Starting phenix.real_space_refine on Tue Feb 3 20:37:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kmq_62441/02_2026/9kmq_62441.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kmq_62441/02_2026/9kmq_62441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kmq_62441/02_2026/9kmq_62441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kmq_62441/02_2026/9kmq_62441.map" model { file = "/net/cci-nas-00/data/ceres_data/9kmq_62441/02_2026/9kmq_62441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kmq_62441/02_2026/9kmq_62441.cif" } resolution = 3.3 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= 0.001 sd= 0.052 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 56 5.16 5 C 4419 2.51 5 N 1070 2.21 5 O 1131 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 6676 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3331 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 13, 'TRANS': 416} Chain breaks: 1 Chain: "A" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3345 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 13, 'TRANS': 418} Chain breaks: 1 Time building chain proxies: 1.50, per 1000 atoms: 0.22 Number of scatterers: 6676 At special positions: 0 Unit cell: (114.48, 76.68, 82.08, 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 56 16.00 O 1131 8.00 N 1070 7.00 C 4419 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: 0.49 Conformation dependent library (CDL) restraints added in 200.3 milliseconds 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1560 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 85.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 23 through 45 removed outlier: 5.358A pdb=" N GLY B 35 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N PHE B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 59 removed outlier: 4.390A pdb=" N VAL B 49 " --> pdb=" O CYS B 45 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LYS B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 97 removed outlier: 4.971A pdb=" N ALA B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 93 " --> pdb=" O MET B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 121 removed outlier: 3.742A pdb=" N ALA B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 151 removed outlier: 3.517A pdb=" N TRP B 142 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR B 151 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 160 through 165 removed outlier: 3.779A pdb=" N LYS B 164 " --> pdb=" O GLU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 175 Processing helix chain 'B' and resid 175 through 199 removed outlier: 4.362A pdb=" N GLY B 179 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 186 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 213 Processing helix chain 'B' and resid 214 through 229 removed outlier: 5.326A pdb=" N TYR B 220 " --> pdb=" O PRO B 216 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TRP B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ARG B 223 " --> pdb=" O ASP B 219 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 242 removed outlier: 4.030A pdb=" N ALA B 233 " --> pdb=" O GLY B 229 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS B 242 " --> pdb=" O TYR B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 300 Processing helix chain 'B' and resid 300 through 323 removed outlier: 4.234A pdb=" N ILE B 304 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU B 313 " --> pdb=" O THR B 309 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER B 319 " --> pdb=" O ILE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 331 removed outlier: 3.584A pdb=" N PHE B 328 " --> pdb=" O GLN B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.668A pdb=" N VAL B 340 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 360 removed outlier: 3.911A pdb=" N MET B 346 " --> pdb=" O ALA B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 370 removed outlier: 4.196A pdb=" N TYR B 365 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TRP B 366 " --> pdb=" O PHE B 362 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA B 370 " --> pdb=" O TRP B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 Processing helix chain 'B' and resid 377 through 398 removed outlier: 3.741A pdb=" N GLN B 381 " --> pdb=" O ARG B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 405 removed outlier: 4.059A pdb=" N THR B 404 " --> pdb=" O ASP B 400 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS B 405 " --> pdb=" O TYR B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 423 removed outlier: 4.146A pdb=" N LEU B 411 " --> pdb=" O PHE B 407 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE B 417 " --> pdb=" O TYR B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 427 Processing helix chain 'B' and resid 440 through 462 Processing helix chain 'B' and resid 462 through 468 removed outlier: 3.920A pdb=" N LEU B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 493 removed outlier: 3.577A pdb=" N ILE B 475 " --> pdb=" O GLN B 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 45 removed outlier: 5.754A pdb=" N GLY A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N PHE A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 58 removed outlier: 4.091A pdb=" N GLY A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 97 removed outlier: 4.845A pdb=" N ALA A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 122 removed outlier: 3.619A pdb=" N ALA A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 149 removed outlier: 3.661A pdb=" N TRP A 142 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 143 " --> pdb=" O PHE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 162 removed outlier: 3.672A pdb=" N GLU A 160 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 175 Processing helix chain 'A' and resid 176 through 200 removed outlier: 3.726A pdb=" N VAL A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 213 Processing helix chain 'A' and resid 214 through 228 removed outlier: 5.035A pdb=" N TYR A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TRP A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG A 223 " --> pdb=" O ASP A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 242 removed outlier: 4.142A pdb=" N ALA A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS A 242 " --> pdb=" O TYR A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 299 Processing helix chain 'A' and resid 299 through 323 removed outlier: 3.856A pdb=" N ALA A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 331 removed outlier: 3.537A pdb=" N PHE A 328 " --> pdb=" O GLN A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix Processing helix chain 'A' and resid 341 through 360 removed outlier: 3.533A pdb=" N MET A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 371 removed outlier: 4.097A pdb=" N TRP A 366 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 378 through 398 Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 406 through 423 removed outlier: 3.511A pdb=" N GLY A 423 " --> pdb=" O PHE A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 435 removed outlier: 3.845A pdb=" N THR A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) Proline residue: A 432 - end of helix removed outlier: 3.557A pdb=" N LEU A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 462 Processing helix chain 'A' and resid 462 through 469 removed outlier: 3.940A pdb=" N LEU A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASN A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 493 453 hydrogen bonds defined for protein. 1347 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: 0.68 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1992 1.35 - 1.47: 1857 1.47 - 1.58: 2895 1.58 - 1.70: 0 1.70 - 1.82: 104 Bond restraints: 6848 Sorted by residual: bond pdb=" CG1 ILE B 481 " pdb=" CD1 ILE B 481 " ideal model delta sigma weight residual 1.513 1.440 0.073 3.90e-02 6.57e+02 3.52e+00 bond pdb=" N ILE B 481 " pdb=" CA ILE B 481 " ideal model delta sigma weight residual 1.459 1.471 -0.012 1.30e-02 5.92e+03 8.72e-01 bond pdb=" CB GLU A 434 " pdb=" CG GLU A 434 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.44e-01 bond pdb=" CB ASP B 39 " pdb=" CG ASP B 39 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.59e-01 bond pdb=" CB MET A 243 " pdb=" CG MET A 243 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.49e-01 ... (remaining 6843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 9144 2.59 - 5.18: 90 5.18 - 7.77: 15 7.77 - 10.36: 1 10.36 - 12.95: 3 Bond angle restraints: 9253 Sorted by residual: angle pdb=" CB MET A 243 " pdb=" CG MET A 243 " pdb=" SD MET A 243 " ideal model delta sigma weight residual 112.70 124.95 -12.25 3.00e+00 1.11e-01 1.67e+01 angle pdb=" CA LEU A 398 " pdb=" CB LEU A 398 " pdb=" CG LEU A 398 " ideal model delta sigma weight residual 116.30 129.25 -12.95 3.50e+00 8.16e-02 1.37e+01 angle pdb=" CA ILE B 481 " pdb=" CB ILE B 481 " pdb=" CG1 ILE B 481 " ideal model delta sigma weight residual 110.40 116.09 -5.69 1.70e+00 3.46e-01 1.12e+01 angle pdb=" CA GLU A 434 " pdb=" CB GLU A 434 " pdb=" CG GLU A 434 " ideal model delta sigma weight residual 114.10 120.69 -6.59 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CA LEU B 411 " pdb=" CB LEU B 411 " pdb=" CG LEU B 411 " ideal model delta sigma weight residual 116.30 127.77 -11.47 3.50e+00 8.16e-02 1.07e+01 ... (remaining 9248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 3266 16.43 - 32.85: 496 32.85 - 49.28: 147 49.28 - 65.71: 34 65.71 - 82.13: 2 Dihedral angle restraints: 3945 sinusoidal: 1489 harmonic: 2456 Sorted by residual: dihedral pdb=" CA TYR B 151 " pdb=" C TYR B 151 " pdb=" N PRO B 152 " pdb=" CA PRO B 152 " ideal model delta harmonic sigma weight residual -180.00 -153.46 -26.54 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA LEU B 153 " pdb=" C LEU B 153 " pdb=" N SER B 154 " pdb=" CA SER B 154 " ideal model delta harmonic sigma weight residual 180.00 159.19 20.81 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ALA A 155 " pdb=" C ALA A 155 " pdb=" N THR A 156 " pdb=" CA THR A 156 " ideal model delta harmonic sigma weight residual 180.00 161.50 18.50 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 3942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 651 0.032 - 0.064: 269 0.064 - 0.097: 99 0.097 - 0.129: 20 0.129 - 0.161: 4 Chirality restraints: 1043 Sorted by residual: chirality pdb=" CB THR A 306 " pdb=" CA THR A 306 " pdb=" OG1 THR A 306 " pdb=" CG2 THR A 306 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" CB ILE B 481 " pdb=" CA ILE B 481 " pdb=" CG1 ILE B 481 " pdb=" CG2 ILE B 481 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" CA PRO B 152 " pdb=" N PRO B 152 " pdb=" C PRO B 152 " pdb=" CB PRO B 152 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 1040 not shown) Planarity restraints: 1132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 434 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" CD GLU A 434 " -0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU A 434 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 434 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 423 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A 424 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 424 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 424 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 496 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" C VAL B 496 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL B 496 " 0.010 2.00e-02 2.50e+03 pdb=" N PRO B 497 " 0.009 2.00e-02 2.50e+03 ... (remaining 1129 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 250 2.72 - 3.27: 7037 3.27 - 3.81: 10909 3.81 - 4.36: 12427 4.36 - 4.90: 22216 Nonbonded interactions: 52839 Sorted by model distance: nonbonded pdb=" O SER B 319 " pdb=" OG1 THR B 323 " model vdw 2.176 3.040 nonbonded pdb=" O ALA B 155 " pdb=" OG SER B 159 " model vdw 2.236 3.040 nonbonded pdb=" O TYR B 413 " pdb=" OG1 THR B 416 " model vdw 2.249 3.040 nonbonded pdb=" O GLY A 489 " pdb=" OG1 THR A 493 " model vdw 2.257 3.040 nonbonded pdb=" O ALA B 330 " pdb=" NZ LYS B 403 " model vdw 2.268 3.120 ... (remaining 52834 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 244 or resid 293 through 499)) selection = chain 'B' } 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: 1.250 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.400 Find NCS groups from input model: 0.060 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 0.073 6848 Z= 0.131 Angle : 0.683 12.949 9253 Z= 0.340 Chirality : 0.040 0.161 1043 Planarity : 0.003 0.044 1132 Dihedral : 17.235 82.133 2385 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.05 % Allowed : 28.90 % Favored : 67.05 % 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: 0.30 (0.30), residues: 854 helix: 1.19 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -2.38 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 213 TYR 0.019 0.001 TYR B 238 PHE 0.018 0.001 PHE A 295 TRP 0.016 0.001 TRP B 222 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6848) covalent geometry : angle 0.68335 ( 9253) hydrogen bonds : bond 0.12008 ( 453) hydrogen bonds : angle 5.63594 ( 1347) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: B 105 ARG cc_start: 0.6693 (mmt180) cc_final: 0.6462 (mtt180) REVERT: B 358 LEU cc_start: 0.7732 (tp) cc_final: 0.7359 (tt) REVERT: B 382 LEU cc_start: 0.8334 (mt) cc_final: 0.8051 (mm) REVERT: A 23 MET cc_start: 0.7890 (mpp) cc_final: 0.7482 (pmm) REVERT: A 26 MET cc_start: 0.7074 (pmm) cc_final: 0.6565 (mmp) REVERT: A 61 ASP cc_start: 0.6932 (p0) cc_final: 0.6665 (p0) REVERT: A 177 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7197 (mmm) REVERT: A 299 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.7209 (m90) REVERT: A 331 MET cc_start: 0.7500 (mmm) cc_final: 0.6950 (tpp) REVERT: A 466 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8205 (mt) outliers start: 28 outliers final: 23 residues processed: 162 average time/residue: 0.0473 time to fit residues: 11.4594 Evaluate side-chains 160 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.0170 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 HIS A 486 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.173327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.142140 restraints weight = 10965.658| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.80 r_work: 0.3695 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6848 Z= 0.120 Angle : 0.601 11.596 9253 Z= 0.300 Chirality : 0.040 0.143 1043 Planarity : 0.003 0.037 1132 Dihedral : 6.274 49.319 968 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.05 % Allowed : 26.01 % Favored : 69.94 % 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: 0.48 (0.30), residues: 854 helix: 1.23 (0.22), residues: 621 sheet: None (None), residues: 0 loop : -2.22 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 167 TYR 0.016 0.001 TYR B 161 PHE 0.011 0.001 PHE B 311 TRP 0.015 0.001 TRP B 222 HIS 0.002 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6848) covalent geometry : angle 0.60073 ( 9253) hydrogen bonds : bond 0.03750 ( 453) hydrogen bonds : angle 4.47670 ( 1347) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 101 LEU cc_start: 0.7813 (tt) cc_final: 0.6923 (mp) REVERT: B 105 ARG cc_start: 0.7015 (mmt180) cc_final: 0.6455 (mtt180) REVERT: B 161 TYR cc_start: 0.7592 (t80) cc_final: 0.7263 (t80) REVERT: B 358 LEU cc_start: 0.7719 (tp) cc_final: 0.7346 (tt) REVERT: B 382 LEU cc_start: 0.8329 (mt) cc_final: 0.8022 (mm) REVERT: A 23 MET cc_start: 0.7752 (mpp) cc_final: 0.7277 (pmm) REVERT: A 26 MET cc_start: 0.7140 (pmm) cc_final: 0.6656 (mmp) REVERT: A 61 ASP cc_start: 0.7008 (p0) cc_final: 0.6745 (p0) REVERT: A 243 MET cc_start: 0.7912 (mmm) cc_final: 0.7680 (mmm) REVERT: A 331 MET cc_start: 0.7368 (mmm) cc_final: 0.6719 (tpp) outliers start: 28 outliers final: 13 residues processed: 171 average time/residue: 0.0490 time to fit residues: 12.0963 Evaluate side-chains 151 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 486 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 53 optimal weight: 0.0270 chunk 29 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 0.0770 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.172670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.141440 restraints weight = 10974.599| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.81 r_work: 0.3686 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6848 Z= 0.118 Angle : 0.591 10.304 9253 Z= 0.292 Chirality : 0.039 0.145 1043 Planarity : 0.003 0.037 1132 Dihedral : 5.392 53.182 934 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 4.05 % Allowed : 25.43 % Favored : 70.52 % 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: 0.43 (0.30), residues: 854 helix: 1.23 (0.22), residues: 626 sheet: None (None), residues: 0 loop : -2.43 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 441 TYR 0.014 0.001 TYR B 161 PHE 0.011 0.001 PHE A 422 TRP 0.016 0.001 TRP B 222 HIS 0.008 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6848) covalent geometry : angle 0.59144 ( 9253) hydrogen bonds : bond 0.03683 ( 453) hydrogen bonds : angle 4.35133 ( 1347) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.200 Fit side-chains REVERT: B 101 LEU cc_start: 0.7730 (tt) cc_final: 0.6993 (mp) REVERT: B 105 ARG cc_start: 0.7071 (mmt180) cc_final: 0.6469 (mtt180) REVERT: B 161 TYR cc_start: 0.7661 (t80) cc_final: 0.7326 (t80) REVERT: B 241 MET cc_start: 0.7144 (tpp) cc_final: 0.6877 (tpp) REVERT: B 334 ILE cc_start: 0.7993 (mm) cc_final: 0.7559 (mt) REVERT: B 358 LEU cc_start: 0.7771 (tp) cc_final: 0.7408 (tt) REVERT: B 382 LEU cc_start: 0.8383 (mt) cc_final: 0.8074 (mm) REVERT: A 26 MET cc_start: 0.7138 (pmm) cc_final: 0.6683 (mmp) REVERT: A 61 ASP cc_start: 0.7055 (p0) cc_final: 0.6784 (p0) REVERT: A 243 MET cc_start: 0.7905 (mmm) cc_final: 0.7540 (mmm) REVERT: A 331 MET cc_start: 0.7489 (mmm) cc_final: 0.6866 (tpp) outliers start: 28 outliers final: 20 residues processed: 161 average time/residue: 0.0463 time to fit residues: 11.1758 Evaluate side-chains 158 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN A 209 HIS A 214 GLN A 486 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.170237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.138979 restraints weight = 11075.510| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.79 r_work: 0.3656 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6848 Z= 0.138 Angle : 0.603 8.924 9253 Z= 0.301 Chirality : 0.040 0.133 1043 Planarity : 0.003 0.033 1132 Dihedral : 5.433 59.100 933 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 6.21 % Allowed : 22.54 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.44 (0.30), residues: 854 helix: 1.23 (0.22), residues: 627 sheet: None (None), residues: 0 loop : -2.41 (0.39), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 441 TYR 0.012 0.001 TYR B 365 PHE 0.014 0.001 PHE A 422 TRP 0.018 0.002 TRP B 222 HIS 0.003 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6848) covalent geometry : angle 0.60314 ( 9253) hydrogen bonds : bond 0.03971 ( 453) hydrogen bonds : angle 4.36082 ( 1347) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: B 101 LEU cc_start: 0.7737 (tt) cc_final: 0.7084 (mp) REVERT: B 105 ARG cc_start: 0.7166 (mmt180) cc_final: 0.6538 (mtt180) REVERT: B 161 TYR cc_start: 0.7649 (t80) cc_final: 0.7348 (t80) REVERT: B 241 MET cc_start: 0.7225 (tpp) cc_final: 0.6958 (tpp) REVERT: B 334 ILE cc_start: 0.8030 (mm) cc_final: 0.7575 (mt) REVERT: B 382 LEU cc_start: 0.8404 (mt) cc_final: 0.8126 (mm) REVERT: A 23 MET cc_start: 0.7606 (pmm) cc_final: 0.7112 (pmm) REVERT: A 26 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6807 (mmp) REVERT: A 61 ASP cc_start: 0.7178 (p0) cc_final: 0.6902 (p0) REVERT: A 243 MET cc_start: 0.7821 (mmm) cc_final: 0.7468 (mmm) REVERT: A 331 MET cc_start: 0.7504 (mmm) cc_final: 0.7106 (tpp) outliers start: 43 outliers final: 29 residues processed: 168 average time/residue: 0.0458 time to fit residues: 11.4890 Evaluate side-chains 165 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 26 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 HIS A 486 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.171048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.139643 restraints weight = 11151.836| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.85 r_work: 0.3662 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6848 Z= 0.127 Angle : 0.640 13.770 9253 Z= 0.307 Chirality : 0.040 0.155 1043 Planarity : 0.003 0.035 1132 Dihedral : 5.372 56.390 933 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.48 % Allowed : 25.00 % Favored : 70.52 % 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 (0.30), residues: 854 helix: 1.27 (0.22), residues: 622 sheet: None (None), residues: 0 loop : -2.39 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 441 TYR 0.011 0.001 TYR B 365 PHE 0.012 0.001 PHE B 311 TRP 0.018 0.001 TRP B 222 HIS 0.003 0.000 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6848) covalent geometry : angle 0.64041 ( 9253) hydrogen bonds : bond 0.03826 ( 453) hydrogen bonds : angle 4.33714 ( 1347) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: B 101 LEU cc_start: 0.7747 (tt) cc_final: 0.7274 (mt) REVERT: B 105 ARG cc_start: 0.7145 (mmt180) cc_final: 0.6514 (mtt180) REVERT: B 171 ILE cc_start: 0.8564 (mm) cc_final: 0.8249 (mt) REVERT: B 241 MET cc_start: 0.7214 (tpp) cc_final: 0.6887 (tpp) REVERT: B 334 ILE cc_start: 0.8021 (mm) cc_final: 0.7564 (mt) REVERT: B 382 LEU cc_start: 0.8398 (mt) cc_final: 0.8111 (mm) REVERT: A 23 MET cc_start: 0.7586 (pmm) cc_final: 0.7114 (pmm) REVERT: A 26 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6769 (mmp) REVERT: A 61 ASP cc_start: 0.7134 (p0) cc_final: 0.6829 (p0) REVERT: A 243 MET cc_start: 0.7756 (mmm) cc_final: 0.7439 (mmm) REVERT: A 345 GLU cc_start: 0.7756 (pp20) cc_final: 0.7517 (pp20) outliers start: 31 outliers final: 23 residues processed: 160 average time/residue: 0.0566 time to fit residues: 13.0488 Evaluate side-chains 163 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 45 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.170970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.139409 restraints weight = 11072.314| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.88 r_work: 0.3659 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6848 Z= 0.127 Angle : 0.635 12.851 9253 Z= 0.308 Chirality : 0.040 0.163 1043 Planarity : 0.003 0.037 1132 Dihedral : 5.074 47.563 931 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 4.91 % Allowed : 24.42 % Favored : 70.66 % 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 (0.30), residues: 854 helix: 1.24 (0.22), residues: 626 sheet: None (None), residues: 0 loop : -2.38 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 167 TYR 0.013 0.001 TYR B 161 PHE 0.012 0.001 PHE B 311 TRP 0.018 0.002 TRP B 222 HIS 0.003 0.000 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6848) covalent geometry : angle 0.63513 ( 9253) hydrogen bonds : bond 0.03809 ( 453) hydrogen bonds : angle 4.32222 ( 1347) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: B 101 LEU cc_start: 0.7740 (tt) cc_final: 0.7293 (mt) REVERT: B 105 ARG cc_start: 0.7154 (mmt180) cc_final: 0.6526 (mtt180) REVERT: B 161 TYR cc_start: 0.7655 (t80) cc_final: 0.7421 (t80) REVERT: B 241 MET cc_start: 0.7326 (tpp) cc_final: 0.6527 (tpp) REVERT: B 334 ILE cc_start: 0.8022 (mm) cc_final: 0.7550 (mt) REVERT: B 382 LEU cc_start: 0.8394 (mt) cc_final: 0.8059 (mt) REVERT: A 23 MET cc_start: 0.7478 (pmm) cc_final: 0.7071 (pmm) REVERT: A 26 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6855 (mmp) REVERT: A 61 ASP cc_start: 0.7185 (p0) cc_final: 0.6880 (p0) REVERT: A 243 MET cc_start: 0.7715 (mmm) cc_final: 0.7410 (mmm) REVERT: A 293 MET cc_start: 0.6288 (mtm) cc_final: 0.5912 (mpp) REVERT: A 331 MET cc_start: 0.7346 (mmm) cc_final: 0.6876 (tpp) outliers start: 34 outliers final: 25 residues processed: 160 average time/residue: 0.0424 time to fit residues: 10.2123 Evaluate side-chains 160 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.170577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.139327 restraints weight = 10996.533| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.86 r_work: 0.3653 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6848 Z= 0.132 Angle : 0.637 12.397 9253 Z= 0.311 Chirality : 0.040 0.137 1043 Planarity : 0.003 0.038 1132 Dihedral : 5.105 47.597 931 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.19 % Allowed : 26.01 % Favored : 69.80 % 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: 0.45 (0.30), residues: 854 helix: 1.21 (0.22), residues: 626 sheet: None (None), residues: 0 loop : -2.33 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 441 TYR 0.013 0.001 TYR B 161 PHE 0.012 0.001 PHE B 311 TRP 0.018 0.002 TRP B 222 HIS 0.003 0.000 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6848) covalent geometry : angle 0.63704 ( 9253) hydrogen bonds : bond 0.03891 ( 453) hydrogen bonds : angle 4.36282 ( 1347) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: B 101 LEU cc_start: 0.7771 (tt) cc_final: 0.7322 (mt) REVERT: B 105 ARG cc_start: 0.7073 (mmt180) cc_final: 0.6465 (mtt180) REVERT: B 161 TYR cc_start: 0.7561 (t80) cc_final: 0.7349 (t80) REVERT: B 334 ILE cc_start: 0.8105 (mm) cc_final: 0.7628 (mt) REVERT: B 382 LEU cc_start: 0.8411 (mt) cc_final: 0.8084 (mt) REVERT: A 23 MET cc_start: 0.7586 (pmm) cc_final: 0.7168 (pmm) REVERT: A 26 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6845 (mmp) REVERT: A 61 ASP cc_start: 0.7167 (p0) cc_final: 0.6860 (p0) REVERT: A 243 MET cc_start: 0.7697 (mmm) cc_final: 0.7395 (mmm) REVERT: A 293 MET cc_start: 0.6326 (mtm) cc_final: 0.5952 (mpp) REVERT: A 331 MET cc_start: 0.7432 (mmm) cc_final: 0.6949 (tpp) outliers start: 29 outliers final: 25 residues processed: 158 average time/residue: 0.0453 time to fit residues: 10.6459 Evaluate side-chains 163 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 67 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.171669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.139888 restraints weight = 11045.706| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.95 r_work: 0.3667 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6848 Z= 0.122 Angle : 0.644 12.343 9253 Z= 0.311 Chirality : 0.040 0.146 1043 Planarity : 0.003 0.035 1132 Dihedral : 5.076 47.564 931 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.76 % Allowed : 26.59 % Favored : 69.65 % 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: 0.57 (0.30), residues: 854 helix: 1.31 (0.22), residues: 620 sheet: None (None), residues: 0 loop : -2.21 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 167 TYR 0.011 0.001 TYR B 161 PHE 0.011 0.001 PHE B 311 TRP 0.018 0.002 TRP B 222 HIS 0.003 0.000 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6848) covalent geometry : angle 0.64369 ( 9253) hydrogen bonds : bond 0.03676 ( 453) hydrogen bonds : angle 4.33543 ( 1347) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: B 101 LEU cc_start: 0.7765 (tt) cc_final: 0.7334 (mt) REVERT: B 105 ARG cc_start: 0.6958 (mmt180) cc_final: 0.6381 (mtt180) REVERT: B 161 TYR cc_start: 0.7649 (t80) cc_final: 0.7357 (t80) REVERT: B 334 ILE cc_start: 0.8113 (mm) cc_final: 0.7651 (mt) REVERT: B 382 LEU cc_start: 0.8406 (mt) cc_final: 0.7982 (mt) REVERT: A 23 MET cc_start: 0.7561 (pmm) cc_final: 0.7159 (pmm) REVERT: A 26 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6851 (mmp) REVERT: A 61 ASP cc_start: 0.7202 (p0) cc_final: 0.6921 (p0) REVERT: A 243 MET cc_start: 0.7727 (mmm) cc_final: 0.7465 (mmm) REVERT: A 293 MET cc_start: 0.6349 (mtm) cc_final: 0.6063 (mpp) REVERT: A 331 MET cc_start: 0.7326 (mmm) cc_final: 0.6889 (tpp) REVERT: A 345 GLU cc_start: 0.7695 (pp20) cc_final: 0.7432 (pp20) outliers start: 26 outliers final: 19 residues processed: 159 average time/residue: 0.0427 time to fit residues: 10.0352 Evaluate side-chains 157 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 40 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 HIS ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.173893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.142565 restraints weight = 11249.803| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.94 r_work: 0.3705 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6848 Z= 0.120 Angle : 0.651 12.705 9253 Z= 0.315 Chirality : 0.041 0.181 1043 Planarity : 0.003 0.036 1132 Dihedral : 5.075 47.053 931 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.32 % Allowed : 26.45 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.30), residues: 854 helix: 1.22 (0.22), residues: 626 sheet: None (None), residues: 0 loop : -2.30 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 441 TYR 0.020 0.001 TYR B 161 PHE 0.012 0.001 PHE B 385 TRP 0.017 0.001 TRP B 222 HIS 0.011 0.001 HIS B 302 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 6848) covalent geometry : angle 0.65079 ( 9253) hydrogen bonds : bond 0.03622 ( 453) hydrogen bonds : angle 4.33814 ( 1347) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: B 26 MET cc_start: 0.7567 (tpt) cc_final: 0.7222 (tmm) REVERT: B 101 LEU cc_start: 0.7763 (tt) cc_final: 0.7310 (mt) REVERT: B 105 ARG cc_start: 0.6931 (mmt180) cc_final: 0.6339 (mtt180) REVERT: B 241 MET cc_start: 0.7407 (tpp) cc_final: 0.6561 (tpp) REVERT: B 334 ILE cc_start: 0.8180 (mm) cc_final: 0.7735 (mt) REVERT: B 382 LEU cc_start: 0.8387 (mt) cc_final: 0.7973 (mt) REVERT: B 494 PHE cc_start: 0.6941 (m-80) cc_final: 0.6642 (m-80) REVERT: A 23 MET cc_start: 0.7626 (pmm) cc_final: 0.7250 (pmm) REVERT: A 26 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6849 (mmp) REVERT: A 61 ASP cc_start: 0.7244 (p0) cc_final: 0.6968 (p0) REVERT: A 243 MET cc_start: 0.7700 (mmm) cc_final: 0.7445 (mmm) REVERT: A 293 MET cc_start: 0.6290 (mtm) cc_final: 0.6040 (mpp) outliers start: 23 outliers final: 20 residues processed: 151 average time/residue: 0.0501 time to fit residues: 11.2523 Evaluate side-chains 157 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 0.0970 chunk 80 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 36 optimal weight: 0.1980 chunk 50 optimal weight: 0.0970 chunk 52 optimal weight: 0.9980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.175581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.144645 restraints weight = 11246.908| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.93 r_work: 0.3731 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 6848 Z= 0.111 Angle : 0.646 13.295 9253 Z= 0.312 Chirality : 0.040 0.177 1043 Planarity : 0.003 0.041 1132 Dihedral : 5.068 49.293 931 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.75 % Allowed : 27.46 % Favored : 69.80 % 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: 0.61 (0.30), residues: 854 helix: 1.26 (0.22), residues: 633 sheet: None (None), residues: 0 loop : -2.15 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 167 TYR 0.015 0.001 TYR B 161 PHE 0.012 0.001 PHE B 429 TRP 0.018 0.001 TRP B 222 HIS 0.007 0.001 HIS B 302 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 6848) covalent geometry : angle 0.64595 ( 9253) hydrogen bonds : bond 0.03376 ( 453) hydrogen bonds : angle 4.26218 ( 1347) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.242 Fit side-chains REVERT: B 26 MET cc_start: 0.7570 (tpt) cc_final: 0.7230 (tmm) REVERT: B 101 LEU cc_start: 0.7681 (tt) cc_final: 0.7235 (mt) REVERT: B 105 ARG cc_start: 0.6967 (mmt180) cc_final: 0.6317 (mtt180) REVERT: B 107 TYR cc_start: 0.7533 (m-10) cc_final: 0.7331 (m-10) REVERT: B 241 MET cc_start: 0.7370 (tpp) cc_final: 0.6538 (tpp) REVERT: B 334 ILE cc_start: 0.8113 (mm) cc_final: 0.7643 (mt) REVERT: B 382 LEU cc_start: 0.8337 (mt) cc_final: 0.7885 (mt) REVERT: B 399 TYR cc_start: 0.7771 (t80) cc_final: 0.7413 (t80) REVERT: B 494 PHE cc_start: 0.7009 (m-80) cc_final: 0.6705 (m-80) REVERT: A 23 MET cc_start: 0.7625 (pmm) cc_final: 0.7253 (pmm) REVERT: A 26 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6816 (mmp) REVERT: A 61 ASP cc_start: 0.7327 (p0) cc_final: 0.7056 (p0) REVERT: A 293 MET cc_start: 0.6413 (mtm) cc_final: 0.6172 (mpp) outliers start: 19 outliers final: 18 residues processed: 156 average time/residue: 0.0473 time to fit residues: 11.0199 Evaluate side-chains 157 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 70 optimal weight: 0.0060 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.0670 chunk 36 optimal weight: 0.0040 chunk 41 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 overall best weight: 0.3346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.177516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.146819 restraints weight = 10963.549| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.95 r_work: 0.3738 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 6848 Z= 0.112 Angle : 0.664 13.350 9253 Z= 0.316 Chirality : 0.040 0.167 1043 Planarity : 0.003 0.036 1132 Dihedral : 5.076 55.407 931 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.75 % Allowed : 28.32 % Favored : 68.93 % 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: 0.67 (0.30), residues: 854 helix: 1.33 (0.22), residues: 629 sheet: None (None), residues: 0 loop : -2.12 (0.40), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 167 TYR 0.024 0.001 TYR B 238 PHE 0.016 0.001 PHE A 311 TRP 0.018 0.001 TRP B 222 HIS 0.002 0.000 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6848) covalent geometry : angle 0.66410 ( 9253) hydrogen bonds : bond 0.03250 ( 453) hydrogen bonds : angle 4.21658 ( 1347) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1414.54 seconds wall clock time: 24 minutes 55.36 seconds (1495.36 seconds total)