Starting phenix.real_space_refine on Wed Sep 17 16:21:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b6m_44266/09_2025/9b6m_44266.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b6m_44266/09_2025/9b6m_44266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b6m_44266/09_2025/9b6m_44266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b6m_44266/09_2025/9b6m_44266.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b6m_44266/09_2025/9b6m_44266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b6m_44266/09_2025/9b6m_44266.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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 25 5.16 5 C 6236 2.51 5 N 1646 2.21 5 O 1896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9803 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3108 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 14, 'TRANS': 375} Chain: "B" Number of atoms: 6695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6695 Classifications: {'peptide': 830} Link IDs: {'PTRANS': 24, 'TRANS': 805} Time building chain proxies: 2.31, per 1000 atoms: 0.24 Number of scatterers: 9803 At special positions: 0 Unit cell: (81.34, 101.26, 117.03, 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 25 16.00 O 1896 8.00 N 1646 7.00 C 6236 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: 0.89 Conformation dependent library (CDL) restraints added in 372.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2312 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 32.6% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 74 through 95 removed outlier: 3.908A pdb=" N TYR A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 108 Processing helix chain 'A' and resid 195 through 212 removed outlier: 3.519A pdb=" N THR A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.926A pdb=" N THR A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 274 Processing helix chain 'A' and resid 276 through 291 removed outlier: 3.581A pdb=" N LYS A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 Processing helix chain 'A' and resid 319 through 328 Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'B' and resid 19 through 25 Processing helix chain 'B' and resid 72 through 79 removed outlier: 3.545A pdb=" N TYR B 76 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 removed outlier: 4.208A pdb=" N VAL B 105 " --> pdb=" O ASN B 101 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 126 removed outlier: 3.735A pdb=" N ALA B 122 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS B 123 " --> pdb=" O SER B 119 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 124 " --> pdb=" O GLY B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 154 removed outlier: 3.990A pdb=" N VAL B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 140 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.636A pdb=" N VAL B 173 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY B 174 " --> pdb=" O PRO B 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 170 through 174' Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'B' and resid 223 through 257 removed outlier: 3.641A pdb=" N PHE B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS B 243 " --> pdb=" O ASN B 239 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR B 246 " --> pdb=" O TRP B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 290 Processing helix chain 'B' and resid 303 through 340 removed outlier: 4.042A pdb=" N LYS B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 370 removed outlier: 3.626A pdb=" N GLY B 370 " --> pdb=" O PHE B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 388 Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 475 through 481 removed outlier: 3.987A pdb=" N PHE B 479 " --> pdb=" O ASN B 476 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 480 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP B 481 " --> pdb=" O ARG B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 504 removed outlier: 3.588A pdb=" N ASP B 504 " --> pdb=" O ASP B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 552 removed outlier: 3.812A pdb=" N VAL B 552 " --> pdb=" O ASN B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 635 removed outlier: 3.885A pdb=" N TYR B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE B 635 " --> pdb=" O PHE B 631 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 24 removed outlier: 7.122A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N MET A 141 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS A 153 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 114 removed outlier: 3.592A pdb=" N SER A 113 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 189 Processing sheet with id=AA4, first strand: chain 'A' and resid 233 through 237 removed outlier: 5.994A pdb=" N VAL A 233 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA A 226 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY A 235 " --> pdb=" O TYR A 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 9 removed outlier: 4.063A pdb=" N ILE B 4 " --> pdb=" O CYS A 389 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS A 389 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU A 384 " --> pdb=" O SER B 64 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ILE B 66 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASN A 386 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA7, first strand: chain 'B' and resid 157 through 161 removed outlier: 5.281A pdb=" N ARG B 161 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLU B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 431 through 434 removed outlier: 6.507A pdb=" N ILE B 617 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER B 424 " --> pdb=" O PHE B 615 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N PHE B 615 " --> pdb=" O SER B 424 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 611 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 610 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG B 449 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 431 through 434 removed outlier: 6.507A pdb=" N ILE B 617 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER B 424 " --> pdb=" O PHE B 615 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N PHE B 615 " --> pdb=" O SER B 424 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 442 through 444 removed outlier: 4.029A pdb=" N ILE B 511 " --> pdb=" O GLN B 599 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL B 601 " --> pdb=" O TYR B 509 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N TYR B 509 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE B 524 " --> pdb=" O ILE B 511 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASN B 513 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE B 522 " --> pdb=" O ASN B 513 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU B 531 " --> pdb=" O ILE B 545 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 655 through 658 Processing sheet with id=AB3, first strand: chain 'B' and resid 666 through 668 Processing sheet with id=AB4, first strand: chain 'B' and resid 680 through 681 Processing sheet with id=AB5, first strand: chain 'B' and resid 699 through 703 removed outlier: 4.741A pdb=" N ILE B 722 " --> pdb=" O VAL B 731 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN B 729 " --> pdb=" O LEU B 724 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 761 through 763 removed outlier: 5.788A pdb=" N ILE B 773 " --> pdb=" O VAL B 791 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1029 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: 1.69 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1704 1.31 - 1.44: 2510 1.44 - 1.58: 5734 1.58 - 1.71: 0 1.71 - 1.84: 40 Bond restraints: 9988 Sorted by residual: bond pdb=" C PRO B 546 " pdb=" O PRO B 546 " ideal model delta sigma weight residual 1.235 1.194 0.041 7.90e-03 1.60e+04 2.68e+01 bond pdb=" C PRO A 44 " pdb=" O PRO A 44 " ideal model delta sigma weight residual 1.234 1.187 0.047 1.00e-02 1.00e+04 2.22e+01 bond pdb=" C LEU B 762 " pdb=" O LEU B 762 " ideal model delta sigma weight residual 1.234 1.178 0.056 1.22e-02 6.72e+03 2.10e+01 bond pdb=" CA SER B 247 " pdb=" CB SER B 247 " ideal model delta sigma weight residual 1.528 1.454 0.074 1.66e-02 3.63e+03 2.00e+01 bond pdb=" C VAL A 66 " pdb=" O VAL A 66 " ideal model delta sigma weight residual 1.236 1.277 -0.041 1.00e-02 1.00e+04 1.69e+01 ... (remaining 9983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 9415 1.44 - 2.89: 3513 2.89 - 4.33: 509 4.33 - 5.77: 50 5.77 - 7.21: 8 Bond angle restraints: 13495 Sorted by residual: angle pdb=" N LEU A 239 " pdb=" CA LEU A 239 " pdb=" C LEU A 239 " ideal model delta sigma weight residual 111.28 106.06 5.22 1.09e+00 8.42e-01 2.30e+01 angle pdb=" N THR B 747 " pdb=" CA THR B 747 " pdb=" C THR B 747 " ideal model delta sigma weight residual 113.56 107.22 6.34 1.39e+00 5.18e-01 2.08e+01 angle pdb=" N LYS A 312 " pdb=" CA LYS A 312 " pdb=" C LYS A 312 " ideal model delta sigma weight residual 111.07 106.22 4.85 1.07e+00 8.73e-01 2.05e+01 angle pdb=" CA ASP B 102 " pdb=" CB ASP B 102 " pdb=" CG ASP B 102 " ideal model delta sigma weight residual 112.60 117.12 -4.52 1.00e+00 1.00e+00 2.04e+01 angle pdb=" N MET B 303 " pdb=" CA MET B 303 " pdb=" C MET B 303 " ideal model delta sigma weight residual 113.55 108.01 5.54 1.26e+00 6.30e-01 1.93e+01 ... (remaining 13490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 5110 17.05 - 34.10: 713 34.10 - 51.15: 196 51.15 - 68.20: 42 68.20 - 85.25: 13 Dihedral angle restraints: 6074 sinusoidal: 2497 harmonic: 3577 Sorted by residual: dihedral pdb=" CA LEU B 401 " pdb=" C LEU B 401 " pdb=" N MET B 402 " pdb=" CA MET B 402 " ideal model delta harmonic sigma weight residual 180.00 -159.38 -20.62 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ARG B 369 " pdb=" C ARG B 369 " pdb=" N GLY B 370 " pdb=" CA GLY B 370 " ideal model delta harmonic sigma weight residual -180.00 -160.97 -19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA LYS B 620 " pdb=" C LYS B 620 " pdb=" N ALA B 621 " pdb=" CA ALA B 621 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 6071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 702 0.050 - 0.099: 461 0.099 - 0.149: 288 0.149 - 0.199: 54 0.199 - 0.248: 10 Chirality restraints: 1515 Sorted by residual: chirality pdb=" CA VAL A 346 " pdb=" N VAL A 346 " pdb=" C VAL A 346 " pdb=" CB VAL A 346 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA VAL A 66 " pdb=" N VAL A 66 " pdb=" C VAL A 66 " pdb=" CB VAL A 66 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ILE B 459 " pdb=" N ILE B 459 " pdb=" C ILE B 459 " pdb=" CB ILE B 459 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1512 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 254 " 0.051 2.00e-02 2.50e+03 2.82e-02 1.60e+01 pdb=" CG TYR B 254 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR B 254 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B 254 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR B 254 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR B 254 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 254 " 0.021 2.00e-02 2.50e+03 pdb=" OH TYR B 254 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 253 " -0.031 2.00e-02 2.50e+03 2.00e-02 9.99e+00 pdb=" CG TRP B 253 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP B 253 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 253 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 253 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TRP B 253 " -0.033 2.00e-02 2.50e+03 pdb=" CE3 TRP B 253 " 0.027 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 253 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 253 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 253 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 821 " 0.035 2.00e-02 2.50e+03 2.30e-02 9.27e+00 pdb=" CG PHE B 821 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE B 821 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 821 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE B 821 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE B 821 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE B 821 " 0.028 2.00e-02 2.50e+03 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 568 2.72 - 3.27: 10391 3.27 - 3.81: 15465 3.81 - 4.36: 21004 4.36 - 4.90: 33474 Nonbonded interactions: 80902 Sorted by model distance: nonbonded pdb=" N ASP A 130 " pdb=" OD1 ASP A 130 " model vdw 2.175 3.120 nonbonded pdb=" OH TYR A 81 " pdb=" O THR A 143 " model vdw 2.206 3.040 nonbonded pdb=" N GLU A 62 " pdb=" OE1 GLU A 62 " model vdw 2.207 3.120 nonbonded pdb=" OG SER A 340 " pdb=" OE1 GLN B 263 " model vdw 2.208 3.040 nonbonded pdb=" OD1 ASP A 195 " pdb=" OH TYR A 355 " model vdw 2.217 3.040 ... (remaining 80897 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.370 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 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 : 0.012 0.074 9988 Z= 0.899 Angle : 1.411 7.213 13495 Z= 1.008 Chirality : 0.079 0.248 1515 Planarity : 0.006 0.028 1728 Dihedral : 17.293 85.249 3762 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.25 % Favored : 93.34 % Rotamer: Outliers : 4.07 % Allowed : 22.17 % Favored : 73.76 % 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 aren not related in a simple way. whole: -1.12 (0.23), residues: 1216 helix: 0.46 (0.27), residues: 372 sheet: -0.51 (0.43), residues: 149 loop : -1.51 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG B 492 TYR 0.051 0.007 TYR B 254 PHE 0.035 0.007 PHE B 821 TRP 0.033 0.006 TRP B 253 HIS 0.016 0.004 HIS B 345 Details of bonding type rmsd covalent geometry : bond 0.01239 ( 9988) covalent geometry : angle 1.41137 (13495) hydrogen bonds : bond 0.22597 ( 360) hydrogen bonds : angle 8.42029 ( 1029) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 18 residues processed: 171 average time/residue: 0.0952 time to fit residues: 22.8776 Evaluate side-chains 133 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 746 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN A 278 GLN A 285 ASN A 354 ASN A 375 ASN B 24 ASN B 194 ASN ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN B 555 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.148535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.122888 restraints weight = 15675.338| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 3.22 r_work: 0.3685 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9988 Z= 0.140 Angle : 0.602 10.168 13495 Z= 0.317 Chirality : 0.044 0.159 1515 Planarity : 0.004 0.038 1728 Dihedral : 6.099 53.473 1335 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.26 % Allowed : 23.08 % Favored : 73.67 % 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 aren not related in a simple way. whole: -0.59 (0.24), residues: 1216 helix: 1.21 (0.28), residues: 368 sheet: -0.64 (0.38), residues: 178 loop : -1.27 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 335 TYR 0.019 0.001 TYR B 743 PHE 0.026 0.001 PHE A 283 TRP 0.012 0.001 TRP B 533 HIS 0.004 0.001 HIS B 290 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9988) covalent geometry : angle 0.60194 (13495) hydrogen bonds : bond 0.04386 ( 360) hydrogen bonds : angle 5.26952 ( 1029) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8260 (mmtt) cc_final: 0.8005 (mttm) REVERT: B 103 CYS cc_start: 0.8167 (m) cc_final: 0.7765 (m) REVERT: B 533 TRP cc_start: 0.8523 (t-100) cc_final: 0.7422 (t-100) outliers start: 36 outliers final: 19 residues processed: 172 average time/residue: 0.0843 time to fit residues: 21.2593 Evaluate side-chains 146 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 793 LYS Chi-restraints excluded: chain B residue 829 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 49 optimal weight: 0.0040 chunk 113 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 44 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 43 optimal weight: 0.0770 chunk 105 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 overall best weight: 0.5752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 728 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.151436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.126934 restraints weight = 15502.227| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 3.15 r_work: 0.3736 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9988 Z= 0.111 Angle : 0.555 9.629 13495 Z= 0.290 Chirality : 0.043 0.147 1515 Planarity : 0.003 0.036 1728 Dihedral : 4.803 41.623 1311 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.98 % Allowed : 23.44 % Favored : 72.58 % 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 aren not related in a simple way. whole: -0.32 (0.24), residues: 1216 helix: 1.53 (0.28), residues: 360 sheet: -0.44 (0.39), residues: 176 loop : -1.15 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 335 TYR 0.010 0.001 TYR B 654 PHE 0.011 0.001 PHE A 272 TRP 0.009 0.001 TRP B 533 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9988) covalent geometry : angle 0.55532 (13495) hydrogen bonds : bond 0.03594 ( 360) hydrogen bonds : angle 4.71863 ( 1029) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 HIS cc_start: 0.8401 (OUTLIER) cc_final: 0.8125 (m-70) REVERT: B 226 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8200 (tp30) REVERT: B 284 ASP cc_start: 0.8583 (m-30) cc_final: 0.8122 (m-30) REVERT: B 301 LYS cc_start: 0.8276 (pttm) cc_final: 0.8020 (pttm) REVERT: B 308 ASP cc_start: 0.8721 (t0) cc_final: 0.8521 (t0) REVERT: B 533 TRP cc_start: 0.8494 (t-100) cc_final: 0.7345 (t-100) REVERT: B 654 TYR cc_start: 0.7020 (OUTLIER) cc_final: 0.6648 (p90) REVERT: B 768 ASP cc_start: 0.7125 (t0) cc_final: 0.6846 (t0) outliers start: 44 outliers final: 26 residues processed: 179 average time/residue: 0.0789 time to fit residues: 21.0133 Evaluate side-chains 150 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 793 LYS Chi-restraints excluded: chain B residue 829 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 20 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 55 optimal weight: 0.1980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 676 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.147841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.121806 restraints weight = 15870.813| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 3.28 r_work: 0.3663 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9988 Z= 0.173 Angle : 0.577 8.603 13495 Z= 0.302 Chirality : 0.044 0.155 1515 Planarity : 0.003 0.035 1728 Dihedral : 4.903 39.143 1309 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.62 % Allowed : 24.71 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.24), residues: 1216 helix: 1.42 (0.28), residues: 360 sheet: -0.63 (0.37), residues: 183 loop : -1.20 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 454 TYR 0.017 0.001 TYR B 654 PHE 0.021 0.002 PHE B 125 TRP 0.011 0.001 TRP B 807 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 9988) covalent geometry : angle 0.57736 (13495) hydrogen bonds : bond 0.03700 ( 360) hydrogen bonds : angle 4.64161 ( 1029) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 129 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 HIS cc_start: 0.8421 (OUTLIER) cc_final: 0.8201 (m-70) REVERT: B 308 ASP cc_start: 0.8740 (t0) cc_final: 0.8486 (t0) REVERT: B 310 ILE cc_start: 0.9069 (mm) cc_final: 0.8763 (mt) REVERT: B 401 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8056 (mp) REVERT: B 533 TRP cc_start: 0.8536 (t-100) cc_final: 0.7277 (t-100) REVERT: B 654 TYR cc_start: 0.6991 (OUTLIER) cc_final: 0.6375 (p90) outliers start: 51 outliers final: 36 residues processed: 169 average time/residue: 0.0791 time to fit residues: 20.0336 Evaluate side-chains 154 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 793 LYS Chi-restraints excluded: chain B residue 795 SER Chi-restraints excluded: chain B residue 829 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.142021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.116345 restraints weight = 15502.644| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 3.17 r_work: 0.3582 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9988 Z= 0.195 Angle : 0.594 8.806 13495 Z= 0.311 Chirality : 0.045 0.162 1515 Planarity : 0.004 0.034 1728 Dihedral : 4.848 27.089 1305 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.62 % Allowed : 26.15 % Favored : 69.23 % 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 aren not related in a simple way. whole: -0.60 (0.24), residues: 1216 helix: 1.22 (0.28), residues: 365 sheet: -0.80 (0.37), residues: 183 loop : -1.23 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 454 TYR 0.019 0.001 TYR B 654 PHE 0.018 0.002 PHE B 125 TRP 0.012 0.001 TRP B 807 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 9988) covalent geometry : angle 0.59427 (13495) hydrogen bonds : bond 0.03751 ( 360) hydrogen bonds : angle 4.63062 ( 1029) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 124 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 HIS cc_start: 0.8397 (OUTLIER) cc_final: 0.8081 (m-70) REVERT: A 370 LYS cc_start: 0.6204 (OUTLIER) cc_final: 0.5856 (mmtm) REVERT: B 226 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8180 (tp30) REVERT: B 308 ASP cc_start: 0.8794 (t0) cc_final: 0.8487 (t0) REVERT: B 310 ILE cc_start: 0.9031 (mm) cc_final: 0.8738 (mt) REVERT: B 533 TRP cc_start: 0.8564 (t-100) cc_final: 0.7347 (t-100) REVERT: B 654 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.6286 (p90) outliers start: 51 outliers final: 40 residues processed: 162 average time/residue: 0.0806 time to fit residues: 19.7175 Evaluate side-chains 161 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 793 LYS Chi-restraints excluded: chain B residue 795 SER Chi-restraints excluded: chain B residue 829 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 111 optimal weight: 4.9990 chunk 37 optimal weight: 0.4980 chunk 45 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 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 = 0.4125 r_free = 0.4125 target = 0.148220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.123225 restraints weight = 15717.378| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 3.17 r_work: 0.3689 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9988 Z= 0.125 Angle : 0.566 15.811 13495 Z= 0.290 Chirality : 0.044 0.168 1515 Planarity : 0.003 0.033 1728 Dihedral : 4.633 26.690 1305 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 5.34 % Allowed : 26.06 % Favored : 68.60 % 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 aren not related in a simple way. whole: -0.47 (0.24), residues: 1216 helix: 1.44 (0.28), residues: 359 sheet: -0.72 (0.38), residues: 173 loop : -1.19 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 454 TYR 0.013 0.001 TYR B 654 PHE 0.015 0.001 PHE B 125 TRP 0.011 0.001 TRP B 807 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9988) covalent geometry : angle 0.56597 (13495) hydrogen bonds : bond 0.03355 ( 360) hydrogen bonds : angle 4.42903 ( 1029) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 125 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 HIS cc_start: 0.8382 (OUTLIER) cc_final: 0.8077 (m-70) REVERT: A 370 LYS cc_start: 0.6254 (OUTLIER) cc_final: 0.5795 (mmtm) REVERT: B 125 PHE cc_start: 0.8637 (t80) cc_final: 0.8431 (t80) REVERT: B 211 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7669 (mm) REVERT: B 308 ASP cc_start: 0.8757 (t0) cc_final: 0.8425 (t0) REVERT: B 310 ILE cc_start: 0.9026 (mm) cc_final: 0.8735 (mt) REVERT: B 479 PHE cc_start: 0.9044 (p90) cc_final: 0.8834 (p90) REVERT: B 533 TRP cc_start: 0.8523 (t-100) cc_final: 0.7327 (t-100) REVERT: B 654 TYR cc_start: 0.7001 (OUTLIER) cc_final: 0.6386 (p90) outliers start: 59 outliers final: 42 residues processed: 171 average time/residue: 0.0821 time to fit residues: 20.8889 Evaluate side-chains 165 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 119 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 793 LYS Chi-restraints excluded: chain B residue 795 SER Chi-restraints excluded: chain B residue 825 ASP Chi-restraints excluded: chain B residue 829 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.140108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.114378 restraints weight = 15537.319| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 3.16 r_work: 0.3549 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9988 Z= 0.239 Angle : 0.640 13.932 13495 Z= 0.331 Chirality : 0.046 0.177 1515 Planarity : 0.004 0.034 1728 Dihedral : 5.000 25.509 1305 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.34 % Allowed : 26.33 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.24), residues: 1216 helix: 1.19 (0.28), residues: 359 sheet: -1.02 (0.37), residues: 173 loop : -1.26 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 335 TYR 0.021 0.002 TYR B 654 PHE 0.035 0.002 PHE A 283 TRP 0.013 0.002 TRP B 807 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00560 ( 9988) covalent geometry : angle 0.64006 (13495) hydrogen bonds : bond 0.03891 ( 360) hydrogen bonds : angle 4.63574 ( 1029) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 116 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 HIS cc_start: 0.8416 (OUTLIER) cc_final: 0.8120 (m-70) REVERT: A 370 LYS cc_start: 0.6277 (OUTLIER) cc_final: 0.5551 (mppt) REVERT: B 308 ASP cc_start: 0.8747 (t0) cc_final: 0.8406 (t0) REVERT: B 310 ILE cc_start: 0.9025 (mm) cc_final: 0.8739 (mt) REVERT: B 528 ASN cc_start: 0.8368 (OUTLIER) cc_final: 0.8166 (p0) REVERT: B 533 TRP cc_start: 0.8575 (t-100) cc_final: 0.7331 (t-100) REVERT: B 819 TRP cc_start: 0.8533 (m100) cc_final: 0.7950 (m100) outliers start: 59 outliers final: 46 residues processed: 162 average time/residue: 0.0798 time to fit residues: 19.6022 Evaluate side-chains 159 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 110 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 528 ASN Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 793 LYS Chi-restraints excluded: chain B residue 795 SER Chi-restraints excluded: chain B residue 825 ASP Chi-restraints excluded: chain B residue 829 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 93 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 37 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 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 = 0.4082 r_free = 0.4082 target = 0.145782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.120675 restraints weight = 15238.082| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.15 r_work: 0.3637 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9988 Z= 0.114 Angle : 0.570 14.852 13495 Z= 0.291 Chirality : 0.044 0.211 1515 Planarity : 0.003 0.035 1728 Dihedral : 4.652 25.610 1305 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.16 % Allowed : 26.97 % Favored : 68.87 % 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 aren not related in a simple way. whole: -0.46 (0.24), residues: 1216 helix: 1.42 (0.28), residues: 361 sheet: -0.71 (0.38), residues: 168 loop : -1.17 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 335 TYR 0.015 0.001 TYR B 743 PHE 0.024 0.001 PHE A 283 TRP 0.011 0.001 TRP B 778 HIS 0.003 0.001 HIS B 290 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9988) covalent geometry : angle 0.57024 (13495) hydrogen bonds : bond 0.03304 ( 360) hydrogen bonds : angle 4.41091 ( 1029) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 119 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLN cc_start: 0.8296 (mm-40) cc_final: 0.7940 (mt0) REVERT: A 206 HIS cc_start: 0.8380 (OUTLIER) cc_final: 0.8086 (m-70) REVERT: A 370 LYS cc_start: 0.6250 (OUTLIER) cc_final: 0.5738 (mmtm) REVERT: B 125 PHE cc_start: 0.8680 (t80) cc_final: 0.8476 (t80) REVERT: B 308 ASP cc_start: 0.8734 (t0) cc_final: 0.8366 (t0) REVERT: B 310 ILE cc_start: 0.8988 (mm) cc_final: 0.8719 (mt) REVERT: B 533 TRP cc_start: 0.8527 (t-100) cc_final: 0.7338 (t-100) REVERT: B 654 TYR cc_start: 0.6958 (OUTLIER) cc_final: 0.6326 (p90) outliers start: 46 outliers final: 37 residues processed: 156 average time/residue: 0.0869 time to fit residues: 19.9786 Evaluate side-chains 152 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 793 LYS Chi-restraints excluded: chain B residue 795 SER Chi-restraints excluded: chain B residue 825 ASP Chi-restraints excluded: chain B residue 829 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 53 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 114 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.144081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.118609 restraints weight = 15315.690| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 3.16 r_work: 0.3613 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9988 Z= 0.151 Angle : 0.587 13.981 13495 Z= 0.301 Chirality : 0.045 0.303 1515 Planarity : 0.003 0.036 1728 Dihedral : 4.710 25.784 1305 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.89 % Allowed : 27.24 % Favored : 68.87 % 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 aren not related in a simple way. whole: -0.55 (0.24), residues: 1216 helix: 1.42 (0.28), residues: 360 sheet: -0.89 (0.38), residues: 170 loop : -1.24 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 335 TYR 0.031 0.001 TYR B 743 PHE 0.022 0.001 PHE A 283 TRP 0.010 0.001 TRP B 807 HIS 0.003 0.001 HIS B 290 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9988) covalent geometry : angle 0.58693 (13495) hydrogen bonds : bond 0.03417 ( 360) hydrogen bonds : angle 4.36053 ( 1029) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7920 (mt0) REVERT: A 206 HIS cc_start: 0.8363 (OUTLIER) cc_final: 0.8063 (m-70) REVERT: A 280 LYS cc_start: 0.7745 (mmtt) cc_final: 0.7489 (mmtp) REVERT: A 370 LYS cc_start: 0.6435 (OUTLIER) cc_final: 0.5915 (mmtm) REVERT: B 308 ASP cc_start: 0.8723 (t0) cc_final: 0.8360 (t0) REVERT: B 310 ILE cc_start: 0.8991 (mm) cc_final: 0.8721 (mt) REVERT: B 533 TRP cc_start: 0.8535 (t-100) cc_final: 0.7303 (t-100) REVERT: B 654 TYR cc_start: 0.7069 (OUTLIER) cc_final: 0.6376 (p90) outliers start: 43 outliers final: 37 residues processed: 149 average time/residue: 0.0833 time to fit residues: 18.5861 Evaluate side-chains 151 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 793 LYS Chi-restraints excluded: chain B residue 825 ASP Chi-restraints excluded: chain B residue 829 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 101 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 0.0010 chunk 72 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 12 optimal weight: 0.0070 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.151375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.127850 restraints weight = 15080.425| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 3.00 r_work: 0.3751 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9988 Z= 0.106 Angle : 0.576 15.060 13495 Z= 0.292 Chirality : 0.044 0.203 1515 Planarity : 0.003 0.037 1728 Dihedral : 4.484 26.638 1305 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.44 % Allowed : 27.87 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.24), residues: 1216 helix: 1.58 (0.28), residues: 361 sheet: -0.65 (0.41), residues: 165 loop : -1.16 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 335 TYR 0.028 0.001 TYR B 743 PHE 0.019 0.001 PHE B 125 TRP 0.012 0.001 TRP B 828 HIS 0.003 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 9988) covalent geometry : angle 0.57624 (13495) hydrogen bonds : bond 0.03050 ( 360) hydrogen bonds : angle 4.21585 ( 1029) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7978 (mt0) REVERT: A 119 LYS cc_start: 0.8165 (mptt) cc_final: 0.7878 (tmmt) REVERT: A 206 HIS cc_start: 0.8291 (OUTLIER) cc_final: 0.8076 (m-70) REVERT: A 370 LYS cc_start: 0.6334 (OUTLIER) cc_final: 0.5969 (mmtm) REVERT: B 308 ASP cc_start: 0.8679 (t0) cc_final: 0.8309 (t0) REVERT: B 310 ILE cc_start: 0.8961 (mm) cc_final: 0.8697 (mt) REVERT: B 654 TYR cc_start: 0.7001 (OUTLIER) cc_final: 0.6650 (p90) outliers start: 38 outliers final: 33 residues processed: 154 average time/residue: 0.0836 time to fit residues: 19.2649 Evaluate side-chains 152 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 793 LYS Chi-restraints excluded: chain B residue 825 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 9 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN ** B 290 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 = 0.4169 r_free = 0.4169 target = 0.151702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.127975 restraints weight = 15241.689| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 3.05 r_work: 0.3746 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 9988 Z= 0.172 Angle : 0.888 59.200 13495 Z= 0.518 Chirality : 0.045 0.202 1515 Planarity : 0.003 0.037 1728 Dihedral : 4.506 26.426 1305 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.35 % Allowed : 28.05 % Favored : 68.60 % Cbeta Deviations : 0.09 % 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 aren not related in a simple way. whole: -0.37 (0.24), residues: 1216 helix: 1.58 (0.28), residues: 361 sheet: -0.63 (0.41), residues: 165 loop : -1.18 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 335 TYR 0.026 0.001 TYR B 743 PHE 0.017 0.001 PHE B 125 TRP 0.010 0.001 TRP B 828 HIS 0.003 0.001 HIS B 290 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9988) covalent geometry : angle 0.88771 (13495) hydrogen bonds : bond 0.03053 ( 360) hydrogen bonds : angle 4.21492 ( 1029) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2005.38 seconds wall clock time: 35 minutes 26.54 seconds (2126.54 seconds total)