Starting phenix.real_space_refine on Wed Feb 4 01:37:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9opw_70727/02_2026/9opw_70727.cif Found real_map, /net/cci-nas-00/data/ceres_data/9opw_70727/02_2026/9opw_70727.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 { model { file = "/net/cci-nas-00/data/ceres_data/9opw_70727/02_2026/9opw_70727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9opw_70727/02_2026/9opw_70727.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9opw_70727/02_2026/9opw_70727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9opw_70727/02_2026/9opw_70727.map" } resolution = 2.86 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= 0.005 sd= 0.141 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: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 5158 2.51 5 N 1385 2.21 5 O 1504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8106 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4006 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 23, 'TRANS': 473} Chain breaks: 3 Chain: "B" Number of atoms: 4100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4100 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 26, 'TRANS': 497} Chain breaks: 2 Time building chain proxies: 1.96, per 1000 atoms: 0.24 Number of scatterers: 8106 At special positions: 0 Unit cell: (85.668, 99.946, 125.906, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1504 8.00 N 1385 7.00 C 5158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.80 Conformation dependent library (CDL) restraints added in 324.6 milliseconds 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 15 sheets defined 40.8% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 65 through 85 removed outlier: 3.683A pdb=" N TYR A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 removed outlier: 4.116A pdb=" N ASN A 106 " --> pdb=" O TYR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 116 removed outlier: 4.193A pdb=" N VAL A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 143 through 155 removed outlier: 3.533A pdb=" N PHE A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.580A pdb=" N LEU A 171 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 201 removed outlier: 3.504A pdb=" N HIS A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 230 removed outlier: 3.659A pdb=" N ALA A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 280 through 291 removed outlier: 4.173A pdb=" N PHE A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.826A pdb=" N ARG A 317 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.595A pdb=" N PHE A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 382 through 403 removed outlier: 4.601A pdb=" N TYR A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N SER A 387 " --> pdb=" O ARG A 383 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 removed outlier: 3.617A pdb=" N LEU A 420 " --> pdb=" O TYR A 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 66 through 86 removed outlier: 3.645A pdb=" N LEU B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 118 Processing helix chain 'B' and resid 130 through 134 Processing helix chain 'B' and resid 146 through 161 removed outlier: 4.044A pdb=" N PHE B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.524A pdb=" N ASP B 176 " --> pdb=" O ARG B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.851A pdb=" N GLN B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 233 removed outlier: 3.635A pdb=" N ALA B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 266 Processing helix chain 'B' and resid 276 through 291 Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 333 through 346 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 369 through 375 Processing helix chain 'B' and resid 376 through 380 Processing helix chain 'B' and resid 381 through 386 removed outlier: 4.045A pdb=" N LEU B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 415 Processing helix chain 'B' and resid 429 through 438 removed outlier: 3.733A pdb=" N GLU B 435 " --> pdb=" O TRP B 431 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN B 436 " --> pdb=" O GLN B 432 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 492 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 6.378A pdb=" N TYR A 33 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLU A 97 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A 35 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL A 99 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLY A 37 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU A 34 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE A 139 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY A 36 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL A 138 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN A 161 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 123 Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 239 removed outlier: 7.592A pdb=" N ILE A 206 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN A 237 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 208 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N THR A 239 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL A 210 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL A 271 " --> pdb=" O TRP A 205 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL A 272 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N PHE A 322 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU A 448 " --> pdb=" O SER A 467 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER A 467 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 450 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 428 through 431 Processing sheet with id=AA5, first strand: chain 'A' and resid 503 through 507 Processing sheet with id=AA6, first strand: chain 'A' and resid 524 through 525 Processing sheet with id=AA7, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AA8, first strand: chain 'B' and resid 30 through 31 removed outlier: 6.467A pdb=" N TYR B 35 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ASP B 98 " --> pdb=" O TYR B 35 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU B 37 " --> pdb=" O ASP B 98 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N PHE B 100 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLY B 39 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA B 140 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLN B 164 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AB1, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.600A pdb=" N VAL B 209 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA B 211 " --> pdb=" O GLU B 240 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU B 242 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLY B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL B 270 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE B 324 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VAL B 321 " --> pdb=" O TRP B 466 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR B 461 " --> pdb=" O THR B 480 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR B 480 " --> pdb=" O TYR B 461 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU B 463 " --> pdb=" O VAL B 478 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 474 " --> pdb=" O VAL B 467 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 442 through 444 removed outlier: 3.532A pdb=" N LEU B 447 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 512 through 513 Processing sheet with id=AB4, first strand: chain 'B' and resid 516 through 517 removed outlier: 3.728A pdb=" N CYS B 523 " --> pdb=" O LYS B 517 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 533 through 534 Processing sheet with id=AB6, first strand: chain 'B' and resid 550 through 551 320 hydrogen bonds defined for protein. 858 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: 1.31 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2168 1.33 - 1.45: 1545 1.45 - 1.57: 4510 1.57 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 8305 Sorted by residual: bond pdb=" C LEU B 90 " pdb=" O LEU B 90 " ideal model delta sigma weight residual 1.235 1.214 0.021 4.70e-03 4.53e+04 2.03e+01 bond pdb=" N HIS A 117 " pdb=" CA HIS A 117 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.53e+00 bond pdb=" N LEU A 121 " pdb=" CA LEU A 121 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.21e-02 6.83e+03 6.43e+00 bond pdb=" N GLU A 118 " pdb=" CA GLU A 118 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.24e-02 6.50e+03 5.99e+00 bond pdb=" N ASP A 119 " pdb=" CA ASP A 119 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.52e-02 4.33e+03 4.08e+00 ... (remaining 8300 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 10911 1.35 - 2.71: 318 2.71 - 4.06: 63 4.06 - 5.41: 5 5.41 - 6.77: 1 Bond angle restraints: 11298 Sorted by residual: angle pdb=" CA TYR A 103 " pdb=" CB TYR A 103 " pdb=" CG TYR A 103 " ideal model delta sigma weight residual 113.90 120.67 -6.77 1.80e+00 3.09e-01 1.41e+01 angle pdb=" N SER B 306 " pdb=" CA SER B 306 " pdb=" C SER B 306 " ideal model delta sigma weight residual 111.02 115.58 -4.56 1.25e+00 6.40e-01 1.33e+01 angle pdb=" CA ASP A 119 " pdb=" C ASP A 119 " pdb=" O ASP A 119 " ideal model delta sigma weight residual 121.54 117.84 3.70 1.16e+00 7.43e-01 1.02e+01 angle pdb=" CA ASP A 119 " pdb=" CB ASP A 119 " pdb=" CG ASP A 119 " ideal model delta sigma weight residual 112.60 115.36 -2.76 1.00e+00 1.00e+00 7.63e+00 angle pdb=" CA TRP A 205 " pdb=" CB TRP A 205 " pdb=" CG TRP A 205 " ideal model delta sigma weight residual 113.60 118.46 -4.86 1.90e+00 2.77e-01 6.55e+00 ... (remaining 11293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 4603 17.49 - 34.98: 264 34.98 - 52.46: 45 52.46 - 69.95: 12 69.95 - 87.44: 6 Dihedral angle restraints: 4930 sinusoidal: 1939 harmonic: 2991 Sorted by residual: dihedral pdb=" CA ILE B 142 " pdb=" C ILE B 142 " pdb=" N GLY B 143 " pdb=" CA GLY B 143 " ideal model delta harmonic sigma weight residual -180.00 -152.18 -27.82 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA ASN A 204 " pdb=" C ASN A 204 " pdb=" N TRP A 205 " pdb=" CA TRP A 205 " ideal model delta harmonic sigma weight residual -180.00 -153.77 -26.23 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA CYS A 499 " pdb=" C CYS A 499 " pdb=" N GLN A 500 " pdb=" CA GLN A 500 " ideal model delta harmonic sigma weight residual 180.00 156.32 23.68 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 4927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 799 0.029 - 0.059: 299 0.059 - 0.088: 83 0.088 - 0.118: 64 0.118 - 0.147: 14 Chirality restraints: 1259 Sorted by residual: chirality pdb=" CA ILE A 490 " pdb=" N ILE A 490 " pdb=" C ILE A 490 " pdb=" CB ILE A 490 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE A 207 " pdb=" N ILE A 207 " pdb=" C ILE A 207 " pdb=" CB ILE A 207 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA VAL A 297 " pdb=" N VAL A 297 " pdb=" C VAL A 297 " pdb=" CB VAL A 297 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 1256 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 105 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO B 106 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 106 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 106 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 103 " -0.008 2.00e-02 2.50e+03 9.77e-03 1.91e+00 pdb=" CG TYR A 103 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 103 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 103 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 103 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 103 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 103 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 103 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 552 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO B 553 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 553 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 553 " -0.018 5.00e-02 4.00e+02 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 679 2.74 - 3.28: 8037 3.28 - 3.82: 12880 3.82 - 4.36: 16129 4.36 - 4.90: 27348 Nonbonded interactions: 65073 Sorted by model distance: nonbonded pdb=" O GLY B 319 " pdb=" OG1 THR B 320 " model vdw 2.206 3.040 nonbonded pdb=" O VAL B 419 " pdb=" OG SER B 420 " model vdw 2.302 3.040 nonbonded pdb=" N GLN A 247 " pdb=" OE1 GLN A 247 " model vdw 2.392 3.120 nonbonded pdb=" OD1 ASP A 531 " pdb=" N GLU A 532 " model vdw 2.410 3.120 nonbonded pdb=" O TYR A 469 " pdb=" N ARG A 473 " model vdw 2.443 3.120 ... (remaining 65068 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: 1.150 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.480 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:7.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 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 : 0.003 0.034 8305 Z= 0.158 Angle : 0.574 6.767 11298 Z= 0.328 Chirality : 0.040 0.147 1259 Planarity : 0.004 0.042 1460 Dihedral : 12.034 87.437 2990 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % 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: -0.08 (0.26), residues: 1007 helix: 0.49 (0.27), residues: 344 sheet: -0.27 (0.38), residues: 175 loop : -0.23 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 54 TYR 0.024 0.002 TYR A 103 PHE 0.010 0.001 PHE B 156 TRP 0.013 0.001 TRP A 205 HIS 0.005 0.001 HIS B 341 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8305) covalent geometry : angle 0.57368 (11298) hydrogen bonds : bond 0.16233 ( 320) hydrogen bonds : angle 5.68903 ( 858) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.312 Fit side-chains REVERT: A 145 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7300 (mp0) REVERT: A 153 PHE cc_start: 0.7867 (m-10) cc_final: 0.7605 (t80) REVERT: A 202 ARG cc_start: 0.8329 (mtt90) cc_final: 0.8090 (mtm110) REVERT: A 433 ASP cc_start: 0.7942 (t0) cc_final: 0.7726 (m-30) REVERT: A 518 ILE cc_start: 0.7829 (mt) cc_final: 0.7562 (mt) REVERT: A 548 GLU cc_start: 0.7164 (tp30) cc_final: 0.6935 (mt-10) REVERT: B 178 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8431 (mp0) REVERT: B 227 SER cc_start: 0.8612 (t) cc_final: 0.8393 (m) REVERT: B 290 HIS cc_start: 0.6370 (m90) cc_final: 0.5949 (m-70) REVERT: B 423 HIS cc_start: 0.7003 (t-90) cc_final: 0.6680 (m-70) REVERT: B 454 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7845 (mt-10) REVERT: B 525 ASP cc_start: 0.7931 (p0) cc_final: 0.7402 (t0) REVERT: B 555 LYS cc_start: 0.7940 (mmmm) cc_final: 0.7695 (mmmm) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.6814 time to fit residues: 141.1495 Evaluate side-chains 96 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 221 GLN A 434 HIS B 58 ASN B 193 GLN B 262 GLN B 394 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.186818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.144738 restraints weight = 9292.180| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.51 r_work: 0.3513 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8305 Z= 0.127 Angle : 0.551 8.783 11298 Z= 0.297 Chirality : 0.042 0.169 1259 Planarity : 0.004 0.045 1460 Dihedral : 4.985 23.817 1096 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.19 % Allowed : 9.47 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.33 (0.27), residues: 1007 helix: 1.15 (0.28), residues: 347 sheet: -0.41 (0.39), residues: 179 loop : -0.11 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 173 TYR 0.017 0.001 TYR A 389 PHE 0.011 0.001 PHE B 160 TRP 0.015 0.001 TRP B 208 HIS 0.007 0.001 HIS B 394 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8305) covalent geometry : angle 0.55073 (11298) hydrogen bonds : bond 0.04385 ( 320) hydrogen bonds : angle 4.24660 ( 858) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.331 Fit side-chains REVERT: A 145 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7137 (mp0) REVERT: A 153 PHE cc_start: 0.7856 (m-10) cc_final: 0.7561 (t80) REVERT: A 194 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.7641 (mtm) REVERT: A 213 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7458 (p0) REVERT: A 456 ASP cc_start: 0.7484 (t0) cc_final: 0.7192 (m-30) REVERT: A 494 MET cc_start: 0.8481 (mtt) cc_final: 0.8258 (mtp) REVERT: A 532 GLU cc_start: 0.6633 (mt-10) cc_final: 0.6311 (mm-30) REVERT: A 548 GLU cc_start: 0.6916 (tp30) cc_final: 0.6639 (mm-30) REVERT: B 110 MET cc_start: 0.8180 (mmp) cc_final: 0.7971 (mmt) REVERT: B 178 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8259 (mp0) REVERT: B 265 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6259 (mm110) REVERT: B 290 HIS cc_start: 0.6535 (m90) cc_final: 0.6157 (m-70) REVERT: B 315 ILE cc_start: 0.7131 (mt) cc_final: 0.6764 (mt) REVERT: B 396 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7335 (mt0) REVERT: B 450 GLN cc_start: 0.8106 (mt0) cc_final: 0.7879 (mt0) REVERT: B 525 ASP cc_start: 0.7940 (p0) cc_final: 0.7445 (t0) REVERT: B 560 LEU cc_start: 0.6530 (tp) cc_final: 0.6116 (tp) outliers start: 29 outliers final: 11 residues processed: 121 average time/residue: 0.5754 time to fit residues: 74.0418 Evaluate side-chains 100 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 492 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 204 ASN A 221 GLN B 63 ASN B 547 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.182312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.140715 restraints weight = 9190.351| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.31 r_work: 0.3438 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8305 Z= 0.187 Angle : 0.584 7.659 11298 Z= 0.309 Chirality : 0.044 0.204 1259 Planarity : 0.004 0.047 1460 Dihedral : 4.953 26.683 1096 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.96 % Allowed : 10.35 % Favored : 85.68 % 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: 0.14 (0.26), residues: 1007 helix: 1.05 (0.28), residues: 353 sheet: -0.62 (0.39), residues: 182 loop : -0.23 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 173 TYR 0.018 0.002 TYR A 103 PHE 0.017 0.002 PHE B 160 TRP 0.011 0.002 TRP B 208 HIS 0.008 0.001 HIS B 341 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 8305) covalent geometry : angle 0.58354 (11298) hydrogen bonds : bond 0.05025 ( 320) hydrogen bonds : angle 4.18649 ( 858) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 81 time to evaluate : 0.399 Fit side-chains REVERT: A 145 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7238 (mp0) REVERT: A 153 PHE cc_start: 0.7992 (m-10) cc_final: 0.7602 (t80) REVERT: A 194 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8111 (mtm) REVERT: A 217 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7869 (tmm160) REVERT: A 251 SER cc_start: 0.7388 (t) cc_final: 0.6899 (p) REVERT: A 407 LYS cc_start: 0.8139 (mptt) cc_final: 0.7898 (mmtt) REVERT: A 463 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7284 (tm-30) REVERT: A 494 MET cc_start: 0.8578 (mtt) cc_final: 0.8355 (mtp) REVERT: A 532 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6569 (mp0) REVERT: A 548 GLU cc_start: 0.6924 (tp30) cc_final: 0.6598 (mm-30) REVERT: B 110 MET cc_start: 0.8182 (mmp) cc_final: 0.7949 (mmp) REVERT: B 142 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8237 (mp) REVERT: B 178 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8387 (mp0) REVERT: B 265 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6440 (mm110) REVERT: B 292 LEU cc_start: 0.7457 (tp) cc_final: 0.7256 (tt) REVERT: B 396 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7651 (mt0) REVERT: B 450 GLN cc_start: 0.8184 (mt0) cc_final: 0.7927 (mt0) REVERT: B 525 ASP cc_start: 0.8175 (p0) cc_final: 0.7587 (t0) outliers start: 36 outliers final: 19 residues processed: 108 average time/residue: 0.6003 time to fit residues: 68.9947 Evaluate side-chains 98 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 516 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 81 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS A 204 ASN A 221 GLN B 63 ASN B 550 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.181261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.139426 restraints weight = 9368.914| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.41 r_work: 0.3429 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8305 Z= 0.207 Angle : 0.591 8.019 11298 Z= 0.311 Chirality : 0.044 0.154 1259 Planarity : 0.005 0.047 1460 Dihedral : 4.964 29.031 1096 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.41 % Allowed : 11.89 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.07 (0.26), residues: 1007 helix: 1.03 (0.28), residues: 353 sheet: -0.64 (0.39), residues: 178 loop : -0.33 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 368 TYR 0.017 0.002 TYR B 281 PHE 0.020 0.002 PHE B 160 TRP 0.014 0.002 TRP B 208 HIS 0.008 0.001 HIS B 341 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 8305) covalent geometry : angle 0.59140 (11298) hydrogen bonds : bond 0.05030 ( 320) hydrogen bonds : angle 4.15160 ( 858) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 76 time to evaluate : 0.357 Fit side-chains REVERT: A 145 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7312 (mp0) REVERT: A 153 PHE cc_start: 0.7973 (m-10) cc_final: 0.7719 (t80) REVERT: A 194 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8024 (mtm) REVERT: A 282 TYR cc_start: 0.7935 (t80) cc_final: 0.7580 (t80) REVERT: A 463 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7234 (tm-30) REVERT: A 532 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6568 (mp0) REVERT: A 548 GLU cc_start: 0.6949 (tp30) cc_final: 0.6612 (mm-30) REVERT: B 142 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8395 (mp) REVERT: B 178 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8121 (mp0) REVERT: B 265 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.6558 (mm110) REVERT: B 292 LEU cc_start: 0.7620 (tp) cc_final: 0.7415 (tt) REVERT: B 396 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7667 (mt0) REVERT: B 447 LEU cc_start: 0.8420 (tp) cc_final: 0.8211 (tt) REVERT: B 450 GLN cc_start: 0.8077 (mt0) cc_final: 0.7798 (mt0) REVERT: B 459 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8586 (mtp) REVERT: B 484 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8291 (p) REVERT: B 525 ASP cc_start: 0.8138 (p0) cc_final: 0.7560 (t0) outliers start: 40 outliers final: 20 residues processed: 105 average time/residue: 0.5292 time to fit residues: 59.3809 Evaluate side-chains 95 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 516 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 394 HIS B 550 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.167894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126725 restraints weight = 9296.094| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.01 r_work: 0.3278 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8305 Z= 0.125 Angle : 0.512 8.788 11298 Z= 0.269 Chirality : 0.041 0.154 1259 Planarity : 0.004 0.047 1460 Dihedral : 4.576 25.358 1096 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.85 % Allowed : 13.33 % Favored : 82.82 % 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: 0.24 (0.27), residues: 1007 helix: 1.33 (0.28), residues: 353 sheet: -0.78 (0.40), residues: 176 loop : -0.26 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 173 TYR 0.019 0.001 TYR B 281 PHE 0.012 0.001 PHE B 160 TRP 0.014 0.001 TRP B 208 HIS 0.005 0.001 HIS B 341 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8305) covalent geometry : angle 0.51211 (11298) hydrogen bonds : bond 0.04038 ( 320) hydrogen bonds : angle 3.98168 ( 858) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 0.324 Fit side-chains REVERT: A 145 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7291 (mp0) REVERT: A 153 PHE cc_start: 0.8005 (m-10) cc_final: 0.7560 (t80) REVERT: A 182 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8765 (ttm-80) REVERT: A 282 TYR cc_start: 0.7997 (t80) cc_final: 0.7655 (t80) REVERT: A 415 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8628 (t) REVERT: A 492 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7896 (mtp) REVERT: A 532 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6609 (mp0) REVERT: A 548 GLU cc_start: 0.6988 (tp30) cc_final: 0.6629 (mm-30) REVERT: B 26 SER cc_start: 0.8561 (OUTLIER) cc_final: 0.8357 (m) REVERT: B 142 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8226 (mp) REVERT: B 178 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8098 (mp0) REVERT: B 231 ASN cc_start: 0.8744 (t0) cc_final: 0.8538 (t0) REVERT: B 265 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.6814 (mm110) REVERT: B 396 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7556 (mt0) REVERT: B 447 LEU cc_start: 0.8414 (tp) cc_final: 0.8207 (tt) REVERT: B 450 GLN cc_start: 0.8247 (mt0) cc_final: 0.7943 (mt0) REVERT: B 459 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8555 (mtp) REVERT: B 484 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.8248 (p) REVERT: B 525 ASP cc_start: 0.8122 (p0) cc_final: 0.7538 (t0) outliers start: 35 outliers final: 15 residues processed: 100 average time/residue: 0.5234 time to fit residues: 56.0501 Evaluate side-chains 97 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 501 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.4980 chunk 40 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 14 optimal weight: 0.0970 chunk 68 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 221 GLN B 550 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.168213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.128448 restraints weight = 9154.176| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.89 r_work: 0.3293 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8305 Z= 0.118 Angle : 0.505 9.032 11298 Z= 0.263 Chirality : 0.041 0.153 1259 Planarity : 0.004 0.048 1460 Dihedral : 4.379 24.163 1096 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.52 % Allowed : 13.77 % Favored : 82.71 % 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: 0.34 (0.27), residues: 1007 helix: 1.46 (0.28), residues: 353 sheet: -0.72 (0.40), residues: 178 loop : -0.24 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 173 TYR 0.019 0.001 TYR B 281 PHE 0.011 0.001 PHE B 160 TRP 0.013 0.001 TRP B 208 HIS 0.004 0.001 HIS B 341 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8305) covalent geometry : angle 0.50537 (11298) hydrogen bonds : bond 0.03889 ( 320) hydrogen bonds : angle 3.88049 ( 858) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 77 time to evaluate : 0.326 Fit side-chains REVERT: A 145 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7501 (mp0) REVERT: A 153 PHE cc_start: 0.8150 (m-10) cc_final: 0.7750 (t80) REVERT: A 182 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8754 (ttm-80) REVERT: A 213 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7571 (p0) REVERT: A 282 TYR cc_start: 0.8040 (t80) cc_final: 0.7707 (t80) REVERT: A 492 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7849 (mtp) REVERT: A 532 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6668 (mp0) REVERT: A 548 GLU cc_start: 0.6991 (tp30) cc_final: 0.6692 (mm-30) REVERT: B 178 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8177 (mp0) REVERT: B 265 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.6793 (mm110) REVERT: B 396 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7529 (mt0) REVERT: B 450 GLN cc_start: 0.8282 (mt0) cc_final: 0.7840 (mp10) REVERT: B 459 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8532 (mtp) REVERT: B 525 ASP cc_start: 0.8148 (p0) cc_final: 0.7616 (t0) outliers start: 32 outliers final: 16 residues processed: 101 average time/residue: 0.5284 time to fit residues: 57.0980 Evaluate side-chains 93 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 492 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 38 optimal weight: 0.0000 chunk 9 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 221 GLN B 203 ASN B 207 ASN B 550 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.169907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.128439 restraints weight = 9311.433| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.07 r_work: 0.3303 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8305 Z= 0.097 Angle : 0.483 9.503 11298 Z= 0.250 Chirality : 0.040 0.152 1259 Planarity : 0.004 0.048 1460 Dihedral : 4.131 22.003 1096 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.19 % Allowed : 14.10 % Favored : 82.71 % 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: 0.53 (0.27), residues: 1007 helix: 1.60 (0.28), residues: 360 sheet: -0.67 (0.40), residues: 175 loop : -0.13 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.021 0.001 TYR B 281 PHE 0.008 0.001 PHE B 398 TRP 0.012 0.001 TRP B 208 HIS 0.004 0.001 HIS B 341 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8305) covalent geometry : angle 0.48255 (11298) hydrogen bonds : bond 0.03474 ( 320) hydrogen bonds : angle 3.78725 ( 858) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 0.321 Fit side-chains REVERT: A 145 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7448 (mp0) REVERT: A 153 PHE cc_start: 0.8122 (m-10) cc_final: 0.7634 (t80) REVERT: A 213 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7516 (p0) REVERT: A 282 TYR cc_start: 0.8003 (t80) cc_final: 0.7700 (t80) REVERT: A 456 ASP cc_start: 0.7661 (t0) cc_final: 0.7150 (m-30) REVERT: A 463 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7471 (mm-40) REVERT: A 532 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6647 (mp0) REVERT: A 548 GLU cc_start: 0.7069 (tp30) cc_final: 0.6632 (mm-30) REVERT: B 178 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8102 (mp0) REVERT: B 262 GLN cc_start: 0.8088 (mm110) cc_final: 0.7847 (mt0) REVERT: B 265 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.6813 (mm110) REVERT: B 396 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7480 (mt0) REVERT: B 450 GLN cc_start: 0.8393 (mt0) cc_final: 0.7941 (mp10) REVERT: B 459 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8543 (mtp) REVERT: B 525 ASP cc_start: 0.8019 (p0) cc_final: 0.7473 (t0) outliers start: 29 outliers final: 14 residues processed: 98 average time/residue: 0.5712 time to fit residues: 59.7316 Evaluate side-chains 95 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 TRP Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 492 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 550 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.168338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.129609 restraints weight = 9248.122| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.87 r_work: 0.3294 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8305 Z= 0.126 Angle : 0.512 9.338 11298 Z= 0.265 Chirality : 0.041 0.148 1259 Planarity : 0.004 0.049 1460 Dihedral : 4.232 23.169 1096 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.30 % Allowed : 14.54 % Favored : 82.16 % 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: 0.47 (0.27), residues: 1007 helix: 1.50 (0.28), residues: 360 sheet: -0.68 (0.40), residues: 175 loop : -0.12 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 173 TYR 0.020 0.001 TYR B 281 PHE 0.011 0.001 PHE B 160 TRP 0.011 0.001 TRP B 303 HIS 0.005 0.001 HIS B 341 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8305) covalent geometry : angle 0.51192 (11298) hydrogen bonds : bond 0.03889 ( 320) hydrogen bonds : angle 3.85958 ( 858) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.349 Fit side-chains REVERT: A 145 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7490 (mp0) REVERT: A 282 TYR cc_start: 0.8015 (t80) cc_final: 0.7710 (t80) REVERT: A 456 ASP cc_start: 0.7697 (t0) cc_final: 0.7212 (m-30) REVERT: A 463 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7479 (mm-40) REVERT: A 492 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7861 (mtp) REVERT: A 532 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6688 (mp0) REVERT: A 548 GLU cc_start: 0.6917 (tp30) cc_final: 0.6617 (mm-30) REVERT: B 178 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8170 (mp0) REVERT: B 265 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.6830 (mm110) REVERT: B 396 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7545 (mt0) REVERT: B 450 GLN cc_start: 0.8443 (mt0) cc_final: 0.7967 (mp10) REVERT: B 459 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8533 (mtp) REVERT: B 525 ASP cc_start: 0.8122 (p0) cc_final: 0.7551 (t0) outliers start: 30 outliers final: 16 residues processed: 99 average time/residue: 0.5615 time to fit residues: 59.4865 Evaluate side-chains 97 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 492 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 123 GLN B 550 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.168056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.128927 restraints weight = 9256.649| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.89 r_work: 0.3289 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8305 Z= 0.124 Angle : 0.509 10.047 11298 Z= 0.264 Chirality : 0.041 0.147 1259 Planarity : 0.004 0.049 1460 Dihedral : 4.226 23.638 1096 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.97 % Allowed : 14.98 % Favored : 82.05 % 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: 0.47 (0.27), residues: 1007 helix: 1.48 (0.28), residues: 360 sheet: -0.70 (0.40), residues: 175 loop : -0.10 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 226 TYR 0.021 0.001 TYR B 281 PHE 0.011 0.001 PHE B 160 TRP 0.011 0.001 TRP B 303 HIS 0.004 0.001 HIS B 341 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8305) covalent geometry : angle 0.50915 (11298) hydrogen bonds : bond 0.03894 ( 320) hydrogen bonds : angle 3.87227 ( 858) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.329 Fit side-chains REVERT: A 145 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7493 (mp0) REVERT: A 282 TYR cc_start: 0.8024 (t80) cc_final: 0.7715 (t80) REVERT: A 456 ASP cc_start: 0.7684 (t0) cc_final: 0.7214 (m-30) REVERT: A 463 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7488 (mm-40) REVERT: A 492 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7871 (mtp) REVERT: A 498 ARG cc_start: 0.6813 (mpt180) cc_final: 0.6483 (mmp-170) REVERT: A 532 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6655 (mp0) REVERT: A 548 GLU cc_start: 0.7175 (tp30) cc_final: 0.6777 (mm-30) REVERT: B 110 MET cc_start: 0.8160 (mmm) cc_final: 0.7898 (mmp) REVERT: B 178 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8241 (mp0) REVERT: B 265 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.6774 (mm110) REVERT: B 396 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7553 (mt0) REVERT: B 450 GLN cc_start: 0.8419 (mt0) cc_final: 0.7904 (mp10) REVERT: B 459 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8609 (mtp) REVERT: B 525 ASP cc_start: 0.8127 (p0) cc_final: 0.7557 (t0) outliers start: 27 outliers final: 18 residues processed: 98 average time/residue: 0.5364 time to fit residues: 56.4516 Evaluate side-chains 97 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 492 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 48 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 82 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 550 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.167098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.126845 restraints weight = 9315.823| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.05 r_work: 0.3268 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8305 Z= 0.147 Angle : 0.541 10.648 11298 Z= 0.280 Chirality : 0.041 0.145 1259 Planarity : 0.004 0.049 1460 Dihedral : 4.339 25.202 1096 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.64 % Allowed : 15.75 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.37 (0.27), residues: 1007 helix: 1.39 (0.28), residues: 354 sheet: -0.74 (0.40), residues: 176 loop : -0.12 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 226 TYR 0.022 0.001 TYR B 281 PHE 0.013 0.002 PHE B 160 TRP 0.011 0.002 TRP B 303 HIS 0.005 0.001 HIS B 341 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8305) covalent geometry : angle 0.54053 (11298) hydrogen bonds : bond 0.04220 ( 320) hydrogen bonds : angle 3.96128 ( 858) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.321 Fit side-chains REVERT: A 145 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7455 (mp0) REVERT: A 282 TYR cc_start: 0.8000 (t80) cc_final: 0.7685 (t80) REVERT: A 456 ASP cc_start: 0.7723 (t0) cc_final: 0.7204 (m-30) REVERT: A 463 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7428 (mm-40) REVERT: A 492 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8003 (mtp) REVERT: A 498 ARG cc_start: 0.6650 (mpt180) cc_final: 0.6361 (mmp-170) REVERT: A 532 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6610 (mp0) REVERT: A 548 GLU cc_start: 0.7179 (tp30) cc_final: 0.6758 (mm-30) REVERT: B 178 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8159 (mp0) REVERT: B 265 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.6722 (mm110) REVERT: B 396 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7616 (mt0) REVERT: B 450 GLN cc_start: 0.8446 (mt0) cc_final: 0.7860 (mp10) REVERT: B 459 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8592 (mtp) REVERT: B 525 ASP cc_start: 0.8141 (p0) cc_final: 0.7457 (t0) outliers start: 24 outliers final: 16 residues processed: 92 average time/residue: 0.5464 time to fit residues: 53.9099 Evaluate side-chains 94 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 492 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 77 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 40 optimal weight: 0.2980 chunk 66 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 HIS B 123 GLN B 550 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.168513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.129055 restraints weight = 9285.913| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.02 r_work: 0.3297 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8305 Z= 0.111 Angle : 0.512 10.523 11298 Z= 0.264 Chirality : 0.040 0.147 1259 Planarity : 0.004 0.049 1460 Dihedral : 4.169 23.136 1096 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.53 % Allowed : 15.97 % Favored : 81.50 % 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: 0.51 (0.27), residues: 1007 helix: 1.53 (0.28), residues: 360 sheet: -0.79 (0.40), residues: 179 loop : -0.02 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 173 TYR 0.022 0.001 TYR B 281 PHE 0.009 0.001 PHE B 398 TRP 0.011 0.001 TRP B 208 HIS 0.004 0.001 HIS B 341 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8305) covalent geometry : angle 0.51169 (11298) hydrogen bonds : bond 0.03720 ( 320) hydrogen bonds : angle 3.89345 ( 858) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3026.81 seconds wall clock time: 52 minutes 29.49 seconds (3149.49 seconds total)