Starting phenix.real_space_refine on Tue Jun 10 05:48:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bw3_44947/06_2025/9bw3_44947.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bw3_44947/06_2025/9bw3_44947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bw3_44947/06_2025/9bw3_44947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bw3_44947/06_2025/9bw3_44947.map" model { file = "/net/cci-nas-00/data/ceres_data/9bw3_44947/06_2025/9bw3_44947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bw3_44947/06_2025/9bw3_44947.cif" } resolution = 2.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.127 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 12 5.49 5 Mg 2 5.21 5 S 60 5.16 5 C 7264 2.51 5 N 1888 2.21 5 O 2214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11440 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.80, per 1000 atoms: 0.68 Number of scatterers: 11440 At special positions: 0 Unit cell: (90.958, 81.76, 132.86, 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 12 15.00 Mg 2 11.99 O 2214 8.00 N 1888 7.00 C 7264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.92 Conformation dependent library (CDL) restraints added in 1.7 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: 65 helices and 10 sheets defined 53.7% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 27 through 41 removed outlier: 3.554A 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 70 removed outlier: 4.075A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 4.057A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.705A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 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 195 Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.873A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.793A pdb=" N GLN A 242 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.639A 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 329 removed outlier: 6.056A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.901A 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 366 Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 474 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: 3.520A 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 583 through 589 removed outlier: 4.274A 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 41 removed outlier: 3.548A 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 70 removed outlier: 3.950A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.960A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.721A 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 222 through 237 removed outlier: 3.779A 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 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.573A 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 329 removed outlier: 5.841A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.622A 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 367 removed outlier: 4.174A pdb=" N VAL B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 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 474 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: 3.566A 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 589 removed outlier: 4.403A 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 677 Processing helix chain 'C' and resid 316 through 321 Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.889A pdb=" N GLY A 462 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN A 410 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLY A 464 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 3.736A pdb=" N CYS A 409 " --> pdb=" O CYS A 170 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N CYS A 170 " --> pdb=" O CYS A 409 " (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 658 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 5.890A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 removed outlier: 6.456A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (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 606 Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659 540 hydrogen bonds defined for protein. 1554 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: 5.50 Time building geometry restraints manager: 4.83 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: 3676 1.34 - 1.46: 2718 1.46 - 1.58: 5162 1.58 - 1.69: 20 1.69 - 1.81: 112 Bond restraints: 11688 Sorted by residual: bond pdb=" CA MET A 240 " pdb=" CB MET A 240 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 6.03e-01 bond pdb=" C3' ATP B 803 " pdb=" C4' ATP B 803 " ideal model delta sigma weight residual 1.526 1.519 0.007 1.10e-02 8.26e+03 4.62e-01 bond pdb=" C3' ATP A 803 " pdb=" C4' ATP A 803 " ideal model delta sigma weight residual 1.526 1.520 0.006 1.10e-02 8.26e+03 3.39e-01 bond pdb=" C2' ATP A 803 " pdb=" C3' ATP A 803 " ideal model delta sigma weight residual 1.531 1.524 0.007 1.20e-02 6.94e+03 3.14e-01 bond pdb=" CA MET A 240 " pdb=" C MET A 240 " ideal model delta sigma weight residual 1.523 1.531 -0.007 1.34e-02 5.57e+03 3.02e-01 ... (remaining 11683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 15468 1.19 - 2.38: 234 2.38 - 3.57: 55 3.57 - 4.76: 5 4.76 - 5.95: 12 Bond angle restraints: 15774 Sorted by residual: angle pdb=" C3' ATP B 803 " pdb=" C4' ATP B 803 " pdb=" O4' ATP B 803 " ideal model delta sigma weight residual 105.22 101.89 3.33 1.30e+00 5.94e-01 6.60e+00 angle pdb=" N ASP D 317 " pdb=" CA ASP D 317 " pdb=" CB ASP D 317 " ideal model delta sigma weight residual 113.65 110.21 3.44 1.47e+00 4.63e-01 5.48e+00 angle pdb=" C3' ATP A 803 " pdb=" C4' ATP A 803 " pdb=" C5' ATP A 803 " ideal model delta sigma weight residual 115.19 111.22 3.97 1.76e+00 3.23e-01 5.09e+00 angle pdb=" C3' ATP B 803 " pdb=" C4' ATP B 803 " pdb=" C5' ATP B 803 " ideal model delta sigma weight residual 115.19 111.33 3.86 1.76e+00 3.23e-01 4.81e+00 angle pdb=" C2' ATP B 803 " pdb=" C3' ATP B 803 " pdb=" O3' ATP B 803 " ideal model delta sigma weight residual 111.83 106.03 5.80 2.67e+00 1.40e-01 4.73e+00 ... (remaining 15769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.31: 6763 34.31 - 68.63: 272 68.63 - 102.94: 35 102.94 - 137.25: 0 137.25 - 171.56: 2 Dihedral angle restraints: 7072 sinusoidal: 2948 harmonic: 4124 Sorted by residual: 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 301.68 130.12 171.56 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 135.73 165.95 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' TTP B 801 " pdb=" O5' TTP B 801 " pdb=" PA TTP B 801 " pdb=" O3A TTP B 801 " ideal model delta sinusoidal sigma weight residual 179.97 -105.64 -74.39 1 2.00e+01 2.50e-03 1.75e+01 ... (remaining 7069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1471 0.056 - 0.112: 183 0.112 - 0.169: 18 0.169 - 0.225: 0 0.225 - 0.281: 6 Chirality restraints: 1678 Sorted by residual: chirality pdb=" C2' ATP A 803 " pdb=" C1' ATP A 803 " pdb=" C3' ATP A 803 " pdb=" O2' ATP A 803 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C2' ATP B 803 " pdb=" C1' ATP B 803 " pdb=" C3' ATP B 803 " pdb=" O2' ATP B 803 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C3' ATP B 803 " pdb=" C2' ATP B 803 " pdb=" C4' ATP B 803 " pdb=" O3' ATP B 803 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 1675 not shown) Planarity restraints: 2012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 6 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO B 7 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 7 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 7 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 37 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" C PHE B 37 " 0.025 2.00e-02 2.50e+03 pdb=" O PHE B 37 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL B 38 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 37 " -0.007 2.00e-02 2.50e+03 1.33e-02 1.77e+00 pdb=" C PHE A 37 " 0.023 2.00e-02 2.50e+03 pdb=" O PHE A 37 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL A 38 " -0.008 2.00e-02 2.50e+03 ... (remaining 2009 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 112 2.51 - 3.11: 8797 3.11 - 3.71: 19496 3.71 - 4.30: 30010 4.30 - 4.90: 47556 Nonbonded interactions: 105971 Sorted by model distance: nonbonded pdb=" O1B TTP A 801 " pdb="MG MG A 802 " model vdw 1.919 2.170 nonbonded pdb=" O2A TTP B 801 " pdb="MG MG B 802 " model vdw 1.928 2.170 nonbonded pdb=" O PRO B 616 " pdb=" OH TYR B 626 " model vdw 1.993 3.040 nonbonded pdb=" OG1 THR A 663 " pdb=" OE2 GLU C 313 " model vdw 2.018 3.040 nonbonded pdb=" OH TYR B 64 " pdb=" OE2 GLU B 116 " model vdw 2.021 3.040 ... (remaining 105966 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' selection = chain 'B' } 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=0.43 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: 0.800 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 34.920 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:31.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 : 0.008 0.834 11689 Z= 0.777 Angle : 0.423 5.947 15774 Z= 0.233 Chirality : 0.041 0.281 1678 Planarity : 0.003 0.055 2012 Dihedral : 17.839 171.565 4420 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 22.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.81 % Allowed : 18.10 % Favored : 81.09 % 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: 1.54 (0.22), residues: 1382 helix: 1.67 (0.20), residues: 668 sheet: 0.46 (0.39), residues: 146 loop : 0.54 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 9 HIS 0.003 0.001 HIS A 568 PHE 0.015 0.001 PHE A 487 TYR 0.010 0.001 TYR B 101 ARG 0.003 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.14600 ( 538) hydrogen bonds : angle 6.27045 ( 1554) covalent geometry : bond 0.00192 (11688) covalent geometry : angle 0.42284 (15774) Misc. bond : bond 0.83368 ( 1) *********************** 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 168 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 1.566 Fit side-chains REVERT: A 315 ASP cc_start: 0.8093 (p0) cc_final: 0.7834 (p0) outliers start: 10 outliers final: 7 residues processed: 167 average time/residue: 1.6550 time to fit residues: 298.8353 Evaluate side-chains 158 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 0.0870 chunk 55 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 34 HIS ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN B 34 HIS B 320 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 = 0.3794 r_free = 0.3794 target = 0.155942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.125798 restraints weight = 10920.203| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.41 r_work: 0.3332 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11689 Z= 0.202 Angle : 0.559 5.584 15774 Z= 0.306 Chirality : 0.044 0.169 1678 Planarity : 0.004 0.049 2012 Dihedral : 10.729 175.717 1634 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.52 % Allowed : 15.10 % Favored : 82.39 % 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: 1.19 (0.22), residues: 1382 helix: 1.30 (0.20), residues: 662 sheet: 0.45 (0.42), residues: 126 loop : 0.45 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 9 HIS 0.005 0.001 HIS B 372 PHE 0.022 0.002 PHE A 100 TYR 0.016 0.002 TYR A 606 ARG 0.007 0.001 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.04566 ( 538) hydrogen bonds : angle 5.53621 ( 1554) covalent geometry : bond 0.00459 (11688) covalent geometry : angle 0.55869 (15774) Misc. bond : bond 0.00135 ( 1) *********************** 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 200 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 1.767 Fit side-chains REVERT: A 209 LYS cc_start: 0.8452 (ttpt) cc_final: 0.8224 (ttpt) REVERT: A 294 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7677 (mt-10) REVERT: A 336 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8474 (ttmt) REVERT: A 348 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7929 (ttp) REVERT: B 52 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7503 (tmtm) outliers start: 31 outliers final: 19 residues processed: 187 average time/residue: 1.8961 time to fit residues: 381.0779 Evaluate side-chains 181 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 634 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 584 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 19 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 44 ASN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 109 ASN B 320 ASN B 668 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.159049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128976 restraints weight = 11140.891| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.43 r_work: 0.3372 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11689 Z= 0.132 Angle : 0.489 5.798 15774 Z= 0.268 Chirality : 0.041 0.143 1678 Planarity : 0.003 0.046 2012 Dihedral : 10.279 172.299 1632 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.27 % Allowed : 15.58 % Favored : 82.14 % 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: 1.22 (0.22), residues: 1382 helix: 1.36 (0.20), residues: 664 sheet: 0.29 (0.42), residues: 126 loop : 0.46 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 9 HIS 0.004 0.001 HIS B 372 PHE 0.018 0.002 PHE B 261 TYR 0.012 0.001 TYR B 574 ARG 0.006 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 538) hydrogen bonds : angle 5.21781 ( 1554) covalent geometry : bond 0.00290 (11688) covalent geometry : angle 0.48857 (15774) Misc. bond : bond 0.00045 ( 1) *********************** 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 203 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 1.461 Fit side-chains REVERT: A 61 ASN cc_start: 0.7720 (m110) cc_final: 0.7206 (m-40) REVERT: A 66 GLU cc_start: 0.7227 (tp30) cc_final: 0.6900 (tp30) REVERT: A 209 LYS cc_start: 0.8424 (ttpt) cc_final: 0.8176 (ttpt) REVERT: A 294 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7561 (mt-10) REVERT: A 659 LYS cc_start: 0.7404 (mttt) cc_final: 0.6900 (mmpt) REVERT: B 52 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7514 (tmtm) REVERT: B 190 MET cc_start: 0.8876 (mtm) cc_final: 0.8644 (mtt) REVERT: C 316 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7274 (ptpp) outliers start: 28 outliers final: 14 residues processed: 189 average time/residue: 2.0667 time to fit residues: 418.4019 Evaluate side-chains 173 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 316 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 63 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 44 ASN A 232 ASN A 568 HIS ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 320 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.155484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.125259 restraints weight = 11090.696| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.41 r_work: 0.3322 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11689 Z= 0.230 Angle : 0.570 6.102 15774 Z= 0.311 Chirality : 0.044 0.151 1678 Planarity : 0.004 0.043 2012 Dihedral : 10.607 175.366 1626 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.76 % Allowed : 16.23 % Favored : 81.01 % 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: 0.97 (0.22), residues: 1382 helix: 1.14 (0.19), residues: 660 sheet: 0.16 (0.41), residues: 130 loop : 0.36 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 9 HIS 0.006 0.001 HIS B 372 PHE 0.022 0.002 PHE B 261 TYR 0.017 0.002 TYR A 57 ARG 0.005 0.001 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.04444 ( 538) hydrogen bonds : angle 5.46075 ( 1554) covalent geometry : bond 0.00525 (11688) covalent geometry : angle 0.57037 (15774) Misc. bond : bond 0.00073 ( 1) *********************** 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 197 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 1.317 Fit side-chains REVERT: A 66 GLU cc_start: 0.7253 (tp30) cc_final: 0.6856 (tp30) REVERT: A 294 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7517 (mt-10) REVERT: A 315 ASP cc_start: 0.8150 (p0) cc_final: 0.7934 (p0) REVERT: A 317 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8277 (mtt) REVERT: A 336 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8453 (ttmt) REVERT: A 348 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7975 (ttp) REVERT: B 52 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7591 (tmtm) REVERT: B 267 ILE cc_start: 0.6788 (OUTLIER) cc_final: 0.6377 (tp) REVERT: B 658 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8313 (mt) outliers start: 34 outliers final: 15 residues processed: 184 average time/residue: 1.4304 time to fit residues: 282.3679 Evaluate side-chains 177 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 0 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 44 ASN A 232 ASN A 568 HIS ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 320 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.157917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.128055 restraints weight = 11000.527| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.41 r_work: 0.3356 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11689 Z= 0.148 Angle : 0.502 6.542 15774 Z= 0.274 Chirality : 0.041 0.138 1678 Planarity : 0.003 0.041 2012 Dihedral : 10.306 174.121 1626 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.19 % Allowed : 16.64 % Favored : 81.17 % 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: 1.06 (0.22), residues: 1382 helix: 1.25 (0.20), residues: 662 sheet: 0.02 (0.41), residues: 134 loop : 0.40 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 9 HIS 0.005 0.001 HIS B 372 PHE 0.020 0.002 PHE B 261 TYR 0.016 0.001 TYR A 57 ARG 0.006 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 538) hydrogen bonds : angle 5.22628 ( 1554) covalent geometry : bond 0.00331 (11688) covalent geometry : angle 0.50157 (15774) Misc. bond : bond 0.00033 ( 1) *********************** 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 189 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 1.265 Fit side-chains REVERT: A 66 GLU cc_start: 0.7228 (tp30) cc_final: 0.6871 (tp30) REVERT: A 294 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7576 (mt-10) REVERT: A 315 ASP cc_start: 0.8156 (p0) cc_final: 0.7949 (p0) REVERT: A 336 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8434 (ttmt) REVERT: A 348 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7734 (ttp) REVERT: A 659 LYS cc_start: 0.7497 (mttt) cc_final: 0.6958 (mmpt) REVERT: B 52 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7568 (tmtm) REVERT: B 60 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6620 (mm-30) REVERT: B 658 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8283 (mt) outliers start: 27 outliers final: 14 residues processed: 178 average time/residue: 1.5054 time to fit residues: 286.8167 Evaluate side-chains 174 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 13 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 44 ASN A 232 ASN A 568 HIS ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 320 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.156265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.126090 restraints weight = 11165.012| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.42 r_work: 0.3332 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11689 Z= 0.193 Angle : 0.539 7.987 15774 Z= 0.293 Chirality : 0.043 0.143 1678 Planarity : 0.004 0.043 2012 Dihedral : 10.452 175.239 1626 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.60 % Allowed : 16.31 % Favored : 81.09 % 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: 0.94 (0.22), residues: 1382 helix: 1.16 (0.20), residues: 660 sheet: 0.01 (0.42), residues: 130 loop : 0.34 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 9 HIS 0.005 0.001 HIS B 372 PHE 0.021 0.002 PHE B 261 TYR 0.015 0.002 TYR A 574 ARG 0.006 0.001 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 538) hydrogen bonds : angle 5.33398 ( 1554) covalent geometry : bond 0.00438 (11688) covalent geometry : angle 0.53883 (15774) Misc. bond : bond 0.00046 ( 1) *********************** 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 187 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 2.251 Fit side-chains REVERT: A 66 GLU cc_start: 0.7312 (tp30) cc_final: 0.6950 (tp30) REVERT: A 294 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7563 (mt-10) REVERT: A 315 ASP cc_start: 0.8155 (p0) cc_final: 0.7914 (p0) REVERT: A 317 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8115 (mtt) REVERT: A 336 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8479 (ttmt) REVERT: A 348 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7885 (ttp) REVERT: A 402 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7984 (mp0) REVERT: B 52 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7611 (tmtm) REVERT: B 267 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.6464 (tp) REVERT: B 384 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.7481 (pm20) REVERT: B 658 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8302 (mt) outliers start: 32 outliers final: 16 residues processed: 175 average time/residue: 1.9971 time to fit residues: 379.0861 Evaluate side-chains 178 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 3 optimal weight: 0.0770 chunk 15 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 44 ASN A 232 ASN A 568 HIS ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 320 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.158483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.128607 restraints weight = 11159.369| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.42 r_work: 0.3364 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11689 Z= 0.139 Angle : 0.497 8.687 15774 Z= 0.270 Chirality : 0.041 0.136 1678 Planarity : 0.003 0.040 2012 Dihedral : 10.202 173.422 1626 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.44 % Allowed : 16.80 % Favored : 80.76 % 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: 1.02 (0.22), residues: 1382 helix: 1.28 (0.20), residues: 662 sheet: -0.15 (0.42), residues: 134 loop : 0.34 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 9 HIS 0.004 0.001 HIS B 372 PHE 0.019 0.002 PHE B 261 TYR 0.011 0.001 TYR B 574 ARG 0.006 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 538) hydrogen bonds : angle 5.15024 ( 1554) covalent geometry : bond 0.00310 (11688) covalent geometry : angle 0.49672 (15774) Misc. bond : bond 0.00043 ( 1) *********************** 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 190 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 1.530 Fit side-chains REVERT: A 66 GLU cc_start: 0.7270 (tp30) cc_final: 0.6938 (tp30) REVERT: A 336 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8459 (ttmt) REVERT: A 348 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7715 (ttp) REVERT: A 402 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7983 (mp0) REVERT: A 659 LYS cc_start: 0.7380 (mttt) cc_final: 0.6913 (mmpt) REVERT: B 52 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7603 (tmtm) REVERT: B 658 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8276 (mt) outliers start: 30 outliers final: 16 residues processed: 176 average time/residue: 1.8356 time to fit residues: 346.3703 Evaluate side-chains 177 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 316 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 64 optimal weight: 0.0980 chunk 127 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 44 ASN A 232 ASN A 568 HIS ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 320 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.159604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.129800 restraints weight = 11089.540| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.43 r_work: 0.3385 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11689 Z= 0.120 Angle : 0.477 6.628 15774 Z= 0.260 Chirality : 0.040 0.136 1678 Planarity : 0.003 0.038 2012 Dihedral : 9.868 169.433 1623 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.44 % Allowed : 16.80 % Favored : 80.76 % 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: 1.10 (0.22), residues: 1382 helix: 1.38 (0.20), residues: 662 sheet: -0.18 (0.42), residues: 134 loop : 0.35 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 9 HIS 0.004 0.001 HIS B 372 PHE 0.017 0.002 PHE B 261 TYR 0.010 0.001 TYR A 574 ARG 0.010 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 538) hydrogen bonds : angle 5.03570 ( 1554) covalent geometry : bond 0.00264 (11688) covalent geometry : angle 0.47652 (15774) Misc. bond : bond 0.00016 ( 1) *********************** 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 202 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 1.284 Fit side-chains REVERT: A 60 GLU cc_start: 0.6498 (pt0) cc_final: 0.5773 (tp30) REVERT: A 66 GLU cc_start: 0.7307 (tp30) cc_final: 0.6980 (tp30) REVERT: A 294 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7437 (mt-10) REVERT: A 336 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8451 (ttmt) REVERT: A 348 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7687 (ttp) REVERT: A 402 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7981 (mp0) REVERT: A 659 LYS cc_start: 0.7346 (mttt) cc_final: 0.6885 (mmpt) REVERT: B 52 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7683 (tmtm) REVERT: B 60 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6625 (mm-30) REVERT: B 267 ILE cc_start: 0.6867 (OUTLIER) cc_final: 0.6465 (tp) REVERT: B 658 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8258 (mt) REVERT: B 665 ARG cc_start: 0.8330 (tmt170) cc_final: 0.8117 (tmt170) outliers start: 30 outliers final: 16 residues processed: 188 average time/residue: 1.7074 time to fit residues: 344.1751 Evaluate side-chains 186 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 35 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 24 optimal weight: 6.9990 chunk 76 optimal weight: 0.0570 chunk 83 optimal weight: 7.9990 chunk 98 optimal weight: 0.0670 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 44 ASN A 232 ASN A 568 HIS ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.161792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.132637 restraints weight = 11116.159| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.41 r_work: 0.3424 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11689 Z= 0.102 Angle : 0.467 7.624 15774 Z= 0.252 Chirality : 0.040 0.133 1678 Planarity : 0.003 0.036 2012 Dihedral : 9.572 163.771 1623 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.95 % Allowed : 17.53 % Favored : 80.52 % 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: 1.20 (0.22), residues: 1382 helix: 1.49 (0.20), residues: 664 sheet: -0.24 (0.42), residues: 134 loop : 0.40 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 9 HIS 0.003 0.001 HIS B 438 PHE 0.020 0.001 PHE A 74 TYR 0.019 0.001 TYR B 57 ARG 0.008 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 538) hydrogen bonds : angle 4.88645 ( 1554) covalent geometry : bond 0.00221 (11688) covalent geometry : angle 0.46704 (15774) Misc. bond : bond 0.00006 ( 1) *********************** 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 189 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 1.263 Fit side-chains REVERT: A 60 GLU cc_start: 0.6404 (pt0) cc_final: 0.5730 (tp30) REVERT: A 66 GLU cc_start: 0.7210 (tp30) cc_final: 0.6923 (tp30) REVERT: A 294 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7392 (mt-10) REVERT: A 384 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.7365 (pp20) REVERT: A 402 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: A 659 LYS cc_start: 0.7317 (mttt) cc_final: 0.6944 (mmpt) REVERT: B 17 MET cc_start: 0.8727 (mmm) cc_final: 0.8447 (mmp) REVERT: B 267 ILE cc_start: 0.6831 (OUTLIER) cc_final: 0.6404 (tp) REVERT: B 315 ASP cc_start: 0.7971 (p0) cc_final: 0.7609 (p0) REVERT: B 539 LYS cc_start: 0.8094 (mmtm) cc_final: 0.7888 (mmtm) REVERT: B 658 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8279 (mt) outliers start: 24 outliers final: 12 residues processed: 180 average time/residue: 1.4973 time to fit residues: 288.6269 Evaluate side-chains 177 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 316 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 87 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 232 ASN A 568 HIS ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS ** B 320 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 = 0.3832 r_free = 0.3832 target = 0.159126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.129580 restraints weight = 11099.371| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.40 r_work: 0.3372 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11689 Z= 0.140 Angle : 0.496 7.074 15774 Z= 0.270 Chirality : 0.041 0.140 1678 Planarity : 0.003 0.052 2012 Dihedral : 9.799 169.009 1623 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.54 % Allowed : 18.43 % Favored : 80.03 % 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: 1.10 (0.22), residues: 1382 helix: 1.41 (0.20), residues: 662 sheet: -0.28 (0.42), residues: 134 loop : 0.35 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 9 HIS 0.004 0.001 HIS B 372 PHE 0.018 0.002 PHE B 261 TYR 0.015 0.001 TYR A 612 ARG 0.012 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 538) hydrogen bonds : angle 5.04928 ( 1554) covalent geometry : bond 0.00312 (11688) covalent geometry : angle 0.49618 (15774) Misc. bond : bond 0.00016 ( 1) ********************** 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 184 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 1.384 Fit side-chains REVERT: A 60 GLU cc_start: 0.6442 (pt0) cc_final: 0.5776 (tp30) REVERT: A 66 GLU cc_start: 0.7240 (tp30) cc_final: 0.6938 (tp30) REVERT: A 294 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7408 (mt-10) REVERT: A 402 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7981 (mp0) REVERT: A 659 LYS cc_start: 0.7392 (mttt) cc_final: 0.6927 (mmpt) REVERT: B 60 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6769 (mm-30) REVERT: B 267 ILE cc_start: 0.6840 (OUTLIER) cc_final: 0.6435 (tp) REVERT: B 539 LYS cc_start: 0.8124 (mmtm) cc_final: 0.7905 (mmtm) REVERT: B 658 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8246 (mt) outliers start: 19 outliers final: 11 residues processed: 178 average time/residue: 1.4839 time to fit residues: 282.7494 Evaluate side-chains 176 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 44 ASN A 232 ASN A 568 HIS ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 320 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.156987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.127231 restraints weight = 11088.431| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.40 r_work: 0.3345 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11689 Z= 0.183 Angle : 0.545 8.597 15774 Z= 0.295 Chirality : 0.043 0.143 1678 Planarity : 0.004 0.052 2012 Dihedral : 10.219 175.360 1623 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.38 % Allowed : 18.59 % Favored : 80.03 % 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: 0.93 (0.22), residues: 1382 helix: 1.19 (0.20), residues: 662 sheet: -0.20 (0.43), residues: 130 loop : 0.31 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 9 HIS 0.005 0.001 HIS B 372 PHE 0.021 0.002 PHE B 261 TYR 0.017 0.002 TYR A 612 ARG 0.011 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 538) hydrogen bonds : angle 5.24692 ( 1554) covalent geometry : bond 0.00416 (11688) covalent geometry : angle 0.54505 (15774) Misc. bond : bond 0.00033 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10808.67 seconds wall clock time: 192 minutes 38.92 seconds (11558.92 seconds total)