Starting phenix.real_space_refine on Thu Jul 2 06:07:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gl2_51434/07_2026/9gl2_51434.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gl2_51434/07_2026/9gl2_51434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gl2_51434/07_2026/9gl2_51434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gl2_51434/07_2026/9gl2_51434.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gl2_51434/07_2026/9gl2_51434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gl2_51434/07_2026/9gl2_51434.map" } resolution = 3.2 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 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= -0.000 sd= 1.000 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: 7 Type Number sf(0) Gaussians P 2 5.49 5 S 49 5.16 5 Cl 1 4.86 5 C 4548 2.51 5 N 1246 2.21 5 O 1301 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7149 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1854 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 3 Chain: "B" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2538 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain: "G" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 380 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "R" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2300 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 12, 'TRANS': 278} Chain breaks: 1 Chain: "R" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'CLR': 1, 'T7M': 1, 'ZKV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'T7M:plan-1': 1, 'T7M:plan-2': 1, 'T7M:plan-3': 1, 'T7M:plan-4': 1, 'T7M:plan-5': 1, 'T7M:plan-6': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 1.47, per 1000 atoms: 0.21 Number of scatterers: 7149 At special positions: 0 Unit cell: (78.518, 99.33, 124.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 49 16.00 P 2 15.00 F 2 9.00 O 1301 8.00 N 1246 7.00 C 4548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.65 Conformation dependent library (CDL) restraints added in 409.7 milliseconds 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1690 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 8 sheets defined 47.7% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 4.133A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.672A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.628A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 314 through 318 removed outlier: 4.143A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.644A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 11 through 25 removed outlier: 4.331A pdb=" N LYS B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.737A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 20 Processing helix chain 'G' and resid 21 through 25 removed outlier: 3.748A pdb=" N ASN G 24 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'R' and resid 35 through 64 removed outlier: 3.615A pdb=" N THR R 39 " --> pdb=" O TYR R 35 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU R 42 " --> pdb=" O ILE R 38 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL R 57 " --> pdb=" O GLY R 53 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA R 62 " --> pdb=" O VAL R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 100 removed outlier: 4.463A pdb=" N LEU R 90 " --> pdb=" O SER R 86 " (cutoff:3.500A) Proline residue: R 91 - end of helix Processing helix chain 'R' and resid 108 through 140 removed outlier: 3.869A pdb=" N LEU R 127 " --> pdb=" O SER R 123 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS R 128 " --> pdb=" O ILE R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 148 removed outlier: 3.522A pdb=" N ARG R 148 " --> pdb=" O TYR R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 169 removed outlier: 3.984A pdb=" N ALA R 153 " --> pdb=" O THR R 149 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY R 164 " --> pdb=" O THR R 160 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE R 169 " --> pdb=" O PHE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 194 through 204 removed outlier: 4.301A pdb=" N THR R 200 " --> pdb=" O THR R 196 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE R 204 " --> pdb=" O THR R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 232 removed outlier: 3.572A pdb=" N PHE R 219 " --> pdb=" O TYR R 215 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA R 222 " --> pdb=" O ILE R 218 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL R 230 " --> pdb=" O ILE R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 326 through 371 removed outlier: 4.372A pdb=" N ALA R 331 " --> pdb=" O ARG R 327 " (cutoff:3.500A) Proline residue: R 360 - end of helix removed outlier: 4.184A pdb=" N LEU R 366 " --> pdb=" O PHE R 362 " (cutoff:3.500A) Proline residue: R 369 - end of helix Processing helix chain 'R' and resid 372 through 375 removed outlier: 3.573A pdb=" N CYS R 375 " --> pdb=" O GLU R 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 372 through 375' Processing helix chain 'R' and resid 378 through 391 removed outlier: 5.065A pdb=" N ILE R 384 " --> pdb=" O LEU R 380 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE R 385 " --> pdb=" O LEU R 381 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN R 386 " --> pdb=" O GLY R 382 " (cutoff:3.500A) Processing helix chain 'R' and resid 391 through 401 Proline residue: R 397 - end of helix Processing helix chain 'R' and resid 404 through 411 Processing helix chain 'R' and resid 412 through 414 No H-bonds generated for 'chain 'R' and resid 412 through 414' Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.728A pdb=" N PHE A 208 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP A 223 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A 360 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.670A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.867A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 79 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.435A 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: 6.511A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.529A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.295A 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: 3.758A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.677A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.500A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 990 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: 0.96 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1145 1.30 - 1.43: 1921 1.43 - 1.56: 4152 1.56 - 1.69: 3 1.69 - 1.82: 70 Bond restraints: 7291 Sorted by residual: bond pdb=" C14 ZKV R 503 " pdb=" N03 ZKV R 503 " ideal model delta sigma weight residual 1.347 1.436 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" O4 T7M R 502 " pdb=" P4 T7M R 502 " ideal model delta sigma weight residual 1.704 1.625 0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C09 ZKV R 503 " pdb=" F02 ZKV R 503 " ideal model delta sigma weight residual 1.413 1.345 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" O13 T7M R 502 " pdb=" P1 T7M R 502 " ideal model delta sigma weight residual 1.659 1.597 0.062 2.00e-02 2.50e+03 9.74e+00 bond pdb=" C14 ZKV R 503 " pdb=" O01 ZKV R 503 " ideal model delta sigma weight residual 1.223 1.174 0.049 2.00e-02 2.50e+03 5.91e+00 ... (remaining 7286 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 9633 1.93 - 3.86: 196 3.86 - 5.80: 41 5.80 - 7.73: 5 7.73 - 9.66: 4 Bond angle restraints: 9879 Sorted by residual: angle pdb=" N LEU R 115 " pdb=" CA LEU R 115 " pdb=" C LEU R 115 " ideal model delta sigma weight residual 111.07 105.83 5.24 1.07e+00 8.73e-01 2.40e+01 angle pdb=" C ASN G 59 " pdb=" N PRO G 60 " pdb=" CA PRO G 60 " ideal model delta sigma weight residual 119.64 114.76 4.88 1.01e+00 9.80e-01 2.33e+01 angle pdb=" N TRP R 387 " pdb=" CA TRP R 387 " pdb=" C TRP R 387 " ideal model delta sigma weight residual 111.82 116.83 -5.01 1.16e+00 7.43e-01 1.87e+01 angle pdb=" N SER A 252 " pdb=" CA SER A 252 " pdb=" C SER A 252 " ideal model delta sigma weight residual 112.92 117.53 -4.61 1.23e+00 6.61e-01 1.41e+01 angle pdb=" N ASN A 254 " pdb=" CA ASN A 254 " pdb=" C ASN A 254 " ideal model delta sigma weight residual 111.07 107.22 3.85 1.07e+00 8.73e-01 1.30e+01 ... (remaining 9874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.67: 4191 24.67 - 49.33: 219 49.33 - 74.00: 25 74.00 - 98.66: 4 98.66 - 123.33: 3 Dihedral angle restraints: 4442 sinusoidal: 1838 harmonic: 2604 Sorted by residual: dihedral pdb=" C10 CLR R 501 " pdb=" C1 CLR R 501 " pdb=" C2 CLR R 501 " pdb=" C3 CLR R 501 " ideal model delta sinusoidal sigma weight residual -56.83 66.50 -123.33 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" CA GLN A 227 " pdb=" C GLN A 227 " pdb=" N ARG A 228 " pdb=" CA ARG A 228 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" C1 CLR R 501 " pdb=" C2 CLR R 501 " pdb=" C3 CLR R 501 " pdb=" O1 CLR R 501 " ideal model delta sinusoidal sigma weight residual 180.04 72.04 108.00 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 4439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 852 0.049 - 0.097: 220 0.097 - 0.146: 48 0.146 - 0.195: 5 0.195 - 0.243: 1 Chirality restraints: 1126 Sorted by residual: chirality pdb=" CB VAL A 224 " pdb=" CA VAL A 224 " pdb=" CG1 VAL A 224 " pdb=" CG2 VAL A 224 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA ILE R 385 " pdb=" N ILE R 385 " pdb=" C ILE R 385 " pdb=" CB ILE R 385 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.05e-01 chirality pdb=" CB THR B 196 " pdb=" CA THR B 196 " pdb=" OG1 THR B 196 " pdb=" CG2 THR B 196 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.17e-01 ... (remaining 1123 not shown) Planarity restraints: 1237 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN R 100 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.97e+00 pdb=" C ASN R 100 " -0.042 2.00e-02 2.50e+03 pdb=" O ASN R 100 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS R 101 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 206 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO R 207 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO R 207 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 207 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 149 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO R 150 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO R 150 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 150 " 0.019 5.00e-02 4.00e+02 ... (remaining 1234 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1281 2.77 - 3.30: 6939 3.30 - 3.83: 11932 3.83 - 4.37: 13899 4.37 - 4.90: 24025 Nonbonded interactions: 58076 Sorted by model distance: nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.237 3.120 nonbonded pdb=" OD2 ASP R 116 " pdb=" OH TYR R 390 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.270 3.040 nonbonded pdb=" OH TYR A 253 " pdb=" O SER A 306 " model vdw 2.280 3.040 nonbonded pdb=" O ASP A 274 " pdb=" ND2 ASN A 278 " model vdw 2.293 3.120 ... (remaining 58071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.490 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 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 : 0.004 0.089 7292 Z= 0.198 Angle : 0.704 9.661 9881 Z= 0.378 Chirality : 0.045 0.243 1126 Planarity : 0.004 0.037 1237 Dihedral : 14.850 123.325 2749 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.53 % Favored : 96.35 % Rotamer: Outliers : 0.26 % Allowed : 1.05 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.29), residues: 877 helix: 0.46 (0.28), residues: 356 sheet: -0.12 (0.42), residues: 166 loop : -0.97 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.017 0.002 TYR A 358 PHE 0.015 0.001 PHE R 112 TRP 0.015 0.002 TRP R 387 HIS 0.007 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.20 ( 7291) covalent geometry : angle 0.70396 / 0.38 ( 9879) SS BOND : bond 0.00224 / 0.12 ( 1) SS BOND : angle 0.98142 / 0.52 ( 2) hydrogen bonds : bond 0.17639 / 12.11 ( 345) hydrogen bonds : angle 6.80617 / 4.79 ( 990) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: B 61 MET cc_start: 0.7734 (tmm) cc_final: 0.7469 (tmm) REVERT: R 112 PHE cc_start: 0.5509 (OUTLIER) cc_final: 0.4694 (t80) outliers start: 2 outliers final: 0 residues processed: 119 average time/residue: 0.0620 time to fit residues: 10.2739 Evaluate side-chains 102 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0010 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.221906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.195193 restraints weight = 8380.208| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 1.98 r_work: 0.4172 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7292 Z= 0.114 Angle : 0.551 6.278 9881 Z= 0.294 Chirality : 0.042 0.188 1126 Planarity : 0.004 0.034 1237 Dihedral : 7.113 57.504 1103 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.79 % Allowed : 8.12 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.29), residues: 877 helix: 0.54 (0.27), residues: 368 sheet: -0.11 (0.43), residues: 158 loop : -0.89 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.011 0.001 TYR R 390 PHE 0.017 0.001 PHE R 112 TRP 0.012 0.001 TRP A 277 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 7291) covalent geometry : angle 0.55131 / 0.29 ( 9879) SS BOND : bond 0.00415 / 0.22 ( 1) SS BOND : angle 1.02764 / 0.60 ( 2) hydrogen bonds : bond 0.04058 / 2.73 ( 345) hydrogen bonds : angle 4.94235 / 3.47 ( 990) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 GLU cc_start: 0.6544 (tt0) cc_final: 0.6308 (tm-30) REVERT: B 188 MET cc_start: 0.7367 (mtm) cc_final: 0.7027 (mtm) REVERT: R 112 PHE cc_start: 0.6905 (OUTLIER) cc_final: 0.5499 (t80) outliers start: 6 outliers final: 5 residues processed: 113 average time/residue: 0.0853 time to fit residues: 12.6242 Evaluate side-chains 117 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 112 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.212842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.185157 restraints weight = 8359.973| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 2.00 r_work: 0.4074 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3934 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7292 Z= 0.195 Angle : 0.633 7.163 9881 Z= 0.336 Chirality : 0.045 0.157 1126 Planarity : 0.004 0.046 1237 Dihedral : 7.164 56.825 1103 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.83 % Allowed : 12.30 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.29), residues: 877 helix: 0.31 (0.27), residues: 375 sheet: -0.47 (0.40), residues: 175 loop : -0.84 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 232 TYR 0.018 0.002 TYR A 358 PHE 0.017 0.002 PHE B 235 TRP 0.020 0.002 TRP A 277 HIS 0.006 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 ( 7291) covalent geometry : angle 0.63225 / 0.34 ( 9879) SS BOND : bond 0.01310 / 0.69 ( 1) SS BOND : angle 1.97759 / 1.15 ( 2) hydrogen bonds : bond 0.04425 / 2.94 ( 345) hydrogen bonds : angle 4.96704 / 3.47 ( 990) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 112 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.5591 (t80) outliers start: 14 outliers final: 9 residues processed: 120 average time/residue: 0.0933 time to fit residues: 14.9157 Evaluate side-chains 119 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 112 PHE Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.0770 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 100 ASN R 386 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.217917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.190593 restraints weight = 8440.095| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 2.00 r_work: 0.4132 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7292 Z= 0.119 Angle : 0.541 7.020 9881 Z= 0.288 Chirality : 0.041 0.159 1126 Planarity : 0.003 0.037 1237 Dihedral : 6.954 58.470 1103 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.57 % Allowed : 13.74 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.29), residues: 877 helix: 0.61 (0.27), residues: 375 sheet: -0.19 (0.42), residues: 158 loop : -0.87 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 225 TYR 0.020 0.002 TYR R 195 PHE 0.014 0.001 PHE B 199 TRP 0.014 0.001 TRP A 277 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 7291) covalent geometry : angle 0.54050 / 0.29 ( 9879) SS BOND : bond 0.00594 / 0.31 ( 1) SS BOND : angle 1.03700 / 0.61 ( 2) hydrogen bonds : bond 0.03650 / 2.44 ( 345) hydrogen bonds : angle 4.66970 / 3.28 ( 990) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 TYR cc_start: 0.6588 (OUTLIER) cc_final: 0.6294 (p90) REVERT: B 188 MET cc_start: 0.7273 (mtm) cc_final: 0.6982 (mtm) REVERT: R 112 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.5829 (t80) outliers start: 12 outliers final: 6 residues processed: 115 average time/residue: 0.0893 time to fit residues: 13.8339 Evaluate side-chains 117 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 112 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.217124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.189751 restraints weight = 8448.747| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 2.00 r_work: 0.4123 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7292 Z= 0.124 Angle : 0.543 7.311 9881 Z= 0.290 Chirality : 0.041 0.152 1126 Planarity : 0.004 0.049 1237 Dihedral : 6.763 59.168 1103 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.70 % Allowed : 14.53 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.29), residues: 877 helix: 0.69 (0.27), residues: 375 sheet: -0.18 (0.42), residues: 156 loop : -0.86 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 27 TYR 0.016 0.002 TYR A 253 PHE 0.013 0.001 PHE B 199 TRP 0.014 0.001 TRP R 387 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 7291) covalent geometry : angle 0.54332 / 0.29 ( 9879) SS BOND : bond 0.00713 / 0.38 ( 1) SS BOND : angle 1.11116 / 0.65 ( 2) hydrogen bonds : bond 0.03621 / 2.43 ( 345) hydrogen bonds : angle 4.54357 / 3.19 ( 990) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASP cc_start: 0.7910 (t0) cc_final: 0.7593 (t0) REVERT: A 360 TYR cc_start: 0.6741 (OUTLIER) cc_final: 0.6307 (p90) REVERT: B 188 MET cc_start: 0.7345 (mtm) cc_final: 0.7101 (mtm) REVERT: B 246 ASP cc_start: 0.7682 (m-30) cc_final: 0.7270 (m-30) REVERT: G 46 LYS cc_start: 0.8195 (pttp) cc_final: 0.7861 (mptt) REVERT: R 112 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.5754 (t80) outliers start: 13 outliers final: 7 residues processed: 120 average time/residue: 0.0930 time to fit residues: 14.9137 Evaluate side-chains 119 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 112 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 81 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 40 optimal weight: 0.3980 chunk 73 optimal weight: 0.0050 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 0.1980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 72 ASN R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.220828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.193879 restraints weight = 8364.789| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 1.98 r_work: 0.4161 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7292 Z= 0.098 Angle : 0.503 9.072 9881 Z= 0.266 Chirality : 0.040 0.164 1126 Planarity : 0.003 0.040 1237 Dihedral : 6.342 59.901 1103 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.83 % Allowed : 15.31 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.29), residues: 877 helix: 0.94 (0.28), residues: 375 sheet: -0.20 (0.42), residues: 156 loop : -0.84 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 27 TYR 0.013 0.001 TYR A 253 PHE 0.012 0.001 PHE B 199 TRP 0.012 0.001 TRP R 387 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 7291) covalent geometry : angle 0.50275 / 0.27 ( 9879) SS BOND : bond 0.00348 / 0.18 ( 1) SS BOND : angle 0.57501 / 0.34 ( 2) hydrogen bonds : bond 0.03228 / 2.17 ( 345) hydrogen bonds : angle 4.33024 / 3.04 ( 990) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASP cc_start: 0.7881 (t0) cc_final: 0.7608 (t0) REVERT: A 360 TYR cc_start: 0.6509 (OUTLIER) cc_final: 0.6199 (p90) REVERT: B 188 MET cc_start: 0.7254 (mtm) cc_final: 0.6998 (mtm) REVERT: B 246 ASP cc_start: 0.7752 (m-30) cc_final: 0.7416 (m-30) REVERT: R 100 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7569 (t0) REVERT: R 101 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8258 (mtmm) REVERT: R 112 PHE cc_start: 0.6970 (OUTLIER) cc_final: 0.5835 (t80) outliers start: 14 outliers final: 8 residues processed: 123 average time/residue: 0.0939 time to fit residues: 15.2886 Evaluate side-chains 125 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 101 LYS Chi-restraints excluded: chain R residue 112 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 86 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.218268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.191338 restraints weight = 8445.464| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 1.98 r_work: 0.4137 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7292 Z= 0.118 Angle : 0.531 8.446 9881 Z= 0.280 Chirality : 0.041 0.148 1126 Planarity : 0.004 0.052 1237 Dihedral : 6.413 59.665 1103 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.49 % Allowed : 15.58 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.29), residues: 877 helix: 0.89 (0.27), residues: 375 sheet: -0.10 (0.42), residues: 151 loop : -0.92 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 27 TYR 0.018 0.001 TYR A 253 PHE 0.013 0.001 PHE B 235 TRP 0.012 0.001 TRP R 387 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 7291) covalent geometry : angle 0.53087 / 0.28 ( 9879) SS BOND : bond 0.00622 / 0.33 ( 1) SS BOND : angle 0.86943 / 0.51 ( 2) hydrogen bonds : bond 0.03407 / 2.28 ( 345) hydrogen bonds : angle 4.34552 / 3.06 ( 990) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASP cc_start: 0.7883 (t0) cc_final: 0.7604 (t0) REVERT: A 360 TYR cc_start: 0.6711 (OUTLIER) cc_final: 0.6263 (p90) REVERT: B 188 MET cc_start: 0.7353 (mtm) cc_final: 0.7119 (mtm) REVERT: B 246 ASP cc_start: 0.7761 (m-30) cc_final: 0.7444 (m-30) REVERT: R 100 ASN cc_start: 0.7919 (OUTLIER) cc_final: 0.7639 (t0) REVERT: R 101 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8308 (mtmm) REVERT: R 112 PHE cc_start: 0.6962 (OUTLIER) cc_final: 0.5859 (t80) REVERT: R 172 MET cc_start: 0.6911 (mmm) cc_final: 0.6551 (mmm) outliers start: 19 outliers final: 11 residues processed: 123 average time/residue: 0.0913 time to fit residues: 15.1657 Evaluate side-chains 128 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 101 LYS Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 112 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 62 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 0.0020 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 100 ASN R 126 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.219201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.192288 restraints weight = 8520.396| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 1.98 r_work: 0.4147 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7292 Z= 0.109 Angle : 0.519 8.641 9881 Z= 0.273 Chirality : 0.041 0.150 1126 Planarity : 0.004 0.049 1237 Dihedral : 6.334 58.931 1103 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.36 % Allowed : 15.58 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.29), residues: 877 helix: 0.95 (0.27), residues: 375 sheet: -0.07 (0.42), residues: 151 loop : -0.91 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 27 TYR 0.015 0.001 TYR A 253 PHE 0.012 0.001 PHE B 199 TRP 0.012 0.001 TRP R 387 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 7291) covalent geometry : angle 0.51872 / 0.27 ( 9879) SS BOND : bond 0.00515 / 0.27 ( 1) SS BOND : angle 0.77004 / 0.45 ( 2) hydrogen bonds : bond 0.03291 / 2.21 ( 345) hydrogen bonds : angle 4.29233 / 3.02 ( 990) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASP cc_start: 0.7866 (t0) cc_final: 0.7622 (t0) REVERT: A 360 TYR cc_start: 0.6739 (OUTLIER) cc_final: 0.6213 (p90) REVERT: B 188 MET cc_start: 0.7312 (mtm) cc_final: 0.7086 (mtm) REVERT: B 246 ASP cc_start: 0.7779 (m-30) cc_final: 0.7484 (m-30) REVERT: G 46 LYS cc_start: 0.8253 (pttp) cc_final: 0.7915 (mptt) REVERT: R 112 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.5971 (t80) REVERT: R 172 MET cc_start: 0.6848 (mmm) cc_final: 0.6570 (mmm) outliers start: 18 outliers final: 12 residues processed: 124 average time/residue: 0.0913 time to fit residues: 15.2462 Evaluate side-chains 126 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 112 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 24 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 87 optimal weight: 0.0570 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.217162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.191995 restraints weight = 8273.127| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 1.85 r_work: 0.4152 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4015 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7292 Z= 0.112 Angle : 0.540 8.593 9881 Z= 0.283 Chirality : 0.041 0.191 1126 Planarity : 0.004 0.050 1237 Dihedral : 6.348 58.365 1103 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.23 % Allowed : 15.31 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.29), residues: 877 helix: 0.96 (0.28), residues: 376 sheet: -0.09 (0.42), residues: 151 loop : -0.88 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 27 TYR 0.016 0.001 TYR A 253 PHE 0.012 0.001 PHE B 235 TRP 0.012 0.001 TRP R 387 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 7291) covalent geometry : angle 0.53944 / 0.28 ( 9879) SS BOND : bond 0.00553 / 0.29 ( 1) SS BOND : angle 0.81473 / 0.48 ( 2) hydrogen bonds : bond 0.03341 / 2.24 ( 345) hydrogen bonds : angle 4.30084 / 3.02 ( 990) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASP cc_start: 0.7912 (t0) cc_final: 0.7650 (t0) REVERT: A 360 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.6270 (p90) REVERT: B 172 GLU cc_start: 0.8401 (tp30) cc_final: 0.8168 (tp30) REVERT: G 46 LYS cc_start: 0.8363 (pttp) cc_final: 0.7947 (mptt) REVERT: R 100 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7752 (t0) REVERT: R 112 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6194 (t80) REVERT: R 223 ARG cc_start: 0.7089 (ttt180) cc_final: 0.6822 (ttt180) REVERT: R 227 ARG cc_start: 0.6667 (mtm110) cc_final: 0.6368 (mtt-85) outliers start: 17 outliers final: 11 residues processed: 126 average time/residue: 0.0953 time to fit residues: 16.0415 Evaluate side-chains 127 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 112 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 20 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.215261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.190178 restraints weight = 8342.900| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 1.86 r_work: 0.4139 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.4001 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7292 Z= 0.122 Angle : 0.575 10.904 9881 Z= 0.299 Chirality : 0.042 0.173 1126 Planarity : 0.004 0.058 1237 Dihedral : 6.446 57.870 1103 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.83 % Allowed : 16.23 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.29), residues: 877 helix: 0.83 (0.27), residues: 376 sheet: -0.13 (0.42), residues: 151 loop : -0.88 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 27 TYR 0.016 0.001 TYR A 253 PHE 0.012 0.001 PHE B 235 TRP 0.015 0.002 TRP R 102 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 7291) covalent geometry : angle 0.57488 / 0.30 ( 9879) SS BOND : bond 0.00658 / 0.35 ( 1) SS BOND : angle 0.99226 / 0.58 ( 2) hydrogen bonds : bond 0.03411 / 2.29 ( 345) hydrogen bonds : angle 4.41332 / 3.08 ( 990) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASP cc_start: 0.7917 (t0) cc_final: 0.7634 (t0) REVERT: A 360 TYR cc_start: 0.6924 (OUTLIER) cc_final: 0.6317 (p90) REVERT: B 172 GLU cc_start: 0.8483 (tp30) cc_final: 0.8216 (tp30) REVERT: G 46 LYS cc_start: 0.8297 (pttp) cc_final: 0.7897 (mptt) REVERT: R 112 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.6256 (t80) REVERT: R 227 ARG cc_start: 0.6618 (mtm110) cc_final: 0.6291 (mtt-85) outliers start: 14 outliers final: 12 residues processed: 120 average time/residue: 0.0954 time to fit residues: 15.2199 Evaluate side-chains 125 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 112 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.0770 chunk 56 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 19 optimal weight: 0.0030 chunk 23 optimal weight: 6.9990 overall best weight: 0.4348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.217636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.192605 restraints weight = 8338.076| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 1.87 r_work: 0.4165 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.4026 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7292 Z= 0.103 Angle : 0.552 9.704 9881 Z= 0.286 Chirality : 0.041 0.163 1126 Planarity : 0.004 0.051 1237 Dihedral : 6.295 57.700 1103 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.31 % Allowed : 16.62 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.29), residues: 877 helix: 0.95 (0.28), residues: 376 sheet: -0.17 (0.42), residues: 156 loop : -0.81 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 27 TYR 0.014 0.001 TYR A 253 PHE 0.011 0.001 PHE B 235 TRP 0.011 0.001 TRP R 387 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 7291) covalent geometry : angle 0.55245 / 0.29 ( 9879) SS BOND : bond 0.00371 / 0.20 ( 1) SS BOND : angle 0.64723 / 0.37 ( 2) hydrogen bonds : bond 0.03220 / 2.16 ( 345) hydrogen bonds : angle 4.34795 / 3.04 ( 990) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1923.58 seconds wall clock time: 33 minutes 52.62 seconds (2032.62 seconds total)