Starting phenix.real_space_refine on Wed May 14 05:21:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxc_45004/05_2025/9bxc_45004.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxc_45004/05_2025/9bxc_45004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bxc_45004/05_2025/9bxc_45004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxc_45004/05_2025/9bxc_45004.map" model { file = "/net/cci-nas-00/data/ceres_data/9bxc_45004/05_2025/9bxc_45004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxc_45004/05_2025/9bxc_45004.cif" } resolution = 2.76 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= 0.003 sd= 0.101 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 2 5.21 5 S 60 5.16 5 C 7284 2.51 5 N 1898 2.21 5 O 2236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11496 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.94, per 1000 atoms: 0.60 Number of scatterers: 11496 At special positions: 0 Unit cell: (91.26, 84.162, 131.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 16 15.00 Mg 2 11.99 O 2236 8.00 N 1898 7.00 C 7284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 170 " - pdb=" SG CYS A 409 " distance=2.03 Simple disulfide: pdb=" SG CYS B 170 " - pdb=" SG CYS B 409 " distance=2.03 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: 2.83 Conformation dependent library (CDL) restraints added in 1.5 seconds 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2652 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 10 sheets defined 53.7% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 7 through 14 Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 27 through 40 removed outlier: 3.771A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 4.259A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.788A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.639A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 removed outlier: 3.524A pdb=" N ASN A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 194 Processing helix chain 'A' and resid 222 through 237 removed outlier: 4.065A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 257 through 264 removed outlier: 3.528A pdb=" N THR A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.661A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 318 through 328 removed outlier: 5.965A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 367 removed outlier: 4.231A pdb=" N VAL A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 443 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.568A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 582 through 588 removed outlier: 4.060A pdb=" N TYR A 586 " --> pdb=" O GLY A 582 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 677 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 27 through 40 removed outlier: 3.613A pdb=" N GLU B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.044A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 86 Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.634A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 removed outlier: 3.514A pdb=" N THR B 264 " --> pdb=" O ASP B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.647A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 328 removed outlier: 5.482A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 443 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.562A pdb=" N LEU B 546 " --> pdb=" O LYS B 542 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.256A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.812A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.234A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 removed outlier: 6.022A pdb=" N PHE A 171 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ASN A 202 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU A 173 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA5, first strand: chain 'A' and resid 655 through 659 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.818A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.878A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AA9, first strand: chain 'B' and resid 601 through 605 Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659 519 hydrogen bonds defined for protein. 1497 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: 3.31 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3683 1.34 - 1.46: 2824 1.46 - 1.58: 5105 1.58 - 1.70: 24 1.70 - 1.82: 112 Bond restraints: 11748 Sorted by residual: bond pdb=" CB PRO D 314 " pdb=" CG PRO D 314 " ideal model delta sigma weight residual 1.492 1.576 -0.084 5.00e-02 4.00e+02 2.81e+00 bond pdb=" CB GLU A 66 " pdb=" CG GLU A 66 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" CB GLU A 75 " pdb=" CG GLU A 75 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.51e+00 bond pdb=" CB CYS A 170 " pdb=" SG CYS A 170 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CB ASP A 215 " pdb=" CG ASP A 215 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.19e+00 ... (remaining 11743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 15539 1.51 - 3.02: 255 3.02 - 4.52: 51 4.52 - 6.03: 20 6.03 - 7.54: 3 Bond angle restraints: 15868 Sorted by residual: angle pdb=" N VAL A 273 " pdb=" CA VAL A 273 " pdb=" C VAL A 273 " ideal model delta sigma weight residual 113.71 109.94 3.77 9.50e-01 1.11e+00 1.57e+01 angle pdb=" CA PRO D 314 " pdb=" N PRO D 314 " pdb=" CD PRO D 314 " ideal model delta sigma weight residual 112.00 107.19 4.81 1.40e+00 5.10e-01 1.18e+01 angle pdb=" CA VAL C 312 " pdb=" CB VAL C 312 " pdb=" CG1 VAL C 312 " ideal model delta sigma weight residual 110.40 116.18 -5.78 1.70e+00 3.46e-01 1.16e+01 angle pdb=" C VAL C 312 " pdb=" CA VAL C 312 " pdb=" CB VAL C 312 " ideal model delta sigma weight residual 111.29 116.82 -5.53 1.64e+00 3.72e-01 1.14e+01 angle pdb=" C GLN B 239 " pdb=" N MET B 240 " pdb=" CA MET B 240 " ideal model delta sigma weight residual 121.54 127.53 -5.99 1.91e+00 2.74e-01 9.84e+00 ... (remaining 15863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.73: 6597 29.73 - 59.46: 458 59.46 - 89.19: 38 89.19 - 118.93: 3 118.93 - 148.66: 4 Dihedral angle restraints: 7100 sinusoidal: 2976 harmonic: 4124 Sorted by residual: dihedral pdb=" CB CYS B 170 " pdb=" SG CYS B 170 " pdb=" SG CYS B 409 " pdb=" CB CYS B 409 " ideal model delta sinusoidal sigma weight residual -86.00 -170.25 84.25 1 1.00e+01 1.00e-02 8.64e+01 dihedral pdb=" C2 TTP A 801 " pdb=" C1' TTP A 801 " pdb=" N1 TTP A 801 " pdb=" O4' TTP A 801 " ideal model delta sinusoidal sigma weight residual 301.68 153.03 148.66 1 2.00e+01 2.50e-03 4.45e+01 dihedral pdb=" C2 TTP B 802 " pdb=" C1' TTP B 802 " pdb=" N1 TTP B 802 " pdb=" O4' TTP B 802 " ideal model delta sinusoidal sigma weight residual 301.68 156.37 145.31 1 2.00e+01 2.50e-03 4.37e+01 ... (remaining 7097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1054 0.031 - 0.063: 455 0.063 - 0.094: 114 0.094 - 0.126: 57 0.126 - 0.157: 6 Chirality restraints: 1686 Sorted by residual: chirality pdb=" CA ASP A 398 " pdb=" N ASP A 398 " pdb=" C ASP A 398 " pdb=" CB ASP A 398 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CA ASP A 215 " pdb=" N ASP A 215 " pdb=" C ASP A 215 " pdb=" CB ASP A 215 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA ILE B 652 " pdb=" N ILE B 652 " pdb=" C ILE B 652 " pdb=" CB ILE B 652 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 1683 not shown) Planarity restraints: 2014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 37 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C PHE B 37 " 0.032 2.00e-02 2.50e+03 pdb=" O PHE B 37 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL B 38 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 37 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C PHE A 37 " 0.029 2.00e-02 2.50e+03 pdb=" O PHE A 37 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A 38 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 313 " 0.027 5.00e-02 4.00e+02 4.01e-02 2.58e+00 pdb=" N PRO D 314 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 314 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 314 " 0.023 5.00e-02 4.00e+02 ... (remaining 2011 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 270 2.67 - 3.23: 11141 3.23 - 3.79: 20492 3.79 - 4.34: 28879 4.34 - 4.90: 46230 Nonbonded interactions: 107012 Sorted by model distance: nonbonded pdb=" O2A TTP A 801 " pdb="MG MG A 802 " model vdw 2.118 2.170 nonbonded pdb=" O PRO B 616 " pdb=" OH TYR B 626 " model vdw 2.132 3.040 nonbonded pdb=" O PRO A 616 " pdb=" OH TYR A 626 " model vdw 2.153 3.040 nonbonded pdb=" O GLU A 119 " pdb=" OG SER A 123 " model vdw 2.175 3.040 nonbonded pdb=" NE2 HIS A 372 " pdb=" O GLN A 516 " model vdw 2.202 3.120 ... (remaining 107007 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 688 or resid 803 through 804)) selection = (chain 'B' and (resid 6 through 688 or resid 803 through 804)) } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.210 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 27.740 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 11750 Z= 0.120 Angle : 0.538 7.538 15872 Z= 0.287 Chirality : 0.040 0.157 1686 Planarity : 0.003 0.040 2014 Dihedral : 18.609 148.658 4442 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.81 % Allowed : 22.00 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.85 (0.22), residues: 1382 helix: 1.08 (0.20), residues: 650 sheet: -0.60 (0.39), residues: 154 loop : 0.51 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 9 HIS 0.004 0.001 HIS B 255 PHE 0.015 0.001 PHE A 100 TYR 0.008 0.001 TYR A 471 ARG 0.007 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.15268 ( 517) hydrogen bonds : angle 6.76712 ( 1497) SS BOND : bond 0.00403 ( 2) SS BOND : angle 2.90084 ( 4) covalent geometry : bond 0.00273 (11748) covalent geometry : angle 0.53571 (15868) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 1.335 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6766 (mp0) REVERT: A 366 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8328 (mtpt) REVERT: B 11 GLN cc_start: 0.6969 (tt0) cc_final: 0.6520 (tt0) REVERT: B 240 MET cc_start: 0.3881 (ppp) cc_final: 0.3387 (ppp) REVERT: B 393 SER cc_start: 0.8840 (t) cc_final: 0.8568 (t) outliers start: 10 outliers final: 6 residues processed: 172 average time/residue: 1.2707 time to fit residues: 236.5337 Evaluate side-chains 153 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 214 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 320 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.147149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121256 restraints weight = 11273.563| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.39 r_work: 0.3194 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 11750 Z= 0.246 Angle : 0.602 6.633 15872 Z= 0.315 Chirality : 0.045 0.168 1686 Planarity : 0.004 0.040 2014 Dihedral : 12.591 157.734 1663 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.81 % Allowed : 19.24 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.48 (0.22), residues: 1382 helix: 0.82 (0.20), residues: 660 sheet: -0.63 (0.42), residues: 134 loop : 0.16 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 9 HIS 0.007 0.001 HIS A 304 PHE 0.020 0.002 PHE A 100 TYR 0.015 0.002 TYR B 574 ARG 0.008 0.001 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.04344 ( 517) hydrogen bonds : angle 5.53994 ( 1497) SS BOND : bond 0.00147 ( 2) SS BOND : angle 3.53156 ( 4) covalent geometry : bond 0.00578 (11748) covalent geometry : angle 0.59948 (15868) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 151 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7587 (mm-30) REVERT: A 75 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7265 (mp0) REVERT: A 316 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: A 632 MET cc_start: 0.9001 (mtt) cc_final: 0.8260 (mtt) REVERT: A 658 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8395 (mp) REVERT: B 11 GLN cc_start: 0.6865 (OUTLIER) cc_final: 0.6518 (tt0) REVERT: B 15 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7387 (mm-30) REVERT: B 30 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7525 (tttm) REVERT: B 43 GLN cc_start: 0.7791 (mt0) cc_final: 0.7558 (mt0) REVERT: B 111 LYS cc_start: 0.7928 (mmmt) cc_final: 0.7617 (mmtm) REVERT: B 240 MET cc_start: 0.3748 (OUTLIER) cc_final: 0.3145 (ppp) REVERT: B 341 LYS cc_start: 0.7853 (mmmm) cc_final: 0.7291 (mtpm) REVERT: B 384 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8105 (pp20) REVERT: B 658 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8123 (mt) outliers start: 47 outliers final: 23 residues processed: 183 average time/residue: 1.4090 time to fit residues: 278.3530 Evaluate side-chains 173 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 318 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 320 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN B 645 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.140095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.113287 restraints weight = 12274.004| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.51 r_work: 0.3187 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11750 Z= 0.154 Angle : 0.542 12.211 15872 Z= 0.281 Chirality : 0.042 0.183 1686 Planarity : 0.003 0.039 2014 Dihedral : 12.054 152.841 1659 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.76 % Allowed : 20.54 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.22), residues: 1382 helix: 0.98 (0.20), residues: 660 sheet: -0.55 (0.43), residues: 134 loop : 0.12 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 9 HIS 0.005 0.001 HIS B 438 PHE 0.018 0.002 PHE B 100 TYR 0.012 0.001 TYR B 574 ARG 0.008 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 517) hydrogen bonds : angle 5.15628 ( 1497) SS BOND : bond 0.00338 ( 2) SS BOND : angle 5.15557 ( 4) covalent geometry : bond 0.00354 (11748) covalent geometry : angle 0.53576 (15868) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 1.265 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7100 (mp0) REVERT: A 316 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: A 658 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8292 (mp) REVERT: B 11 GLN cc_start: 0.6647 (tt0) cc_final: 0.6334 (tt0) REVERT: B 15 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7318 (mm-30) REVERT: B 43 GLN cc_start: 0.7664 (mt0) cc_final: 0.7431 (mt0) REVERT: B 240 MET cc_start: 0.3683 (ppp) cc_final: 0.3111 (ppp) REVERT: B 341 LYS cc_start: 0.7667 (mmmm) cc_final: 0.7045 (mtpt) REVERT: B 348 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7757 (ptp) REVERT: B 384 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8029 (pp20) REVERT: B 393 SER cc_start: 0.8760 (t) cc_final: 0.8487 (t) REVERT: B 658 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7809 (mt) outliers start: 34 outliers final: 10 residues processed: 176 average time/residue: 1.1802 time to fit residues: 225.6030 Evaluate side-chains 160 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 318 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 110 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 320 ASN A 329 ASN A 410 ASN ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.147027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.121778 restraints weight = 11601.075| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.45 r_work: 0.3239 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11750 Z= 0.152 Angle : 0.525 9.000 15872 Z= 0.273 Chirality : 0.041 0.165 1686 Planarity : 0.003 0.039 2014 Dihedral : 11.716 152.238 1648 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.00 % Allowed : 20.29 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.62 (0.22), residues: 1382 helix: 1.06 (0.20), residues: 660 sheet: -0.64 (0.44), residues: 134 loop : 0.09 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 9 HIS 0.005 0.001 HIS A 304 PHE 0.018 0.002 PHE A 100 TYR 0.011 0.001 TYR B 574 ARG 0.009 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 517) hydrogen bonds : angle 5.04458 ( 1497) SS BOND : bond 0.00448 ( 2) SS BOND : angle 4.20430 ( 4) covalent geometry : bond 0.00350 (11748) covalent geometry : angle 0.52096 (15868) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 1.381 Fit side-chains REVERT: A 34 HIS cc_start: 0.8366 (t-90) cc_final: 0.8153 (t70) REVERT: A 75 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7205 (mp0) REVERT: A 316 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: A 362 ASP cc_start: 0.8069 (m-30) cc_final: 0.7859 (m-30) REVERT: A 545 ASN cc_start: 0.8538 (m-40) cc_final: 0.8244 (m-40) REVERT: A 658 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8387 (mt) REVERT: B 11 GLN cc_start: 0.6836 (tt0) cc_final: 0.6538 (tt0) REVERT: B 15 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7458 (mm-30) REVERT: B 43 GLN cc_start: 0.7725 (mt0) cc_final: 0.7458 (mt0) REVERT: B 240 MET cc_start: 0.3539 (OUTLIER) cc_final: 0.2949 (ppp) REVERT: B 348 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7881 (ptp) REVERT: B 384 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7963 (pp20) REVERT: B 393 SER cc_start: 0.8874 (t) cc_final: 0.8610 (t) REVERT: B 610 LYS cc_start: 0.7553 (mtmp) cc_final: 0.7182 (mtmt) REVERT: B 658 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7959 (mt) outliers start: 37 outliers final: 13 residues processed: 172 average time/residue: 1.2727 time to fit residues: 236.9953 Evaluate side-chains 163 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 318 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 121 optimal weight: 0.1980 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 320 ASN ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.140605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.114675 restraints weight = 12058.163| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.43 r_work: 0.3091 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11750 Z= 0.141 Angle : 0.510 7.476 15872 Z= 0.265 Chirality : 0.041 0.163 1686 Planarity : 0.003 0.038 2014 Dihedral : 11.543 150.889 1648 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.33 % Allowed : 20.21 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.67 (0.22), residues: 1382 helix: 1.13 (0.20), residues: 662 sheet: -0.70 (0.44), residues: 134 loop : 0.08 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 9 HIS 0.004 0.001 HIS A 304 PHE 0.017 0.001 PHE A 100 TYR 0.011 0.001 TYR A 498 ARG 0.009 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 517) hydrogen bonds : angle 4.96801 ( 1497) SS BOND : bond 0.00264 ( 2) SS BOND : angle 3.19706 ( 4) covalent geometry : bond 0.00323 (11748) covalent geometry : angle 0.50792 (15868) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 1.440 Fit side-chains REVERT: A 34 HIS cc_start: 0.8215 (t-90) cc_final: 0.7982 (t70) REVERT: A 75 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7055 (mp0) REVERT: A 144 MET cc_start: 0.8708 (mtm) cc_final: 0.8505 (mtm) REVERT: A 316 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: A 545 ASN cc_start: 0.8402 (m-40) cc_final: 0.8053 (m-40) REVERT: A 658 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8194 (mp) REVERT: B 11 GLN cc_start: 0.6415 (tt0) cc_final: 0.6124 (tt0) REVERT: B 15 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7305 (mm-30) REVERT: B 16 ILE cc_start: 0.7819 (mm) cc_final: 0.7608 (mm) REVERT: B 43 GLN cc_start: 0.7682 (mt0) cc_final: 0.7447 (mt0) REVERT: B 139 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6822 (mm-30) REVERT: B 214 LYS cc_start: 0.6479 (OUTLIER) cc_final: 0.6261 (ttpp) REVERT: B 240 MET cc_start: 0.3499 (OUTLIER) cc_final: 0.2864 (ppp) REVERT: B 322 MET cc_start: 0.8586 (mmm) cc_final: 0.8236 (mmm) REVERT: B 348 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7656 (ptp) REVERT: B 384 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7982 (pp20) REVERT: B 393 SER cc_start: 0.8724 (t) cc_final: 0.8414 (t) REVERT: B 421 GLU cc_start: 0.8085 (pt0) cc_final: 0.7725 (pp20) REVERT: B 610 LYS cc_start: 0.7357 (mtmp) cc_final: 0.7036 (mtmt) REVERT: B 658 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7713 (mt) outliers start: 41 outliers final: 14 residues processed: 183 average time/residue: 1.3274 time to fit residues: 262.2511 Evaluate side-chains 168 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 232 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.146755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.120788 restraints weight = 11508.578| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.40 r_work: 0.3198 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11750 Z= 0.253 Angle : 0.590 7.783 15872 Z= 0.306 Chirality : 0.044 0.158 1686 Planarity : 0.004 0.041 2014 Dihedral : 11.972 161.449 1644 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.17 % Allowed : 20.86 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.36 (0.22), residues: 1382 helix: 0.81 (0.20), residues: 662 sheet: -0.81 (0.43), residues: 134 loop : -0.01 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 9 HIS 0.005 0.001 HIS A 304 PHE 0.020 0.002 PHE A 261 TYR 0.014 0.002 TYR A 498 ARG 0.006 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 517) hydrogen bonds : angle 5.28008 ( 1497) SS BOND : bond 0.00172 ( 2) SS BOND : angle 3.29300 ( 4) covalent geometry : bond 0.00598 (11748) covalent geometry : angle 0.58749 (15868) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7131 (mp0) REVERT: A 232 ASN cc_start: 0.8523 (m110) cc_final: 0.8164 (m-40) REVERT: A 316 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: A 335 GLU cc_start: 0.7535 (pt0) cc_final: 0.7156 (pt0) REVERT: A 362 ASP cc_start: 0.8069 (m-30) cc_final: 0.7865 (m-30) REVERT: A 545 ASN cc_start: 0.8612 (m-40) cc_final: 0.8258 (m-40) REVERT: A 632 MET cc_start: 0.8994 (mtt) cc_final: 0.8266 (mtt) REVERT: A 658 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8393 (mp) REVERT: A 660 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.6717 (m-30) REVERT: B 11 GLN cc_start: 0.6917 (tt0) cc_final: 0.6520 (tt0) REVERT: B 15 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7506 (mm-30) REVERT: B 16 ILE cc_start: 0.8081 (mm) cc_final: 0.7878 (mm) REVERT: B 43 GLN cc_start: 0.7801 (mt0) cc_final: 0.7544 (mt0) REVERT: B 240 MET cc_start: 0.3721 (OUTLIER) cc_final: 0.3075 (ppp) REVERT: B 309 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7152 (tm-30) REVERT: B 384 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8125 (pp20) REVERT: B 393 SER cc_start: 0.8875 (t) cc_final: 0.8619 (t) REVERT: B 610 LYS cc_start: 0.7535 (mtmp) cc_final: 0.7221 (mtmt) REVERT: B 639 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.7715 (m-30) REVERT: B 658 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.7961 (mt) outliers start: 39 outliers final: 17 residues processed: 175 average time/residue: 1.3163 time to fit residues: 248.6437 Evaluate side-chains 174 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 90 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 53 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 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 14 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 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 = 0.3697 r_free = 0.3697 target = 0.149883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.124876 restraints weight = 11669.855| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.38 r_work: 0.3269 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11750 Z= 0.146 Angle : 0.524 7.205 15872 Z= 0.271 Chirality : 0.041 0.158 1686 Planarity : 0.003 0.040 2014 Dihedral : 11.584 153.077 1644 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.19 % Allowed : 22.24 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.22), residues: 1382 helix: 1.03 (0.20), residues: 660 sheet: -0.87 (0.43), residues: 134 loop : 0.02 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 9 HIS 0.005 0.001 HIS B 438 PHE 0.017 0.002 PHE A 100 TYR 0.012 0.001 TYR B 574 ARG 0.010 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 517) hydrogen bonds : angle 5.03964 ( 1497) SS BOND : bond 0.00193 ( 2) SS BOND : angle 2.62890 ( 4) covalent geometry : bond 0.00338 (11748) covalent geometry : angle 0.52227 (15868) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 1.351 Fit side-chains REVERT: A 34 HIS cc_start: 0.8368 (t-90) cc_final: 0.8152 (t70) REVERT: A 75 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7225 (mp0) REVERT: A 144 MET cc_start: 0.8737 (mtm) cc_final: 0.8527 (mtm) REVERT: A 316 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: A 328 ASP cc_start: 0.7867 (m-30) cc_final: 0.7605 (m-30) REVERT: A 335 GLU cc_start: 0.7449 (pt0) cc_final: 0.7129 (pt0) REVERT: A 362 ASP cc_start: 0.8086 (m-30) cc_final: 0.7877 (m-30) REVERT: A 453 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8407 (ttt-90) REVERT: A 545 ASN cc_start: 0.8642 (m-40) cc_final: 0.8300 (m-40) REVERT: A 640 MET cc_start: 0.9062 (tpp) cc_final: 0.8835 (tpp) REVERT: A 658 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8406 (mp) REVERT: B 11 GLN cc_start: 0.6826 (tt0) cc_final: 0.6489 (tt0) REVERT: B 43 GLN cc_start: 0.7812 (mt0) cc_final: 0.7572 (mt0) REVERT: B 131 ASN cc_start: 0.8092 (t0) cc_final: 0.7714 (t0) REVERT: B 240 MET cc_start: 0.3628 (OUTLIER) cc_final: 0.3020 (ppp) REVERT: B 384 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7958 (pp20) REVERT: B 393 SER cc_start: 0.8864 (t) cc_final: 0.8608 (t) REVERT: B 421 GLU cc_start: 0.8167 (pt0) cc_final: 0.7863 (pp20) REVERT: B 610 LYS cc_start: 0.7326 (mtmp) cc_final: 0.7035 (mtmt) REVERT: B 658 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7981 (mt) outliers start: 27 outliers final: 15 residues processed: 167 average time/residue: 1.2676 time to fit residues: 229.7370 Evaluate side-chains 166 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 232 ASN ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.147831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.122050 restraints weight = 11472.904| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.40 r_work: 0.3216 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11750 Z= 0.214 Angle : 0.569 7.282 15872 Z= 0.294 Chirality : 0.043 0.156 1686 Planarity : 0.003 0.041 2014 Dihedral : 11.799 160.339 1644 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.44 % Allowed : 22.32 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.36 (0.22), residues: 1382 helix: 0.87 (0.20), residues: 662 sheet: -0.91 (0.43), residues: 134 loop : -0.05 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 9 HIS 0.006 0.001 HIS B 568 PHE 0.020 0.002 PHE B 74 TYR 0.014 0.002 TYR A 498 ARG 0.010 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 517) hydrogen bonds : angle 5.18666 ( 1497) SS BOND : bond 0.00235 ( 2) SS BOND : angle 3.16988 ( 4) covalent geometry : bond 0.00504 (11748) covalent geometry : angle 0.56696 (15868) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 34 HIS cc_start: 0.8395 (t-90) cc_final: 0.8180 (t70) REVERT: A 316 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: A 328 ASP cc_start: 0.7886 (m-30) cc_final: 0.7591 (m-30) REVERT: A 335 GLU cc_start: 0.7456 (pt0) cc_final: 0.7095 (pt0) REVERT: A 453 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8417 (ttt-90) REVERT: A 545 ASN cc_start: 0.8590 (m-40) cc_final: 0.8216 (m-40) REVERT: A 632 MET cc_start: 0.9018 (mtt) cc_final: 0.8301 (mtt) REVERT: A 658 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8366 (mp) REVERT: A 660 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.6644 (m-30) REVERT: B 11 GLN cc_start: 0.6864 (tt0) cc_final: 0.6422 (tm-30) REVERT: B 43 GLN cc_start: 0.7732 (mt0) cc_final: 0.7470 (mt0) REVERT: B 131 ASN cc_start: 0.8136 (t0) cc_final: 0.7758 (t0) REVERT: B 240 MET cc_start: 0.3756 (OUTLIER) cc_final: 0.3096 (ppp) REVERT: B 384 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8126 (pp20) REVERT: B 393 SER cc_start: 0.8882 (t) cc_final: 0.8622 (t) REVERT: B 610 LYS cc_start: 0.7449 (mtmp) cc_final: 0.7173 (mtmt) REVERT: B 658 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7980 (mt) outliers start: 30 outliers final: 17 residues processed: 164 average time/residue: 1.2489 time to fit residues: 222.0529 Evaluate side-chains 168 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 62 optimal weight: 3.9990 chunk 128 optimal weight: 0.4980 chunk 68 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 91 optimal weight: 0.0060 chunk 132 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 232 ASN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.141429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.115634 restraints weight = 12291.319| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.43 r_work: 0.3106 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11750 Z= 0.129 Angle : 0.511 6.554 15872 Z= 0.265 Chirality : 0.041 0.158 1686 Planarity : 0.003 0.040 2014 Dihedral : 11.430 153.281 1644 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.11 % Allowed : 22.89 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.56 (0.22), residues: 1382 helix: 1.10 (0.20), residues: 662 sheet: -1.07 (0.41), residues: 142 loop : 0.05 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 9 HIS 0.006 0.001 HIS B 568 PHE 0.017 0.001 PHE A 100 TYR 0.011 0.001 TYR B 574 ARG 0.009 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03247 ( 517) hydrogen bonds : angle 4.93585 ( 1497) SS BOND : bond 0.00230 ( 2) SS BOND : angle 2.61084 ( 4) covalent geometry : bond 0.00295 (11748) covalent geometry : angle 0.50927 (15868) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.333 Fit side-chains REVERT: A 34 HIS cc_start: 0.8233 (t-90) cc_final: 0.8016 (t70) REVERT: A 75 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7120 (mp0) REVERT: A 144 MET cc_start: 0.8676 (mtm) cc_final: 0.8452 (mtm) REVERT: A 316 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: A 328 ASP cc_start: 0.7650 (m-30) cc_final: 0.7369 (m-30) REVERT: A 545 ASN cc_start: 0.8476 (m-40) cc_final: 0.8112 (m-40) REVERT: A 632 MET cc_start: 0.8941 (mtt) cc_final: 0.8237 (mtt) REVERT: A 640 MET cc_start: 0.9026 (tpp) cc_final: 0.8808 (tpp) REVERT: A 658 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8186 (mp) REVERT: B 11 GLN cc_start: 0.6372 (tt0) cc_final: 0.5722 (mt0) REVERT: B 43 GLN cc_start: 0.7686 (mt0) cc_final: 0.7407 (mt0) REVERT: B 117 ARG cc_start: 0.7917 (mtp180) cc_final: 0.7712 (mmm160) REVERT: B 240 MET cc_start: 0.3551 (OUTLIER) cc_final: 0.2894 (ppp) REVERT: B 384 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7972 (pp20) REVERT: B 393 SER cc_start: 0.8663 (t) cc_final: 0.8353 (t) REVERT: B 421 GLU cc_start: 0.8101 (pt0) cc_final: 0.7728 (pp20) REVERT: B 610 LYS cc_start: 0.7131 (mtmp) cc_final: 0.6873 (mtmt) outliers start: 26 outliers final: 15 residues processed: 166 average time/residue: 1.1944 time to fit residues: 215.4846 Evaluate side-chains 160 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 89 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 129 optimal weight: 0.0170 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 232 ASN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.143949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.116363 restraints weight = 12117.494| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.76 r_work: 0.3209 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11750 Z= 0.136 Angle : 0.526 7.765 15872 Z= 0.272 Chirality : 0.041 0.156 1686 Planarity : 0.003 0.040 2014 Dihedral : 11.342 153.960 1644 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.70 % Allowed : 23.30 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.58 (0.22), residues: 1382 helix: 1.15 (0.20), residues: 662 sheet: -1.13 (0.41), residues: 142 loop : 0.04 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 9 HIS 0.008 0.001 HIS B 568 PHE 0.019 0.002 PHE B 74 TYR 0.011 0.001 TYR A 612 ARG 0.009 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03265 ( 517) hydrogen bonds : angle 4.92230 ( 1497) SS BOND : bond 0.00265 ( 2) SS BOND : angle 3.10544 ( 4) covalent geometry : bond 0.00312 (11748) covalent geometry : angle 0.52340 (15868) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 1.248 Fit side-chains REVERT: A 34 HIS cc_start: 0.8285 (t-90) cc_final: 0.8068 (t70) REVERT: A 75 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7182 (mp0) REVERT: A 144 MET cc_start: 0.8703 (mtm) cc_final: 0.8497 (mtm) REVERT: A 316 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: A 322 MET cc_start: 0.7453 (mmt) cc_final: 0.7118 (mtp) REVERT: A 328 ASP cc_start: 0.7743 (m-30) cc_final: 0.7488 (m-30) REVERT: A 545 ASN cc_start: 0.8464 (m-40) cc_final: 0.8078 (m-40) REVERT: A 640 MET cc_start: 0.9029 (tpp) cc_final: 0.8791 (tpp) REVERT: A 658 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8253 (mp) REVERT: A 686 ARG cc_start: 0.7594 (mtp85) cc_final: 0.6488 (mpt90) REVERT: B 11 GLN cc_start: 0.6575 (tt0) cc_final: 0.5960 (mt0) REVERT: B 43 GLN cc_start: 0.7697 (mt0) cc_final: 0.7436 (mt0) REVERT: B 117 ARG cc_start: 0.7976 (mtp180) cc_final: 0.7774 (mmm160) REVERT: B 131 ASN cc_start: 0.7993 (t0) cc_final: 0.7675 (t0) REVERT: B 240 MET cc_start: 0.3623 (OUTLIER) cc_final: 0.2916 (ppp) REVERT: B 294 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7028 (mm-30) REVERT: B 321 GLU cc_start: 0.8135 (tt0) cc_final: 0.7875 (tt0) REVERT: B 348 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7699 (ptp) REVERT: B 384 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7984 (pp20) REVERT: B 393 SER cc_start: 0.8724 (t) cc_final: 0.8434 (t) REVERT: B 421 GLU cc_start: 0.8165 (pt0) cc_final: 0.7823 (pp20) REVERT: B 610 LYS cc_start: 0.7034 (mtmp) cc_final: 0.6783 (mtmt) outliers start: 21 outliers final: 13 residues processed: 161 average time/residue: 1.2059 time to fit residues: 210.7126 Evaluate side-chains 164 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 19 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 80 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 108 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 232 ASN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.145589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.117496 restraints weight = 11935.818| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.75 r_work: 0.3202 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11750 Z= 0.125 Angle : 0.518 7.533 15872 Z= 0.268 Chirality : 0.041 0.157 1686 Planarity : 0.003 0.038 2014 Dihedral : 11.181 152.315 1644 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.70 % Allowed : 23.46 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.62 (0.22), residues: 1382 helix: 1.16 (0.20), residues: 664 sheet: -1.17 (0.40), residues: 142 loop : 0.10 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 9 HIS 0.009 0.001 HIS B 568 PHE 0.024 0.002 PHE B 98 TYR 0.012 0.001 TYR A 612 ARG 0.011 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03199 ( 517) hydrogen bonds : angle 4.86792 ( 1497) SS BOND : bond 0.00261 ( 2) SS BOND : angle 2.84317 ( 4) covalent geometry : bond 0.00285 (11748) covalent geometry : angle 0.51564 (15868) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8239.65 seconds wall clock time: 143 minutes 15.67 seconds (8595.67 seconds total)