Starting phenix.real_space_refine on Tue Nov 18 07:29:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dlu_7957/11_2025/6dlu_7957_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dlu_7957/11_2025/6dlu_7957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6dlu_7957/11_2025/6dlu_7957_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dlu_7957/11_2025/6dlu_7957_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dlu_7957/11_2025/6dlu_7957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dlu_7957/11_2025/6dlu_7957.map" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 66 5.16 5 C 7512 2.51 5 N 2105 2.21 5 O 2300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11991 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5918 Classifications: {'peptide': 734} Link IDs: {'CIS': 13, 'PTRANS': 26, 'TRANS': 694} Chain breaks: 1 Chain: "P" Number of atoms: 6007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6007 Classifications: {'peptide': 747} Link IDs: {'CIS': 12, 'PTRANS': 26, 'TRANS': 708} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.01, per 1000 atoms: 0.25 Number of scatterers: 11991 At special positions: 0 Unit cell: (216.14, 199.02, 112.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 6 15.00 Mg 2 11.99 O 2300 8.00 N 2105 7.00 C 7512 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 516.1 milliseconds 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2804 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 5 sheets defined 52.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'B' and resid 8 through 19 Processing helix chain 'B' and resid 43 through 53 Processing helix chain 'B' and resid 93 through 110 removed outlier: 3.662A pdb=" N VAL B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 165 removed outlier: 3.992A pdb=" N PHE B 163 " --> pdb=" O MET B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 185 through 194 Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 238 through 244 Processing helix chain 'B' and resid 247 through 262 Processing helix chain 'B' and resid 273 through 290 removed outlier: 3.511A pdb=" N LEU B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 309 removed outlier: 3.710A pdb=" N LEU B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE B 307 " --> pdb=" O GLN B 303 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 removed outlier: 3.820A pdb=" N TYR B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 345 Processing helix chain 'B' and resid 360 through 368 removed outlier: 3.873A pdb=" N PHE B 366 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 376 Processing helix chain 'B' and resid 381 through 395 removed outlier: 3.969A pdb=" N ARG B 385 " --> pdb=" O GLU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 417 Processing helix chain 'B' and resid 420 through 442 removed outlier: 3.509A pdb=" N CYS B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER B 437 " --> pdb=" O SER B 433 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 438 " --> pdb=" O GLU B 434 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG B 440 " --> pdb=" O ILE B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 482 removed outlier: 3.894A pdb=" N GLY B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG B 470 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU B 482 " --> pdb=" O LEU B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 507 Processing helix chain 'B' and resid 609 through 624 removed outlier: 3.959A pdb=" N VAL B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP B 614 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 636 removed outlier: 3.516A pdb=" N GLU B 634 " --> pdb=" O GLY B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 689 Proline residue: B 682 - end of helix removed outlier: 3.714A pdb=" N LEU B 688 " --> pdb=" O THR B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 700 Processing helix chain 'B' and resid 700 through 706 Processing helix chain 'B' and resid 718 through 748 Processing helix chain 'P' and resid 4 through 23 Proline residue: P 11 - end of helix Processing helix chain 'P' and resid 43 through 53 removed outlier: 3.733A pdb=" N VAL P 47 " --> pdb=" O GLY P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 93 through 109 Processing helix chain 'P' and resid 151 through 165 removed outlier: 4.194A pdb=" N PHE P 163 " --> pdb=" O MET P 159 " (cutoff:3.500A) Processing helix chain 'P' and resid 180 through 183 Processing helix chain 'P' and resid 184 through 194 Processing helix chain 'P' and resid 206 through 210 removed outlier: 3.509A pdb=" N LEU P 209 " --> pdb=" O LYS P 206 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET P 210 " --> pdb=" O LEU P 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 206 through 210' Processing helix chain 'P' and resid 216 through 221 Processing helix chain 'P' and resid 238 through 244 Processing helix chain 'P' and resid 247 through 262 Processing helix chain 'P' and resid 273 through 312 Proline residue: P 294 - end of helix removed outlier: 3.798A pdb=" N SER P 306 " --> pdb=" O SER P 302 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE P 307 " --> pdb=" O GLN P 303 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS P 309 " --> pdb=" O LEU P 305 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU P 310 " --> pdb=" O SER P 306 " (cutoff:3.500A) Processing helix chain 'P' and resid 313 through 315 No H-bonds generated for 'chain 'P' and resid 313 through 315' Processing helix chain 'P' and resid 321 through 344 removed outlier: 3.646A pdb=" N LYS P 325 " --> pdb=" O ASP P 321 " (cutoff:3.500A) Processing helix chain 'P' and resid 359 through 367 Processing helix chain 'P' and resid 371 through 376 removed outlier: 3.994A pdb=" N VAL P 375 " --> pdb=" O PRO P 371 " (cutoff:3.500A) Processing helix chain 'P' and resid 383 through 396 removed outlier: 4.336A pdb=" N HIS P 396 " --> pdb=" O ILE P 392 " (cutoff:3.500A) Processing helix chain 'P' and resid 406 through 418 removed outlier: 3.555A pdb=" N LYS P 418 " --> pdb=" O LYS P 414 " (cutoff:3.500A) Processing helix chain 'P' and resid 420 through 442 removed outlier: 3.640A pdb=" N CYS P 424 " --> pdb=" O ILE P 420 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU P 425 " --> pdb=" O ARG P 421 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER P 437 " --> pdb=" O SER P 433 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG P 440 " --> pdb=" O ILE P 436 " (cutoff:3.500A) Processing helix chain 'P' and resid 443 through 447 Processing helix chain 'P' and resid 452 through 482 removed outlier: 4.300A pdb=" N GLY P 469 " --> pdb=" O ARG P 465 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG P 470 " --> pdb=" O GLU P 466 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU P 482 " --> pdb=" O LEU P 478 " (cutoff:3.500A) Processing helix chain 'P' and resid 502 through 508 removed outlier: 3.757A pdb=" N MET P 506 " --> pdb=" O ARG P 502 " (cutoff:3.500A) Processing helix chain 'P' and resid 511 through 516 removed outlier: 4.673A pdb=" N GLN P 515 " --> pdb=" O THR P 511 " (cutoff:3.500A) Processing helix chain 'P' and resid 609 through 624 Processing helix chain 'P' and resid 654 through 689 Proline residue: P 682 - end of helix Processing helix chain 'P' and resid 690 through 699 Processing helix chain 'P' and resid 700 through 708 removed outlier: 3.597A pdb=" N CYS P 708 " --> pdb=" O ASN P 704 " (cutoff:3.500A) Processing helix chain 'P' and resid 710 through 715 removed outlier: 3.909A pdb=" N MET P 715 " --> pdb=" O GLN P 711 " (cutoff:3.500A) Processing helix chain 'P' and resid 718 through 747 removed outlier: 3.754A pdb=" N ALA P 722 " --> pdb=" O SER P 718 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR P 747 " --> pdb=" O GLY P 743 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 73 through 75 Processing sheet with id=AA2, first strand: chain 'B' and resid 73 through 75 removed outlier: 6.653A pdb=" N ILE B 34 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN B 33 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU B 172 " --> pdb=" O GLN B 33 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA B 35 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL B 174 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL B 37 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE B 201 " --> pdb=" O CYS B 169 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE B 171 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B 203 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ALA B 173 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N THR B 205 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER B 175 " --> pdb=" O THR B 205 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 565 through 566 removed outlier: 3.825A pdb=" N LYS B 539 " --> pdb=" O ILE B 528 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 527 " --> pdb=" O ALA B 606 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU B 603 " --> pdb=" O LEU B 588 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 80 through 83 removed outlier: 6.586A pdb=" N ILE P 34 " --> pdb=" O VAL P 135 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL P 174 " --> pdb=" O VAL P 37 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE P 201 " --> pdb=" O CYS P 169 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE P 171 " --> pdb=" O ILE P 201 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL P 203 " --> pdb=" O ILE P 171 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ALA P 173 " --> pdb=" O VAL P 203 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR P 205 " --> pdb=" O ALA P 173 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER P 175 " --> pdb=" O THR P 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 565 through 566 removed outlier: 3.700A pdb=" N LYS P 539 " --> pdb=" O ILE P 528 " (cutoff:3.500A) 586 hydrogen bonds defined for protein. 1701 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: 1.97 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 2082 1.28 - 1.42: 2843 1.42 - 1.56: 7123 1.56 - 1.70: 10 1.70 - 1.84: 122 Bond restraints: 12180 Sorted by residual: bond pdb=" C3' GCP B 801 " pdb=" C4' GCP B 801 " ideal model delta sigma weight residual 1.526 1.292 0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C3' GCP P 801 " pdb=" C4' GCP P 801 " ideal model delta sigma weight residual 1.526 1.293 0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C4' GCP P 801 " pdb=" O4' GCP P 801 " ideal model delta sigma weight residual 1.429 1.620 -0.191 2.00e-02 2.50e+03 9.11e+01 bond pdb=" C4' GCP B 801 " pdb=" O4' GCP B 801 " ideal model delta sigma weight residual 1.429 1.619 -0.190 2.00e-02 2.50e+03 9.04e+01 bond pdb=" C3' GCP P 801 " pdb=" O3' GCP P 801 " ideal model delta sigma weight residual 1.401 1.562 -0.161 2.00e-02 2.50e+03 6.52e+01 ... (remaining 12175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 16128 2.83 - 5.66: 229 5.66 - 8.49: 41 8.49 - 11.32: 14 11.32 - 14.15: 4 Bond angle restraints: 16416 Sorted by residual: angle pdb=" C SER B 582 " pdb=" N LYS B 583 " pdb=" CA LYS B 583 " ideal model delta sigma weight residual 121.70 133.09 -11.39 1.80e+00 3.09e-01 4.00e+01 angle pdb=" C SER P 582 " pdb=" N LYS P 583 " pdb=" CA LYS P 583 " ideal model delta sigma weight residual 121.70 132.97 -11.27 1.80e+00 3.09e-01 3.92e+01 angle pdb=" C GLU P 717 " pdb=" N SER P 718 " pdb=" CA SER P 718 " ideal model delta sigma weight residual 121.70 131.71 -10.01 1.80e+00 3.09e-01 3.09e+01 angle pdb=" C GLU B 717 " pdb=" N SER B 718 " pdb=" CA SER B 718 " ideal model delta sigma weight residual 121.70 131.04 -9.34 1.80e+00 3.09e-01 2.69e+01 angle pdb=" C PHE B 317 " pdb=" N ARG B 318 " pdb=" CA ARG B 318 " ideal model delta sigma weight residual 121.70 130.04 -8.34 1.80e+00 3.09e-01 2.15e+01 ... (remaining 16411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 7170 16.47 - 32.94: 311 32.94 - 49.42: 70 49.42 - 65.89: 22 65.89 - 82.36: 13 Dihedral angle restraints: 7586 sinusoidal: 3266 harmonic: 4320 Sorted by residual: dihedral pdb=" CA ARG P 364 " pdb=" C ARG P 364 " pdb=" N ILE P 365 " pdb=" CA ILE P 365 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA GLU B 368 " pdb=" C GLU B 368 " pdb=" N ARG B 369 " pdb=" CA ARG B 369 " ideal model delta harmonic sigma weight residual 180.00 158.99 21.01 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ARG B 290 " pdb=" C ARG B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 -159.31 -20.69 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 7583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1082 0.038 - 0.077: 539 0.077 - 0.115: 167 0.115 - 0.153: 38 0.153 - 0.191: 4 Chirality restraints: 1830 Sorted by residual: chirality pdb=" C2' GCP B 801 " pdb=" C1' GCP B 801 " pdb=" C3' GCP B 801 " pdb=" O2' GCP B 801 " both_signs ideal model delta sigma weight residual False -2.75 -2.56 -0.19 2.00e-01 2.50e+01 9.14e-01 chirality pdb=" C2' GCP P 801 " pdb=" C1' GCP P 801 " pdb=" C3' GCP P 801 " pdb=" O2' GCP P 801 " both_signs ideal model delta sigma weight residual False -2.75 -2.56 -0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" CA VAL B 544 " pdb=" N VAL B 544 " pdb=" C VAL B 544 " pdb=" CB VAL B 544 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.13e-01 ... (remaining 1827 not shown) Planarity restraints: 2135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 432 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C ILE B 432 " 0.040 2.00e-02 2.50e+03 pdb=" O ILE B 432 " -0.015 2.00e-02 2.50e+03 pdb=" N SER B 433 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU P 330 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C LEU P 330 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU P 330 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN P 331 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 430 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C MET B 430 " -0.032 2.00e-02 2.50e+03 pdb=" O MET B 430 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL B 431 " 0.011 2.00e-02 2.50e+03 ... (remaining 2132 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 61 2.54 - 3.13: 9582 3.13 - 3.72: 17654 3.72 - 4.31: 23917 4.31 - 4.90: 39446 Nonbonded interactions: 90660 Sorted by model distance: nonbonded pdb=" O1B GCP B 801 " pdb="MG MG B 802 " model vdw 1.944 2.170 nonbonded pdb=" OG1 THR B 65 " pdb="MG MG B 802 " model vdw 1.963 2.170 nonbonded pdb=" OG1 THR P 65 " pdb="MG MG P 802 " model vdw 2.002 2.170 nonbonded pdb=" OE2 GLU B 104 " pdb=" NH2 ARG B 107 " model vdw 2.025 3.120 nonbonded pdb=" O2G GCP B 801 " pdb="MG MG B 802 " model vdw 2.035 2.170 ... (remaining 90655 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 'B' and (resid 7 through 747 or resid 801 through 802)) selection = (chain 'P' and (resid 7 through 20 or resid 29 through 802)) } 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 group one per residue 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: 12.610 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.290 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 : 0.009 0.234 12181 Z= 0.398 Angle : 0.945 14.147 16416 Z= 0.488 Chirality : 0.048 0.191 1830 Planarity : 0.004 0.031 2135 Dihedral : 11.137 82.361 4782 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.23 % Allowed : 3.10 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.75 % 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: -2.78 (0.19), residues: 1475 helix: -0.90 (0.18), residues: 695 sheet: -1.67 (0.34), residues: 184 loop : -3.02 (0.19), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 724 TYR 0.022 0.002 TYR B 669 PHE 0.022 0.002 PHE B 366 TRP 0.021 0.003 TRP B 616 HIS 0.009 0.002 HIS P 396 Details of bonding type rmsd covalent geometry : bond 0.00866 (12180) covalent geometry : angle 0.94506 (16416) hydrogen bonds : bond 0.15298 ( 584) hydrogen bonds : angle 6.48159 ( 1701) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 227 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 361 ARG cc_start: 0.7193 (tpt90) cc_final: 0.6722 (tpp-160) REVERT: B 434 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7828 (tm-30) REVERT: B 480 ASP cc_start: 0.8008 (m-30) cc_final: 0.7681 (m-30) REVERT: B 648 MET cc_start: 0.4195 (mpp) cc_final: 0.3877 (mpp) REVERT: B 681 MET cc_start: 0.7568 (ppp) cc_final: 0.7262 (tmm) REVERT: P 1 MET cc_start: 0.7218 (mtt) cc_final: 0.7014 (mtp) REVERT: P 181 LEU cc_start: 0.8820 (tp) cc_final: 0.8592 (tt) REVERT: P 297 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7642 (ttm-80) REVERT: P 356 LEU cc_start: 0.7181 (tt) cc_final: 0.6587 (mt) REVERT: P 376 LYS cc_start: 0.7929 (ttpt) cc_final: 0.7659 (ttpp) REVERT: P 489 ASN cc_start: 0.7964 (t0) cc_final: 0.7252 (p0) REVERT: P 506 MET cc_start: -0.0395 (tpt) cc_final: -0.0913 (tpp) outliers start: 3 outliers final: 0 residues processed: 229 average time/residue: 0.1308 time to fit residues: 41.5939 Evaluate side-chains 124 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 20.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 ASN B 284 GLN B 288 HIS B 692 ASN B 733 HIS P 155 GLN ** P 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 530 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.140496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.107348 restraints weight = 27660.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.106948 restraints weight = 18855.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.108138 restraints weight = 14617.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.108706 restraints weight = 12202.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.108823 restraints weight = 9423.502| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12181 Z= 0.165 Angle : 0.684 11.589 16416 Z= 0.360 Chirality : 0.043 0.170 1830 Planarity : 0.004 0.038 2135 Dihedral : 7.091 87.248 1679 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.51 % Allowed : 7.78 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.75 % 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: -1.60 (0.20), residues: 1475 helix: 0.15 (0.19), residues: 720 sheet: -1.26 (0.37), residues: 178 loop : -2.58 (0.21), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 467 TYR 0.013 0.002 TYR P 314 PHE 0.018 0.002 PHE P 83 TRP 0.010 0.002 TRP P 616 HIS 0.005 0.001 HIS P 367 Details of bonding type rmsd covalent geometry : bond 0.00368 (12180) covalent geometry : angle 0.68365 (16416) hydrogen bonds : bond 0.04642 ( 584) hydrogen bonds : angle 4.69864 ( 1701) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7258 (t0) cc_final: 0.7052 (t0) REVERT: B 434 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7868 (tm-30) REVERT: B 480 ASP cc_start: 0.7966 (m-30) cc_final: 0.7670 (m-30) REVERT: B 648 MET cc_start: 0.4246 (mpp) cc_final: 0.3904 (mpp) REVERT: B 657 ARG cc_start: 0.6870 (ptt-90) cc_final: 0.6484 (ptp90) REVERT: B 681 MET cc_start: 0.7674 (ppp) cc_final: 0.7202 (tmm) REVERT: P 297 ARG cc_start: 0.8247 (ttp80) cc_final: 0.7745 (ttm-80) REVERT: P 361 ARG cc_start: 0.5500 (ttt90) cc_final: 0.4501 (ttt90) REVERT: P 376 LYS cc_start: 0.7967 (ttpt) cc_final: 0.7730 (ttpp) REVERT: P 506 MET cc_start: -0.0441 (tpt) cc_final: -0.0888 (tpp) outliers start: 20 outliers final: 11 residues processed: 147 average time/residue: 0.1262 time to fit residues: 26.3520 Evaluate side-chains 117 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 234 VAL Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 305 LEU Chi-restraints excluded: chain P residue 329 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 70 optimal weight: 6.9990 chunk 21 optimal weight: 0.3980 chunk 82 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 87 optimal weight: 0.2980 chunk 85 optimal weight: 0.5980 chunk 2 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 GLN ** P 367 HIS ** 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 = 0.4028 r_free = 0.4028 target = 0.141785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.109339 restraints weight = 27775.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.108763 restraints weight = 18886.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.109498 restraints weight = 16616.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.110356 restraints weight = 12290.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.110327 restraints weight = 11261.550| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12181 Z= 0.120 Angle : 0.591 11.358 16416 Z= 0.313 Chirality : 0.040 0.150 1830 Planarity : 0.003 0.029 2135 Dihedral : 5.921 88.273 1679 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.81 % Allowed : 9.52 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.75 % 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: -0.86 (0.21), residues: 1475 helix: 0.87 (0.20), residues: 717 sheet: -1.03 (0.37), residues: 178 loop : -2.31 (0.22), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 440 TYR 0.013 0.001 TYR P 354 PHE 0.012 0.001 PHE B 543 TRP 0.009 0.001 TRP B 542 HIS 0.005 0.001 HIS P 367 Details of bonding type rmsd covalent geometry : bond 0.00245 (12180) covalent geometry : angle 0.59075 (16416) hydrogen bonds : bond 0.03763 ( 584) hydrogen bonds : angle 4.12537 ( 1701) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.491 Fit side-chains REVERT: B 361 ARG cc_start: 0.7573 (tpt-90) cc_final: 0.7254 (tpt-90) REVERT: B 434 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7541 (tp30) REVERT: B 486 MET cc_start: 0.7306 (tmm) cc_final: 0.7031 (tmm) REVERT: B 506 MET cc_start: -0.2157 (pmm) cc_final: -0.3702 (ptt) REVERT: B 648 MET cc_start: 0.4394 (mpp) cc_final: 0.3906 (mpp) REVERT: P 361 ARG cc_start: 0.5339 (ttt90) cc_final: 0.4215 (ttt90) REVERT: P 373 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7518 (tm-30) REVERT: P 506 MET cc_start: -0.0476 (tpt) cc_final: -0.0909 (tpp) outliers start: 24 outliers final: 9 residues processed: 139 average time/residue: 0.1216 time to fit residues: 24.1036 Evaluate side-chains 111 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 305 LEU Chi-restraints excluded: chain P residue 329 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 39 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 63 optimal weight: 0.3980 chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 17 GLN P 178 ASN ** P 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.141140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.107602 restraints weight = 27857.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.107875 restraints weight = 16905.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.108765 restraints weight = 13587.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.109085 restraints weight = 11935.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.109377 restraints weight = 8947.351| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12181 Z= 0.128 Angle : 0.598 11.348 16416 Z= 0.312 Chirality : 0.041 0.144 1830 Planarity : 0.003 0.029 2135 Dihedral : 5.733 85.501 1679 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.64 % Allowed : 10.42 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.75 % 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 (0.22), residues: 1475 helix: 1.21 (0.20), residues: 712 sheet: -0.84 (0.38), residues: 178 loop : -2.13 (0.22), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 467 TYR 0.011 0.001 TYR P 314 PHE 0.011 0.001 PHE B 409 TRP 0.010 0.001 TRP B 616 HIS 0.006 0.001 HIS P 367 Details of bonding type rmsd covalent geometry : bond 0.00275 (12180) covalent geometry : angle 0.59781 (16416) hydrogen bonds : bond 0.03583 ( 584) hydrogen bonds : angle 3.99323 ( 1701) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.494 Fit side-chains REVERT: B 140 MET cc_start: 0.8136 (mtt) cc_final: 0.7830 (mtt) REVERT: B 361 ARG cc_start: 0.7592 (tpt-90) cc_final: 0.7213 (tpt-90) REVERT: B 434 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7681 (tp30) REVERT: B 486 MET cc_start: 0.7580 (tmm) cc_final: 0.7135 (tmm) REVERT: B 648 MET cc_start: 0.4468 (mpp) cc_final: 0.4036 (mpp) REVERT: P 361 ARG cc_start: 0.5452 (ttt90) cc_final: 0.4156 (ttm-80) REVERT: P 564 MET cc_start: 0.4440 (tpp) cc_final: 0.2799 (mmm) outliers start: 35 outliers final: 20 residues processed: 138 average time/residue: 0.1239 time to fit residues: 24.4077 Evaluate side-chains 118 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 130 LEU Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain P residue 399 ARG Chi-restraints excluded: chain P residue 434 GLU Chi-restraints excluded: chain P residue 459 ILE Chi-restraints excluded: chain P residue 603 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 108 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 127 optimal weight: 30.0000 chunk 10 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 367 HIS ** 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 = 0.3986 r_free = 0.3986 target = 0.138746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.105976 restraints weight = 27577.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.104633 restraints weight = 18056.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.106516 restraints weight = 14916.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.106508 restraints weight = 11380.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.106554 restraints weight = 9559.792| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12181 Z= 0.144 Angle : 0.603 11.314 16416 Z= 0.313 Chirality : 0.041 0.148 1830 Planarity : 0.003 0.030 2135 Dihedral : 5.733 84.912 1679 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.04 % Allowed : 11.63 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.75 % 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: -0.23 (0.22), residues: 1475 helix: 1.44 (0.20), residues: 713 sheet: -0.73 (0.39), residues: 178 loop : -2.04 (0.23), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 467 TYR 0.012 0.001 TYR B 125 PHE 0.010 0.001 PHE B 409 TRP 0.010 0.001 TRP B 616 HIS 0.005 0.001 HIS P 367 Details of bonding type rmsd covalent geometry : bond 0.00312 (12180) covalent geometry : angle 0.60252 (16416) hydrogen bonds : bond 0.03576 ( 584) hydrogen bonds : angle 3.95018 ( 1701) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.503 Fit side-chains REVERT: B 332 MET cc_start: 0.8411 (tpp) cc_final: 0.8129 (mmt) REVERT: B 361 ARG cc_start: 0.7643 (tpt-90) cc_final: 0.6829 (tpt-90) REVERT: B 434 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7667 (tp30) REVERT: B 486 MET cc_start: 0.7676 (tmm) cc_final: 0.7361 (tmm) REVERT: B 648 MET cc_start: 0.4504 (mpp) cc_final: 0.4054 (mpp) REVERT: P 6 MET cc_start: 0.8563 (tpp) cc_final: 0.8312 (tpp) REVERT: P 361 ARG cc_start: 0.5605 (ttt90) cc_final: 0.4132 (ttt90) REVERT: P 364 ARG cc_start: 0.7029 (ptm160) cc_final: 0.4810 (mtt90) REVERT: P 564 MET cc_start: 0.4389 (tpp) cc_final: 0.2648 (mmm) outliers start: 27 outliers final: 16 residues processed: 121 average time/residue: 0.1265 time to fit residues: 22.2516 Evaluate side-chains 112 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 305 LEU Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain P residue 399 ARG Chi-restraints excluded: chain P residue 459 ILE Chi-restraints excluded: chain P residue 603 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 17 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 121 ASN P 155 GLN P 367 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.135472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.103163 restraints weight = 27717.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.101234 restraints weight = 20730.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.102350 restraints weight = 18464.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.102807 restraints weight = 13997.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.102882 restraints weight = 11614.735| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12181 Z= 0.202 Angle : 0.690 11.352 16416 Z= 0.358 Chirality : 0.044 0.162 1830 Planarity : 0.004 0.071 2135 Dihedral : 6.123 81.272 1679 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.89 % Allowed : 12.01 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.75 % 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 (0.22), residues: 1475 helix: 1.24 (0.20), residues: 713 sheet: -0.67 (0.39), residues: 176 loop : -1.96 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 657 TYR 0.023 0.002 TYR B 125 PHE 0.013 0.002 PHE B 409 TRP 0.014 0.002 TRP P 542 HIS 0.009 0.002 HIS P 396 Details of bonding type rmsd covalent geometry : bond 0.00472 (12180) covalent geometry : angle 0.69030 (16416) hydrogen bonds : bond 0.04275 ( 584) hydrogen bonds : angle 4.24353 ( 1701) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.420 Fit side-chains REVERT: B 361 ARG cc_start: 0.7699 (tpt-90) cc_final: 0.6890 (tpt-90) REVERT: B 434 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8019 (tm-30) REVERT: B 486 MET cc_start: 0.7848 (tmm) cc_final: 0.7552 (tmm) REVERT: B 648 MET cc_start: 0.4758 (mpp) cc_final: 0.4259 (mpp) REVERT: P 6 MET cc_start: 0.8692 (tpp) cc_final: 0.8375 (tpp) REVERT: P 399 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.5100 (tpp-160) REVERT: P 564 MET cc_start: 0.4190 (tpp) cc_final: 0.2605 (mmm) REVERT: P 651 MET cc_start: 0.2416 (tpp) cc_final: 0.2099 (tpt) REVERT: P 670 MET cc_start: 0.8796 (mmm) cc_final: 0.8540 (mmt) outliers start: 25 outliers final: 17 residues processed: 109 average time/residue: 0.1226 time to fit residues: 19.3279 Evaluate side-chains 99 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 399 ARG Chi-restraints excluded: chain P residue 434 GLU Chi-restraints excluded: chain P residue 459 ILE Chi-restraints excluded: chain P residue 603 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 126 optimal weight: 0.2980 chunk 91 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 ASN P 288 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.136519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.103573 restraints weight = 27601.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.102264 restraints weight = 20689.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.102724 restraints weight = 16781.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.104603 restraints weight = 14412.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.104390 restraints weight = 10918.566| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12181 Z= 0.160 Angle : 0.632 11.875 16416 Z= 0.327 Chirality : 0.042 0.150 1830 Planarity : 0.003 0.032 2135 Dihedral : 5.871 78.765 1679 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.51 % Allowed : 13.29 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.75 % 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 (0.22), residues: 1475 helix: 1.43 (0.20), residues: 709 sheet: -0.74 (0.39), residues: 177 loop : -1.84 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 663 TYR 0.017 0.001 TYR B 125 PHE 0.011 0.001 PHE B 409 TRP 0.009 0.001 TRP B 616 HIS 0.005 0.001 HIS P 396 Details of bonding type rmsd covalent geometry : bond 0.00374 (12180) covalent geometry : angle 0.63225 (16416) hydrogen bonds : bond 0.03828 ( 584) hydrogen bonds : angle 4.07331 ( 1701) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.494 Fit side-chains REVERT: B 434 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7758 (tp30) REVERT: B 521 ILE cc_start: -0.2037 (OUTLIER) cc_final: -0.2254 (mt) REVERT: B 648 MET cc_start: 0.4815 (mpp) cc_final: 0.4326 (mpp) REVERT: P 399 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.5160 (tpp-160) REVERT: P 476 MET cc_start: 0.7746 (tpt) cc_final: 0.7408 (tpp) REVERT: P 564 MET cc_start: 0.4231 (tpp) cc_final: 0.2579 (mmm) outliers start: 20 outliers final: 15 residues processed: 102 average time/residue: 0.1148 time to fit residues: 17.5132 Evaluate side-chains 100 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 399 ARG Chi-restraints excluded: chain P residue 434 GLU Chi-restraints excluded: chain P residue 603 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 94 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 143 optimal weight: 0.0000 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 85 HIS P 687 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.138521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.105427 restraints weight = 27385.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.104381 restraints weight = 17637.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.105666 restraints weight = 14388.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.105923 restraints weight = 11617.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.105831 restraints weight = 9920.828| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12181 Z= 0.121 Angle : 0.606 11.349 16416 Z= 0.312 Chirality : 0.041 0.148 1830 Planarity : 0.003 0.031 2135 Dihedral : 5.636 78.459 1679 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.36 % Allowed : 13.67 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.75 % 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 (0.22), residues: 1475 helix: 1.66 (0.20), residues: 715 sheet: -0.67 (0.39), residues: 179 loop : -1.83 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 123 TYR 0.017 0.001 TYR B 125 PHE 0.009 0.001 PHE B 94 TRP 0.010 0.001 TRP B 542 HIS 0.004 0.001 HIS P 396 Details of bonding type rmsd covalent geometry : bond 0.00264 (12180) covalent geometry : angle 0.60592 (16416) hydrogen bonds : bond 0.03370 ( 584) hydrogen bonds : angle 3.87662 ( 1701) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: B 434 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8034 (tp30) REVERT: B 521 ILE cc_start: -0.2057 (OUTLIER) cc_final: -0.2274 (mt) REVERT: B 648 MET cc_start: 0.4621 (mpp) cc_final: 0.4142 (mpp) REVERT: P 364 ARG cc_start: 0.6900 (ptm160) cc_final: 0.5029 (mtt90) REVERT: P 399 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.5138 (tpp-160) REVERT: P 534 MET cc_start: 0.2403 (tmm) cc_final: 0.1783 (tmm) outliers start: 18 outliers final: 11 residues processed: 105 average time/residue: 0.1228 time to fit residues: 18.7543 Evaluate side-chains 99 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 399 ARG Chi-restraints excluded: chain P residue 434 GLU Chi-restraints excluded: chain P residue 459 ILE Chi-restraints excluded: chain P residue 603 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.0870 chunk 61 optimal weight: 30.0000 chunk 83 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.137443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.104615 restraints weight = 27452.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.103495 restraints weight = 18610.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.104665 restraints weight = 14802.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.105071 restraints weight = 11484.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.105129 restraints weight = 9703.473| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12181 Z= 0.135 Angle : 0.627 11.345 16416 Z= 0.323 Chirality : 0.041 0.144 1830 Planarity : 0.003 0.030 2135 Dihedral : 5.627 77.998 1679 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.28 % Allowed : 13.82 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.75 % 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 (0.22), residues: 1475 helix: 1.68 (0.20), residues: 715 sheet: -0.58 (0.40), residues: 179 loop : -1.78 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 440 TYR 0.016 0.001 TYR B 125 PHE 0.008 0.001 PHE P 647 TRP 0.008 0.001 TRP B 616 HIS 0.004 0.001 HIS P 396 Details of bonding type rmsd covalent geometry : bond 0.00306 (12180) covalent geometry : angle 0.62733 (16416) hydrogen bonds : bond 0.03430 ( 584) hydrogen bonds : angle 3.87802 ( 1701) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.506 Fit side-chains REVERT: B 434 GLU cc_start: 0.8561 (tm-30) cc_final: 0.7972 (tp30) REVERT: B 476 MET cc_start: 0.7844 (mmp) cc_final: 0.7637 (mmm) REVERT: B 521 ILE cc_start: -0.2000 (OUTLIER) cc_final: -0.2226 (mt) REVERT: B 648 MET cc_start: 0.4717 (mpp) cc_final: 0.4227 (mpp) REVERT: P 364 ARG cc_start: 0.6916 (ptm160) cc_final: 0.5061 (mtt90) REVERT: P 399 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.5157 (tpp-160) REVERT: P 534 MET cc_start: 0.2412 (tmm) cc_final: 0.1871 (tmm) REVERT: P 564 MET cc_start: 0.4196 (tmm) cc_final: 0.3201 (tpp) outliers start: 17 outliers final: 12 residues processed: 100 average time/residue: 0.1156 time to fit residues: 17.0435 Evaluate side-chains 101 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 399 ARG Chi-restraints excluded: chain P residue 434 GLU Chi-restraints excluded: chain P residue 459 ILE Chi-restraints excluded: chain P residue 603 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 0.1980 chunk 64 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 15 optimal weight: 0.0570 chunk 0 optimal weight: 7.9990 chunk 115 optimal weight: 0.7980 chunk 143 optimal weight: 0.0070 chunk 116 optimal weight: 0.6980 chunk 49 optimal weight: 0.0870 chunk 140 optimal weight: 0.8980 overall best weight: 0.2094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 367 HIS B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.140038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.107238 restraints weight = 27785.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.106272 restraints weight = 19283.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.107722 restraints weight = 14851.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.108058 restraints weight = 10718.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.108183 restraints weight = 9659.588| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12181 Z= 0.114 Angle : 0.605 11.328 16416 Z= 0.310 Chirality : 0.040 0.145 1830 Planarity : 0.003 0.033 2135 Dihedral : 5.389 78.048 1679 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.13 % Allowed : 13.60 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.75 % 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 (0.22), residues: 1475 helix: 1.90 (0.20), residues: 714 sheet: -0.63 (0.38), residues: 185 loop : -1.65 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 440 TYR 0.010 0.001 TYR P 669 PHE 0.010 0.001 PHE B 94 TRP 0.012 0.001 TRP B 542 HIS 0.003 0.000 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00233 (12180) covalent geometry : angle 0.60471 (16416) hydrogen bonds : bond 0.03006 ( 584) hydrogen bonds : angle 3.72252 ( 1701) Misc. bond : bond 0.00001 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.509 Fit side-chains REVERT: B 434 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7861 (tp30) REVERT: B 476 MET cc_start: 0.7801 (mmp) cc_final: 0.7593 (mmm) REVERT: B 521 ILE cc_start: -0.1869 (OUTLIER) cc_final: -0.2103 (mt) REVERT: B 648 MET cc_start: 0.4762 (mpp) cc_final: 0.4243 (mpp) REVERT: P 266 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7067 (mtt90) REVERT: P 361 ARG cc_start: 0.5880 (ttt90) cc_final: 0.3400 (ttm110) REVERT: P 364 ARG cc_start: 0.6466 (ptm160) cc_final: 0.4849 (mtt90) REVERT: P 534 MET cc_start: 0.2320 (tmm) cc_final: 0.1777 (tmm) REVERT: P 564 MET cc_start: 0.4289 (tmm) cc_final: 0.3372 (tpp) REVERT: P 686 MET cc_start: 0.5350 (mtm) cc_final: 0.5005 (ttp) outliers start: 15 outliers final: 10 residues processed: 110 average time/residue: 0.1204 time to fit residues: 19.2282 Evaluate side-chains 102 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 266 ARG Chi-restraints excluded: chain P residue 399 ARG Chi-restraints excluded: chain P residue 434 GLU Chi-restraints excluded: chain P residue 459 ILE Chi-restraints excluded: chain P residue 603 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 4 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 97 optimal weight: 0.0370 chunk 138 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 38 optimal weight: 0.0980 chunk 25 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 overall best weight: 1.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.139112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.105844 restraints weight = 27646.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.104947 restraints weight = 17413.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.106424 restraints weight = 13627.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.106510 restraints weight = 10811.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.106686 restraints weight = 9716.648| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12181 Z= 0.128 Angle : 0.622 11.357 16416 Z= 0.316 Chirality : 0.041 0.178 1830 Planarity : 0.003 0.034 2135 Dihedral : 5.446 78.710 1679 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.13 % Allowed : 13.97 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.75 % 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: 0.40 (0.22), residues: 1475 helix: 1.90 (0.20), residues: 714 sheet: -0.61 (0.39), residues: 182 loop : -1.60 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 440 TYR 0.014 0.001 TYR B 80 PHE 0.008 0.001 PHE B 94 TRP 0.008 0.001 TRP B 542 HIS 0.004 0.001 HIS P 396 Details of bonding type rmsd covalent geometry : bond 0.00290 (12180) covalent geometry : angle 0.62152 (16416) hydrogen bonds : bond 0.03147 ( 584) hydrogen bonds : angle 3.72846 ( 1701) Misc. bond : bond 0.00009 ( 1) =============================================================================== Job complete usr+sys time: 2643.45 seconds wall clock time: 46 minutes 20.73 seconds (2780.73 seconds total)