Starting phenix.real_space_refine on Sun Jun 8 15:18:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b6m_44266/06_2025/9b6m_44266.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b6m_44266/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b6m_44266/06_2025/9b6m_44266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b6m_44266/06_2025/9b6m_44266.map" model { file = "/net/cci-nas-00/data/ceres_data/9b6m_44266/06_2025/9b6m_44266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b6m_44266/06_2025/9b6m_44266.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.52, per 1000 atoms: 0.67 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: 2.67 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.32 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: 3.47 Time building geometry restraints manager: 3.17 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: 1.370 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.420 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.550 ------------------------------------------------------------------------------- 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 : 15.03 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.033 0.006 TRP B 253 HIS 0.016 0.004 HIS B 345 PHE 0.035 0.007 PHE B 821 TYR 0.051 0.007 TYR B 254 ARG 0.014 0.002 ARG B 492 Details of bonding type rmsd hydrogen bonds : bond 0.22597 ( 360) hydrogen bonds : angle 8.42029 ( 1029) covalent geometry : bond 0.01239 ( 9988) covalent geometry : angle 1.41137 (13495) *********************** 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 : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 18 residues processed: 171 average time/residue: 0.2587 time to fit residues: 62.3559 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 : 1.174 ------------------------------------------------------------------------------- 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 103 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 210 ASN A 219 ASN A 278 GLN A 285 ASN A 354 ASN A 375 ASN B 24 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.149963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.124524 restraints weight = 15471.233| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 3.21 r_work: 0.3703 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9988 Z= 0.130 Angle : 0.592 10.233 13495 Z= 0.312 Chirality : 0.044 0.158 1515 Planarity : 0.004 0.037 1728 Dihedral : 6.024 52.673 1335 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.08 % Allowed : 22.71 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.24), residues: 1216 helix: 1.29 (0.28), residues: 368 sheet: -0.52 (0.40), residues: 173 loop : -1.24 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 533 HIS 0.004 0.001 HIS B 290 PHE 0.014 0.001 PHE A 272 TYR 0.016 0.001 TYR B 743 ARG 0.006 0.001 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.04345 ( 360) hydrogen bonds : angle 5.22398 ( 1029) covalent geometry : bond 0.00289 ( 9988) covalent geometry : angle 0.59204 (13495) *********************** 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 181 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 THR cc_start: 0.8963 (p) cc_final: 0.8750 (t) REVERT: B 103 CYS cc_start: 0.8191 (m) cc_final: 0.7801 (m) REVERT: B 533 TRP cc_start: 0.8523 (t-100) cc_final: 0.7396 (t-100) outliers start: 34 outliers final: 18 residues processed: 173 average time/residue: 0.2050 time to fit residues: 51.4736 Evaluate side-chains 147 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 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 29 optimal weight: 0.0000 chunk 82 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 76 optimal weight: 0.0870 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- 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** B 728 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.145841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.120107 restraints weight = 15789.931| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 3.22 r_work: 0.3650 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9988 Z= 0.172 Angle : 0.591 9.255 13495 Z= 0.310 Chirality : 0.045 0.153 1515 Planarity : 0.004 0.036 1728 Dihedral : 5.088 40.282 1311 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.43 % Allowed : 23.44 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.24), residues: 1216 helix: 1.25 (0.27), residues: 367 sheet: -0.65 (0.38), residues: 183 loop : -1.29 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 807 HIS 0.005 0.001 HIS A 209 PHE 0.026 0.002 PHE A 283 TYR 0.019 0.001 TYR B 654 ARG 0.004 0.000 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 360) hydrogen bonds : angle 4.86285 ( 1029) covalent geometry : bond 0.00402 ( 9988) covalent geometry : angle 0.59102 (13495) *********************** 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 188 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 139 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8279 (mmtp) cc_final: 0.8078 (mmtt) REVERT: A 206 HIS cc_start: 0.8425 (OUTLIER) cc_final: 0.8184 (m-70) REVERT: B 103 CYS cc_start: 0.8168 (m) cc_final: 0.7789 (m) REVERT: B 226 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8222 (tp30) REVERT: B 533 TRP cc_start: 0.8506 (t-100) cc_final: 0.7313 (t-100) REVERT: B 654 TYR cc_start: 0.7000 (OUTLIER) cc_final: 0.6148 (p90) REVERT: B 817 LYS cc_start: 0.8301 (mtpp) cc_final: 0.8090 (mtpp) outliers start: 49 outliers final: 32 residues processed: 175 average time/residue: 0.1896 time to fit residues: 49.4513 Evaluate side-chains 155 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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 154 CYS Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 240 SER 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 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 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 408 THR Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 552 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 121 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 0.0870 chunk 91 optimal weight: 6.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- 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 540 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.144387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.119662 restraints weight = 15400.024| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 3.05 r_work: 0.3644 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9988 Z= 0.183 Angle : 0.585 8.910 13495 Z= 0.308 Chirality : 0.045 0.154 1515 Planarity : 0.004 0.036 1728 Dihedral : 5.042 38.628 1309 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.16 % Allowed : 23.71 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.24), residues: 1216 helix: 1.21 (0.28), residues: 367 sheet: -0.76 (0.37), residues: 183 loop : -1.29 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 807 HIS 0.005 0.001 HIS A 209 PHE 0.020 0.002 PHE A 283 TYR 0.018 0.001 TYR B 654 ARG 0.004 0.000 ARG B 454 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 360) hydrogen bonds : angle 4.72581 ( 1029) covalent geometry : bond 0.00430 ( 9988) covalent geometry : angle 0.58541 (13495) *********************** 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 187 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 130 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 HIS cc_start: 0.8412 (OUTLIER) cc_final: 0.8093 (m-70) REVERT: B 226 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8216 (tp30) REVERT: B 310 ILE cc_start: 0.9088 (mm) cc_final: 0.8797 (mt) REVERT: B 401 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8076 (mp) REVERT: B 533 TRP cc_start: 0.8532 (t-100) cc_final: 0.7309 (t-100) REVERT: B 654 TYR cc_start: 0.7132 (OUTLIER) cc_final: 0.6193 (p90) outliers start: 57 outliers final: 39 residues processed: 174 average time/residue: 0.1887 time to fit residues: 48.8114 Evaluate side-chains 161 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 119 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 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 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 200 LEU 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 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 510 THR Chi-restraints excluded: chain B residue 552 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 61 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 0.0980 chunk 22 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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** A 254 HIS ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.146111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.120805 restraints weight = 15135.895| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 3.16 r_work: 0.3645 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9988 Z= 0.115 Angle : 0.551 9.194 13495 Z= 0.287 Chirality : 0.043 0.163 1515 Planarity : 0.003 0.036 1728 Dihedral : 4.811 39.904 1309 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.07 % Allowed : 26.06 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.24), residues: 1216 helix: 1.44 (0.28), residues: 365 sheet: -0.63 (0.38), residues: 178 loop : -1.21 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 807 HIS 0.003 0.001 HIS A 209 PHE 0.017 0.001 PHE A 283 TYR 0.013 0.001 TYR B 743 ARG 0.003 0.000 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 360) hydrogen bonds : angle 4.49722 ( 1029) covalent geometry : bond 0.00266 ( 9988) covalent geometry : angle 0.55103 (13495) *********************** 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 186 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 141 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: A 206 HIS cc_start: 0.8356 (OUTLIER) cc_final: 0.8088 (m-70) REVERT: B 226 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8188 (tp30) REVERT: B 310 ILE cc_start: 0.9035 (mm) cc_final: 0.8755 (mt) REVERT: B 397 LEU cc_start: 0.8454 (mt) cc_final: 0.8093 (mt) REVERT: B 533 TRP cc_start: 0.8520 (t-100) cc_final: 0.7344 (t-100) REVERT: B 654 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.6408 (p90) outliers start: 45 outliers final: 29 residues processed: 177 average time/residue: 0.1942 time to fit residues: 50.8966 Evaluate side-chains 156 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN 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 199 THR Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 222 VAL 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 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 408 THR Chi-restraints excluded: chain B residue 458 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 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 829 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 114 optimal weight: 0.0570 chunk 111 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- 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 ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 676 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.142291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.116702 restraints weight = 15263.699| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 3.16 r_work: 0.3592 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9988 Z= 0.184 Angle : 0.609 15.657 13495 Z= 0.313 Chirality : 0.045 0.267 1515 Planarity : 0.004 0.043 1728 Dihedral : 4.810 26.590 1305 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.62 % Allowed : 25.70 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.24), residues: 1216 helix: 1.30 (0.28), residues: 365 sheet: -0.76 (0.37), residues: 173 loop : -1.28 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 807 HIS 0.003 0.001 HIS A 209 PHE 0.023 0.002 PHE B 125 TYR 0.017 0.001 TYR B 654 ARG 0.004 0.000 ARG B 454 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 360) hydrogen bonds : angle 4.51546 ( 1029) covalent geometry : bond 0.00432 ( 9988) covalent geometry : angle 0.60935 (13495) *********************** 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 182 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 131 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 HIS cc_start: 0.8386 (OUTLIER) cc_final: 0.8098 (m-70) REVERT: B 226 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8153 (tp30) REVERT: B 310 ILE cc_start: 0.9039 (mm) cc_final: 0.8757 (mt) REVERT: B 654 TYR cc_start: 0.7098 (OUTLIER) cc_final: 0.6265 (p90) outliers start: 51 outliers final: 39 residues processed: 167 average time/residue: 0.1891 time to fit residues: 46.8872 Evaluate side-chains 161 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 42 LEU 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 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 B residue 19 THR Chi-restraints excluded: chain B residue 91 MET 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 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 530 ILE Chi-restraints excluded: chain B residue 552 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 720 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 69 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 8.9990 chunk 89 optimal weight: 0.1980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.144420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.118780 restraints weight = 15322.639| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 3.19 r_work: 0.3611 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9988 Z= 0.142 Angle : 0.591 14.229 13495 Z= 0.302 Chirality : 0.044 0.261 1515 Planarity : 0.004 0.044 1728 Dihedral : 4.701 26.130 1305 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.25 % Allowed : 26.33 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.24), residues: 1216 helix: 1.34 (0.28), residues: 366 sheet: -0.71 (0.38), residues: 173 loop : -1.26 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 807 HIS 0.003 0.001 HIS A 209 PHE 0.018 0.001 PHE A 283 TYR 0.014 0.001 TYR B 654 ARG 0.004 0.000 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 360) hydrogen bonds : angle 4.39261 ( 1029) covalent geometry : bond 0.00332 ( 9988) covalent geometry : angle 0.59134 (13495) *********************** 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: 47 poor density : 128 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 HIS cc_start: 0.8381 (OUTLIER) cc_final: 0.8124 (m-70) REVERT: A 369 LYS cc_start: 0.7086 (tppt) cc_final: 0.6801 (ttmt) REVERT: B 226 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8162 (tp30) REVERT: B 310 ILE cc_start: 0.9028 (mm) cc_final: 0.8755 (mt) REVERT: B 533 TRP cc_start: 0.8461 (t-100) cc_final: 0.7225 (t-100) REVERT: B 654 TYR cc_start: 0.7045 (OUTLIER) cc_final: 0.6301 (p90) outliers start: 47 outliers final: 38 residues processed: 163 average time/residue: 0.1948 time to fit residues: 46.9121 Evaluate side-chains 156 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 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 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 B residue 19 THR Chi-restraints excluded: chain B residue 91 MET 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 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 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 530 ILE 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 829 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 94 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.144147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.118266 restraints weight = 15439.385| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 3.20 r_work: 0.3611 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9988 Z= 0.150 Angle : 0.596 14.000 13495 Z= 0.304 Chirality : 0.045 0.282 1515 Planarity : 0.004 0.037 1728 Dihedral : 4.719 25.876 1305 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.62 % Allowed : 26.61 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.24), residues: 1216 helix: 1.33 (0.28), residues: 367 sheet: -0.67 (0.38), residues: 173 loop : -1.25 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 807 HIS 0.003 0.001 HIS B 290 PHE 0.016 0.002 PHE B 125 TYR 0.015 0.001 TYR B 654 ARG 0.004 0.000 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 360) hydrogen bonds : angle 4.36522 ( 1029) covalent geometry : bond 0.00351 ( 9988) covalent geometry : angle 0.59559 (13495) *********************** 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 171 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 120 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 HIS cc_start: 0.8352 (OUTLIER) cc_final: 0.8082 (m-70) REVERT: B 226 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8164 (tp30) REVERT: B 310 ILE cc_start: 0.9017 (mm) cc_final: 0.8751 (mt) REVERT: B 533 TRP cc_start: 0.8492 (t-100) cc_final: 0.7205 (t-100) REVERT: B 654 TYR cc_start: 0.7042 (OUTLIER) cc_final: 0.6305 (p90) outliers start: 51 outliers final: 41 residues processed: 157 average time/residue: 0.1963 time to fit residues: 46.0562 Evaluate side-chains 156 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 113 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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 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 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 B residue 19 THR Chi-restraints excluded: chain B residue 91 MET 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 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 294 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 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 552 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 797 ASP 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 5 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 29 optimal weight: 0.4980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.145368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.119820 restraints weight = 15273.833| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 3.17 r_work: 0.3630 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9988 Z= 0.136 Angle : 0.589 13.884 13495 Z= 0.300 Chirality : 0.045 0.303 1515 Planarity : 0.003 0.035 1728 Dihedral : 4.620 26.403 1305 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.25 % Allowed : 26.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.24), residues: 1216 helix: 1.41 (0.28), residues: 367 sheet: -0.58 (0.39), residues: 168 loop : -1.21 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 807 HIS 0.003 0.001 HIS B 290 PHE 0.015 0.001 PHE B 125 TYR 0.014 0.001 TYR B 743 ARG 0.003 0.000 ARG B 454 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 360) hydrogen bonds : angle 4.29162 ( 1029) covalent geometry : bond 0.00315 ( 9988) covalent geometry : angle 0.58860 (13495) *********************** 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 170 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 123 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: A 206 HIS cc_start: 0.8349 (OUTLIER) cc_final: 0.8119 (m-70) REVERT: A 369 LYS cc_start: 0.7431 (ttmt) cc_final: 0.7063 (ttmt) REVERT: B 125 PHE cc_start: 0.8705 (t80) cc_final: 0.8502 (t80) REVERT: B 226 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8147 (tp30) REVERT: B 310 ILE cc_start: 0.8986 (mm) cc_final: 0.8718 (mt) REVERT: B 654 TYR cc_start: 0.6981 (OUTLIER) cc_final: 0.6354 (p90) outliers start: 47 outliers final: 39 residues processed: 158 average time/residue: 0.1903 time to fit residues: 45.0617 Evaluate side-chains 158 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 324 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 91 MET 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 272 LEU Chi-restraints excluded: chain B residue 294 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 79 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 A 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.148898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.123575 restraints weight = 15179.413| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 3.11 r_work: 0.3672 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9988 Z= 0.114 Angle : 0.582 13.898 13495 Z= 0.296 Chirality : 0.045 0.315 1515 Planarity : 0.003 0.037 1728 Dihedral : 4.503 27.772 1305 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.53 % Allowed : 27.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.24), residues: 1216 helix: 1.53 (0.28), residues: 368 sheet: -0.59 (0.40), residues: 165 loop : -1.14 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 778 HIS 0.002 0.001 HIS A 206 PHE 0.016 0.001 PHE A 372 TYR 0.025 0.001 TYR B 743 ARG 0.002 0.000 ARG B 454 Details of bonding type rmsd hydrogen bonds : bond 0.03128 ( 360) hydrogen bonds : angle 4.17838 ( 1029) covalent geometry : bond 0.00261 ( 9988) covalent geometry : angle 0.58183 (13495) ********************** 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 168 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 206 HIS cc_start: 0.8227 (OUTLIER) cc_final: 0.7997 (m-70) REVERT: A 280 LYS cc_start: 0.7572 (mmtt) cc_final: 0.7301 (mmtm) REVERT: A 369 LYS cc_start: 0.7433 (ttmt) cc_final: 0.7121 (ttmt) REVERT: B 46 GLN cc_start: 0.7084 (mp-120) cc_final: 0.6817 (mp-120) REVERT: B 226 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8148 (tp30) REVERT: B 310 ILE cc_start: 0.8956 (mm) cc_final: 0.8699 (mt) REVERT: B 654 TYR cc_start: 0.7009 (OUTLIER) cc_final: 0.6465 (p90) REVERT: B 766 LYS cc_start: 0.8180 (tmtt) cc_final: 0.7888 (tmtt) outliers start: 39 outliers final: 35 residues processed: 159 average time/residue: 0.1874 time to fit residues: 44.5075 Evaluate side-chains 158 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN 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 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 219 ASN 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 B residue 19 THR Chi-restraints excluded: chain B residue 91 MET 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 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 294 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 408 THR Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 552 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 93 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.147264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.121754 restraints weight = 15278.873| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 3.19 r_work: 0.3650 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 9988 Z= 0.215 Angle : 0.910 59.158 13495 Z= 0.527 Chirality : 0.047 0.320 1515 Planarity : 0.003 0.038 1728 Dihedral : 4.536 27.256 1305 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.71 % Allowed : 27.87 % Favored : 68.42 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.24), residues: 1216 helix: 1.49 (0.28), residues: 368 sheet: -0.58 (0.40), residues: 165 loop : -1.16 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 778 HIS 0.002 0.001 HIS A 209 PHE 0.035 0.002 PHE A 372 TYR 0.023 0.001 TYR B 743 ARG 0.003 0.000 ARG B 454 Details of bonding type rmsd hydrogen bonds : bond 0.03188 ( 360) hydrogen bonds : angle 4.18195 ( 1029) covalent geometry : bond 0.00473 ( 9988) covalent geometry : angle 0.91040 (13495) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4280.95 seconds wall clock time: 74 minutes 49.67 seconds (4489.67 seconds total)