: 79 52.46 - 69.94: 12 69.94 - 87.42: 8 Dihedral angle restraints: 5010 sinusoidal: 1972 harmonic: 3038 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 58.72 34.28 1 1.00e+01 1.00e-02 1.67e+01 dihedral pdb=" CA ASP G 36 " pdb=" C ASP G 36 " pdb=" N LEU G 37 " pdb=" CA LEU G 37 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA TYR R 182 " pdb=" C TYR R 182 " pdb=" N SER R 183 " pdb=" CA SER R 183 " ideal model delta harmonic sigma weight residual 180.00 -160.57 -19.43 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 5007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 754 0.037 - 0.074: 378 0.074 - 0.111: 116 0.111 - 0.148: 38 0.148 - 0.185: 5 Chirality restraints: 1291 Sorted by residual: chirality pdb=" CA HIS L 5 " pdb=" N HIS L 5 " pdb=" C HIS L 5 " pdb=" CB HIS L 5 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.58e-01 chirality pdb=" CA ILE B 273 " pdb=" N ILE B 273 " pdb=" C ILE B 273 " pdb=" CB ILE B 273 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA VAL L 2 " pdb=" N VAL L 2 " pdb=" C VAL L 2 " pdb=" CB VAL L 2 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 1288 not shown) Planarity restraints: 1444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 281 " 0.019 2.00e-02 2.50e+03 1.37e-02 4.69e+00 pdb=" CG TRP A 281 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 281 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 281 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 281 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 281 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 281 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA R 256 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO R 257 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO R 257 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 257 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN N 13 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO N 14 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO N 14 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO N 14 " -0.026 5.00e-02 4.00e+02 ... (remaining 1441 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 907 2.74 - 3.28: 7965 3.28 - 3.82: 13555 3.82 - 4.36: 16080 4.36 - 4.90: 28045 Nonbonded interactions: 66552 Sorted by model distance: nonbonded pdb=" NE1 TRP R 255 " pdb=" OD1 ASN R 291 " model vdw 2.197 2.520 nonbonded pdb=" NH1 ARG A 232 " pdb=" OD2 ASP N 109 " model vdw 2.227 2.520 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.228 2.520 nonbonded pdb=" OE2 GLU R 94 " pdb="CA CA R 501 " model vdw 2.243 2.510 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.244 2.440 ... (remaining 66547 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 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: 1.280 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: 5.160 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 24.780 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 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 : 0.007 0.056 8389 Z= 0.486 Angle : 0.728 10.843 11360 Z= 0.406 Chirality : 0.049 0.185 1291 Planarity : 0.005 0.049 1444 Dihedral : 14.043 87.425 3030 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.11 % Allowed : 0.55 % Favored : 99.33 % 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: -0.98 (0.25), residues: 1025 helix: 0.31 (0.26), residues: 401 sheet: -0.75 (0.32), residues: 234 loop : -1.50 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 281 HIS 0.008 0.002 HIS L 5 PHE 0.030 0.002 PHE B 235 TYR 0.027 0.002 TYR B 59 ARG 0.009 0.001 ARG R 151 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 239 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 240 average time/residue: 1.2710 time to fit residues: 323.2288 Evaluate side-chains 157 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN B 75 GLN B 91 HIS B 259 GLN ** R 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN G 44 HIS L 5 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8389 Z= 0.215 Angle : 0.645 13.330 11360 Z= 0.327 Chirality : 0.042 0.139 1291 Planarity : 0.004 0.046 1444 Dihedral : 4.924 46.607 1137 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.11 % Allowed : 13.65 % Favored : 83.24 % 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: -0.24 (0.26), residues: 1025 helix: 1.12 (0.26), residues: 398 sheet: -0.36 (0.34), residues: 227 loop : -1.31 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.003 0.001 HIS R 261 PHE 0.014 0.001 PHE R 259 TYR 0.017 0.001 TYR R 277 ARG 0.008 0.001 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 170 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.8856 (t0) cc_final: 0.8633 (t0) REVERT: G 14 LYS cc_start: 0.8789 (mmtm) cc_final: 0.8546 (mmtm) REVERT: G 28 ILE cc_start: 0.8149 (mp) cc_final: 0.7863 (mp) outliers start: 28 outliers final: 9 residues processed: 182 average time/residue: 1.1906 time to fit residues: 230.0194 Evaluate side-chains 140 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain G residue 19 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 92 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** R 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 291 ASN L 5 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8389 Z= 0.252 Angle : 0.643 13.495 11360 Z= 0.324 Chirality : 0.042 0.136 1291 Planarity : 0.004 0.044 1444 Dihedral : 4.821 48.801 1135 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.44 % Allowed : 15.32 % Favored : 80.24 % 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: 0.12 (0.26), residues: 1025 helix: 1.50 (0.27), residues: 397 sheet: -0.29 (0.33), residues: 240 loop : -1.13 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.006 0.001 HIS R 261 PHE 0.013 0.001 PHE R 310 TYR 0.017 0.001 TYR R 277 ARG 0.007 0.001 ARG R 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 153 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 MET cc_start: 0.7040 (tpt) cc_final: 0.6726 (tpp) REVERT: G 28 ILE cc_start: 0.7956 (mp) cc_final: 0.7679 (mp) REVERT: N 34 MET cc_start: 0.6599 (OUTLIER) cc_final: 0.6342 (mtt) outliers start: 40 outliers final: 13 residues processed: 174 average time/residue: 1.1705 time to fit residues: 216.6983 Evaluate side-chains 147 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 282 ASN Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 34 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 98 optimal weight: 0.0020 chunk 88 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 230 ASN ** R 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 291 ASN N 82 GLN N 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8389 Z= 0.186 Angle : 0.629 13.469 11360 Z= 0.315 Chirality : 0.042 0.292 1291 Planarity : 0.004 0.042 1444 Dihedral : 4.683 48.200 1135 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.22 % Allowed : 17.43 % Favored : 78.36 % 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: 0.30 (0.27), residues: 1025 helix: 1.63 (0.27), residues: 400 sheet: -0.15 (0.33), residues: 245 loop : -1.07 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS R 261 PHE 0.012 0.001 PHE R 259 TYR 0.024 0.001 TYR L 1 ARG 0.008 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.8864 (t0) cc_final: 0.8607 (t0) REVERT: R 116 MET cc_start: 0.5229 (OUTLIER) cc_final: 0.4954 (tpp) REVERT: G 28 ILE cc_start: 0.7957 (mp) cc_final: 0.7680 (mp) REVERT: N 34 MET cc_start: 0.6661 (OUTLIER) cc_final: 0.6363 (mtt) REVERT: N 83 MET cc_start: 0.6935 (mmp) cc_final: 0.6733 (mmp) REVERT: N 98 ARG cc_start: 0.8692 (ttp80) cc_final: 0.8423 (ttp80) outliers start: 38 outliers final: 13 residues processed: 168 average time/residue: 1.2002 time to fit residues: 214.3572 Evaluate side-chains 148 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 116 MET Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 282 ASN Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 34 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 68 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** R 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8389 Z= 0.198 Angle : 0.633 12.504 11360 Z= 0.315 Chirality : 0.042 0.182 1291 Planarity : 0.004 0.043 1444 Dihedral : 4.602 48.288 1135 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.44 % Allowed : 20.09 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.27), residues: 1025 helix: 1.73 (0.26), residues: 404 sheet: -0.17 (0.32), residues: 250 loop : -1.09 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS R 261 PHE 0.012 0.001 PHE R 310 TYR 0.022 0.001 TYR L 1 ARG 0.007 0.000 ARG R 151 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 145 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 116 MET cc_start: 0.5309 (OUTLIER) cc_final: 0.5003 (tpp) REVERT: G 28 ILE cc_start: 0.8042 (mp) cc_final: 0.7801 (mp) REVERT: N 34 MET cc_start: 0.6694 (OUTLIER) cc_final: 0.6389 (mtt) REVERT: N 98 ARG cc_start: 0.8715 (ttp80) cc_final: 0.8494 (ttp80) outliers start: 31 outliers final: 15 residues processed: 158 average time/residue: 1.1765 time to fit residues: 197.6986 Evaluate side-chains 155 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 116 MET Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 282 ASN Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 34 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 81 optimal weight: 0.0020 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 75 GLN ** R 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8389 Z= 0.220 Angle : 0.669 13.939 11360 Z= 0.330 Chirality : 0.042 0.136 1291 Planarity : 0.004 0.043 1444 Dihedral : 4.620 48.313 1135 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.77 % Allowed : 20.75 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.27), residues: 1025 helix: 1.77 (0.27), residues: 403 sheet: -0.20 (0.32), residues: 250 loop : -1.06 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 47 HIS 0.003 0.001 HIS R 261 PHE 0.014 0.001 PHE R 45 TYR 0.022 0.001 TYR L 1 ARG 0.008 0.001 ARG R 151 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 0.947 Fit side-chains REVERT: G 28 ILE cc_start: 0.8089 (mp) cc_final: 0.7849 (mp) REVERT: N 34 MET cc_start: 0.6681 (OUTLIER) cc_final: 0.6404 (mtt) REVERT: N 98 ARG cc_start: 0.8738 (ttp80) cc_final: 0.8514 (ttp80) outliers start: 34 outliers final: 13 residues processed: 157 average time/residue: 1.1500 time to fit residues: 192.2678 Evaluate side-chains 147 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 282 ASN Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 34 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 59 GLN B 75 GLN ** R 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8389 Z= 0.205 Angle : 0.672 12.997 11360 Z= 0.333 Chirality : 0.042 0.137 1291 Planarity : 0.003 0.043 1444 Dihedral : 4.572 47.923 1135 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.88 % Allowed : 20.87 % Favored : 75.25 % 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: 0.45 (0.27), residues: 1025 helix: 1.82 (0.27), residues: 403 sheet: -0.15 (0.32), residues: 248 loop : -1.03 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP N 47 HIS 0.003 0.001 HIS R 261 PHE 0.014 0.001 PHE R 45 TYR 0.018 0.001 TYR L 1 ARG 0.009 0.001 ARG R 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 142 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: B 226 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7101 (tp30) REVERT: B 234 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7370 (m-80) REVERT: G 28 ILE cc_start: 0.8151 (mp) cc_final: 0.7919 (mp) REVERT: N 34 MET cc_start: 0.6685 (OUTLIER) cc_final: 0.6456 (mtt) REVERT: N 98 ARG cc_start: 0.8734 (ttp80) cc_final: 0.8519 (ttp80) outliers start: 35 outliers final: 15 residues processed: 158 average time/residue: 1.1609 time to fit residues: 195.4973 Evaluate side-chains 145 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 282 ASN Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 34 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 94 optimal weight: 0.0370 chunk 85 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.0980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 155 ASN ** R 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8389 Z= 0.186 Angle : 0.714 12.689 11360 Z= 0.348 Chirality : 0.042 0.146 1291 Planarity : 0.004 0.043 1444 Dihedral : 4.479 47.517 1135 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.77 % Allowed : 22.53 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.27), residues: 1025 helix: 1.88 (0.27), residues: 403 sheet: 0.05 (0.34), residues: 232 loop : -1.00 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 47 HIS 0.003 0.001 HIS R 261 PHE 0.014 0.001 PHE R 45 TYR 0.017 0.001 TYR L 1 ARG 0.008 0.001 ARG R 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 151 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7285 (m-80) REVERT: R 291 ASN cc_start: 0.7858 (t0) cc_final: 0.7567 (t0) REVERT: N 34 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.6482 (mtt) REVERT: N 98 ARG cc_start: 0.8716 (ttp80) cc_final: 0.8473 (ttp80) outliers start: 25 outliers final: 13 residues processed: 162 average time/residue: 1.2174 time to fit residues: 209.2695 Evaluate side-chains 145 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 282 ASN Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 34 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 0.0570 chunk 28 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 91 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN B 75 GLN ** R 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN N 39 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8389 Z= 0.213 Angle : 0.748 14.452 11360 Z= 0.362 Chirality : 0.042 0.155 1291 Planarity : 0.004 0.075 1444 Dihedral : 4.548 47.653 1135 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.89 % Allowed : 23.64 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.27), residues: 1025 helix: 1.81 (0.27), residues: 396 sheet: -0.03 (0.33), residues: 244 loop : -0.95 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 47 HIS 0.003 0.001 HIS R 261 PHE 0.012 0.001 PHE B 199 TYR 0.018 0.001 TYR L 1 ARG 0.021 0.001 ARG R 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 234 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7291 (m-80) REVERT: R 291 ASN cc_start: 0.7819 (t0) cc_final: 0.7493 (t0) REVERT: N 34 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6525 (mtt) REVERT: N 98 ARG cc_start: 0.8714 (ttp80) cc_final: 0.8455 (ttp80) outliers start: 26 outliers final: 13 residues processed: 155 average time/residue: 1.1685 time to fit residues: 192.9957 Evaluate side-chains 151 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 282 ASN Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 34 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** R 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8389 Z= 0.324 Angle : 0.798 15.524 11360 Z= 0.390 Chirality : 0.044 0.238 1291 Planarity : 0.004 0.069 1444 Dihedral : 4.777 49.401 1135 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.33 % Allowed : 23.97 % Favored : 73.70 % 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: 0.39 (0.27), residues: 1025 helix: 1.63 (0.27), residues: 399 sheet: -0.10 (0.33), residues: 246 loop : -0.93 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 47 HIS 0.003 0.001 HIS R 261 PHE 0.015 0.002 PHE R 45 TYR 0.020 0.001 TYR L 1 ARG 0.021 0.001 ARG R 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: R 56 ASN cc_start: 0.7430 (m-40) cc_final: 0.6835 (t0) REVERT: N 34 MET cc_start: 0.6850 (OUTLIER) cc_final: 0.6644 (mtt) REVERT: N 98 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8544 (ttp80) outliers start: 21 outliers final: 13 residues processed: 148 average time/residue: 1.1892 time to fit residues: 187.0978 Evaluate side-chains 146 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 282 ASN Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 34 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 0.3980 chunk 71 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.129788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.092426 restraints weight = 16110.261| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.91 r_work: 0.3122 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8389 Z= 0.272 Angle : 0.783 16.346 11360 Z= 0.384 Chirality : 0.043 0.211 1291 Planarity : 0.004 0.059 1444 Dihedral : 4.793 48.905 1135 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.89 % Allowed : 24.75 % Favored : 73.36 % 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: 0.40 (0.27), residues: 1025 helix: 1.63 (0.27), residues: 399 sheet: -0.04 (0.33), residues: 243 loop : -0.95 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 47 HIS 0.004 0.001 HIS G 44 PHE 0.031 0.002 PHE B 292 TYR 0.022 0.001 TYR L 1 ARG 0.019 0.001 ARG R 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3894.44 seconds wall clock time: 69 minutes 36.98 seconds (4176.98 seconds total)