Starting phenix.real_space_refine on Fri Jul 3 01:26:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bw3_44947/07_2026/9bw3_44947.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bw3_44947/07_2026/9bw3_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_44947/07_2026/9bw3_44947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bw3_44947/07_2026/9bw3_44947.map" model { file = "/net/cci-nas-00/data/ceres_data/9bw3_44947/07_2026/9bw3_44947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bw3_44947/07_2026/9bw3_44947.cif" } resolution = 2.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.127 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 2.78, per 1000 atoms: 0.24 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: 1.00 Conformation dependent library (CDL) restraints added in 525.0 milliseconds 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: 0.37 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: 2.10 Time building geometry restraints manager: 1.33 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=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.608 0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" O3B TTP A 801 " pdb=" PG TTP A 801 " ideal model delta sigma weight residual 1.748 1.608 0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" O3A TTP A 801 " pdb=" PB TTP A 801 " ideal model delta sigma weight residual 1.675 1.608 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C4 TTP A 801 " pdb=" N3 TTP A 801 " ideal model delta sigma weight residual 1.385 1.334 0.051 2.00e-02 2.50e+03 6.58e+00 ... (remaining 11683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 15643 2.11 - 4.22: 83 4.22 - 6.34: 36 6.34 - 8.45: 7 8.45 - 10.56: 5 Bond angle restraints: 15774 Sorted by residual: angle pdb=" O1A TTP A 801 " pdb=" PA TTP A 801 " pdb=" O2A TTP A 801 " ideal model delta sigma weight residual 121.23 110.67 10.56 3.00e+00 1.11e-01 1.24e+01 angle pdb=" O1A TTP B 801 " pdb=" PA TTP B 801 " pdb=" O2A TTP B 801 " ideal model delta sigma weight residual 121.23 110.96 10.27 3.00e+00 1.11e-01 1.17e+01 angle pdb=" O3B TTP B 801 " pdb=" PG TTP B 801 " pdb=" O3G TTP B 801 " ideal model delta sigma weight residual 100.73 109.67 -8.94 3.00e+00 1.11e-01 8.88e+00 angle pdb=" O1B TTP B 801 " pdb=" PB TTP B 801 " pdb=" O2B TTP B 801 " ideal model delta sigma weight residual 119.36 110.63 8.73 3.00e+00 1.11e-01 8.46e+00 angle pdb=" O1B TTP A 801 " pdb=" PB TTP A 801 " pdb=" O2B TTP A 801 " ideal model delta sigma weight residual 119.36 110.69 8.67 3.00e+00 1.11e-01 8.35e+00 ... (remaining 15769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 6147 17.47 - 34.94: 677 34.94 - 52.41: 218 52.41 - 69.88: 48 69.88 - 87.35: 30 Dihedral angle restraints: 7120 sinusoidal: 2996 harmonic: 4124 Sorted by residual: dihedral pdb=" CG ARG A 331 " pdb=" CD ARG A 331 " pdb=" NE ARG A 331 " pdb=" CZ ARG A 331 " ideal model delta sinusoidal sigma weight residual -90.00 -41.69 -48.31 2 1.50e+01 4.44e-03 1.19e+01 dihedral pdb=" CA ASP A 660 " pdb=" CB ASP A 660 " pdb=" CG ASP A 660 " pdb=" OD1 ASP A 660 " ideal model delta sinusoidal sigma weight residual -30.00 -88.75 58.75 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASN A 14 " pdb=" CB ASN A 14 " pdb=" CG ASN A 14 " pdb=" OD1 ASN A 14 " ideal model delta sinusoidal sigma weight residual -90.00 -161.30 71.30 2 2.00e+01 2.50e-03 1.08e+01 ... (remaining 7117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1468 0.056 - 0.112: 183 0.112 - 0.169: 21 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: 0.02 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: 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.960 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 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= 0.788 Angle : 0.528 10.562 15774 Z= 0.256 Chirality : 0.041 0.281 1678 Planarity : 0.003 0.055 2012 Dihedral : 17.472 87.351 4468 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (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 ARG 0.003 0.000 ARG A 331 TYR 0.010 0.001 TYR B 101 PHE 0.015 0.001 PHE A 487 TRP 0.007 0.001 TRP A 9 HIS 0.003 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 (11688) covalent geometry : angle 0.52759 / 0.26 (15774) hydrogen bonds : bond 0.14600 / 9.83 ( 538) hydrogen bonds : angle 6.27045 / 4.44 ( 1554) Misc. bond : bond 0.83368 / 43.88 ( 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 : 0.452 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: 0.6362 time to fit residues: 114.6973 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 : 0.449 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0050 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN A 34 HIS A 232 ASN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN 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 = 0.3780 r_free = 0.3780 target = 0.154667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.124385 restraints weight = 11038.782| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.41 r_work: 0.3309 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11689 Z= 0.252 Angle : 0.592 6.165 15774 Z= 0.328 Chirality : 0.046 0.172 1678 Planarity : 0.004 0.049 2012 Dihedral : 8.006 65.648 1682 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.76 % Allowed : 14.77 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.22), residues: 1382 helix: 1.16 (0.20), residues: 660 sheet: 0.37 (0.41), residues: 126 loop : 0.38 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 331 TYR 0.017 0.002 TYR B 574 PHE 0.024 0.003 PHE A 100 TRP 0.010 0.003 TRP A 558 HIS 0.006 0.001 HIS B 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.25 (11688) covalent geometry : angle 0.59209 / 0.33 (15774) hydrogen bonds : bond 0.04834 / 3.24 ( 538) hydrogen bonds : angle 5.64467 / 3.96 ( 1554) Misc. bond : bond 0.00139 / 0.07 ( 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 197 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 0.446 Fit side-chains REVERT: A 209 LYS cc_start: 0.8463 (ttpt) cc_final: 0.8250 (ttpt) REVERT: A 294 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7618 (mt-10) REVERT: A 336 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8508 (ttmt) REVERT: A 348 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8093 (ttp) REVERT: B 52 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7572 (tmtm) REVERT: C 316 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7350 (ptpp) outliers start: 34 outliers final: 17 residues processed: 184 average time/residue: 0.6473 time to fit residues: 128.0391 Evaluate side-chains 179 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 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 584 ILE Chi-restraints excluded: chain A residue 599 GLU 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 C residue 316 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 129 optimal weight: 0.0070 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 106 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3828 r_free = 0.3828 target = 0.159065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.129167 restraints weight = 11141.355| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.43 r_work: 0.3376 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1254 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= 0.119 Angle : 0.466 4.812 15774 Z= 0.261 Chirality : 0.040 0.141 1678 Planarity : 0.003 0.045 2012 Dihedral : 7.432 62.117 1681 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.19 % Allowed : 15.99 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.22), residues: 1382 helix: 1.34 (0.20), residues: 664 sheet: 0.30 (0.41), residues: 134 loop : 0.46 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 331 TYR 0.011 0.001 TYR B 574 PHE 0.018 0.002 PHE A 74 TRP 0.009 0.002 TRP A 9 HIS 0.004 0.001 HIS B 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (11688) covalent geometry : angle 0.46606 / 0.26 (15774) hydrogen bonds : bond 0.03653 / 2.45 ( 538) hydrogen bonds : angle 5.20075 / 3.65 ( 1554) Misc. bond : bond 0.00067 / 0.04 ( 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 201 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.571 Fit side-chains REVERT: A 61 ASN cc_start: 0.7753 (m110) cc_final: 0.7251 (m-40) REVERT: A 66 GLU cc_start: 0.7189 (tp30) cc_final: 0.6869 (tp30) REVERT: A 209 LYS cc_start: 0.8410 (ttpt) cc_final: 0.8165 (ttpt) REVERT: A 294 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7526 (mt-10) REVERT: A 315 ASP cc_start: 0.8150 (p0) cc_final: 0.7932 (p0) REVERT: A 348 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7686 (ttp) REVERT: A 599 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8208 (mt-10) REVERT: A 659 LYS cc_start: 0.7336 (mttt) cc_final: 0.6877 (mmpt) REVERT: B 52 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7514 (tmtm) outliers start: 27 outliers final: 14 residues processed: 188 average time/residue: 0.6209 time to fit residues: 125.5286 Evaluate side-chains 178 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 537 SER Chi-restraints excluded: chain A residue 599 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 28 optimal weight: 0.4980 chunk 41 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.159740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.129755 restraints weight = 11107.462| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.43 r_work: 0.3379 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1402 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= 0.123 Angle : 0.460 4.990 15774 Z= 0.257 Chirality : 0.040 0.135 1678 Planarity : 0.003 0.040 2012 Dihedral : 7.119 63.068 1674 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.68 % Allowed : 16.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.22), residues: 1382 helix: 1.39 (0.20), residues: 662 sheet: 0.11 (0.41), residues: 134 loop : 0.48 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 331 TYR 0.019 0.001 TYR A 57 PHE 0.017 0.002 PHE B 261 TRP 0.010 0.002 TRP A 9 HIS 0.004 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (11688) covalent geometry : angle 0.45967 / 0.26 (15774) hydrogen bonds : bond 0.03555 / 2.38 ( 538) hydrogen bonds : angle 5.09756 / 3.59 ( 1554) Misc. bond : bond 0.00045 / 0.02 ( 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 201 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.264 Fit side-chains REVERT: A 61 ASN cc_start: 0.7713 (m110) cc_final: 0.7172 (m-40) REVERT: A 66 GLU cc_start: 0.7143 (tp30) cc_final: 0.6859 (tp30) REVERT: A 209 LYS cc_start: 0.8416 (ttpt) cc_final: 0.8187 (ttpt) REVERT: A 294 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7566 (mt-10) REVERT: A 336 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8348 (ttmt) REVERT: A 348 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7679 (ttp) REVERT: A 599 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8246 (mt-10) REVERT: A 659 LYS cc_start: 0.7402 (mttt) cc_final: 0.6939 (mmpt) REVERT: B 52 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7572 (tmtm) REVERT: B 658 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8288 (mt) outliers start: 33 outliers final: 13 residues processed: 188 average time/residue: 0.6273 time to fit residues: 126.4877 Evaluate side-chains 179 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 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 599 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 273 VAL 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 67 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS A 44 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.156341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125652 restraints weight = 11097.879| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.43 r_work: 0.3335 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1428 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 : 0.475 6.585 15774 Z= 0.265 Chirality : 0.041 0.135 1678 Planarity : 0.003 0.039 2012 Dihedral : 7.018 65.030 1671 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.44 % Allowed : 16.64 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.22), residues: 1382 helix: 1.39 (0.20), residues: 662 sheet: 0.02 (0.42), residues: 134 loop : 0.48 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 331 TYR 0.012 0.001 TYR A 574 PHE 0.018 0.002 PHE B 261 TRP 0.009 0.002 TRP A 9 HIS 0.004 0.001 HIS B 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (11688) covalent geometry : angle 0.47451 / 0.26 (15774) hydrogen bonds : bond 0.03672 / 2.47 ( 538) hydrogen bonds : angle 5.13459 / 3.62 ( 1554) Misc. bond : bond 0.00042 / 0.02 ( 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 198 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.473 Fit side-chains REVERT: A 66 GLU cc_start: 0.7192 (tp30) cc_final: 0.6840 (tp30) REVERT: A 131 ASN cc_start: 0.7900 (t0) cc_final: 0.7633 (t0) REVERT: A 294 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7492 (mt-10) REVERT: A 336 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8393 (ttmt) REVERT: A 348 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7714 (ttp) REVERT: A 402 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: A 599 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8152 (mt-10) REVERT: A 659 LYS cc_start: 0.7482 (mttt) cc_final: 0.6953 (mmpt) REVERT: B 52 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7575 (tmtm) REVERT: B 658 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8233 (mt) REVERT: C 316 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7546 (ptpp) outliers start: 30 outliers final: 12 residues processed: 185 average time/residue: 0.6677 time to fit residues: 132.4308 Evaluate side-chains 181 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 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 599 GLU 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 267 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 316 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 96 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS A 44 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.159106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.129191 restraints weight = 11184.268| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.43 r_work: 0.3372 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11689 Z= 0.133 Angle : 0.470 5.818 15774 Z= 0.261 Chirality : 0.040 0.136 1678 Planarity : 0.003 0.039 2012 Dihedral : 7.022 65.761 1671 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.44 % Allowed : 16.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.22), residues: 1382 helix: 1.40 (0.20), residues: 662 sheet: -0.06 (0.42), residues: 134 loop : 0.48 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 235 TYR 0.020 0.001 TYR B 57 PHE 0.018 0.002 PHE B 261 TRP 0.010 0.002 TRP A 9 HIS 0.004 0.001 HIS B 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (11688) covalent geometry : angle 0.46993 / 0.26 (15774) hydrogen bonds : bond 0.03582 / 2.40 ( 538) hydrogen bonds : angle 5.08622 / 3.58 ( 1554) Misc. bond : bond 0.00234 / 0.12 ( 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 193 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.378 Fit side-chains REVERT: A 60 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.5794 (tp30) REVERT: A 61 ASN cc_start: 0.7686 (m110) cc_final: 0.7122 (m-40) REVERT: A 66 GLU cc_start: 0.7200 (tp30) cc_final: 0.6874 (tp30) REVERT: A 131 ASN cc_start: 0.7916 (t0) cc_final: 0.7632 (t0) REVERT: A 294 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7450 (mt-10) REVERT: A 348 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7685 (ttp) REVERT: A 599 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8211 (mt-10) REVERT: A 604 ARG cc_start: 0.7777 (mmt-90) cc_final: 0.7562 (mmt-90) REVERT: A 659 LYS cc_start: 0.7388 (mttt) cc_final: 0.6892 (mmpt) REVERT: B 52 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7700 (tmtm) REVERT: B 60 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6608 (mm-30) REVERT: B 658 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8270 (mt) outliers start: 30 outliers final: 14 residues processed: 178 average time/residue: 0.6597 time to fit residues: 126.0031 Evaluate side-chains 179 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 232 ASN Chi-restraints excluded: chain A residue 273 VAL 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 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 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 107 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 53 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS A 44 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.158969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.129095 restraints weight = 11024.539| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.41 r_work: 0.3369 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11689 Z= 0.143 Angle : 0.481 8.273 15774 Z= 0.266 Chirality : 0.041 0.138 1678 Planarity : 0.003 0.037 2012 Dihedral : 7.009 66.890 1671 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.19 % Allowed : 16.88 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.22), residues: 1382 helix: 1.37 (0.20), residues: 662 sheet: -0.11 (0.42), residues: 134 loop : 0.43 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 331 TYR 0.012 0.001 TYR A 574 PHE 0.019 0.002 PHE B 261 TRP 0.009 0.002 TRP A 9 HIS 0.005 0.001 HIS B 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (11688) covalent geometry : angle 0.48088 / 0.27 (15774) hydrogen bonds : bond 0.03672 / 2.47 ( 538) hydrogen bonds : angle 5.11546 / 3.60 ( 1554) Misc. bond : bond 0.00202 / 0.11 ( 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 189 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.502 Fit side-chains REVERT: A 66 GLU cc_start: 0.7210 (tp30) cc_final: 0.6883 (tp30) REVERT: A 131 ASN cc_start: 0.7896 (t0) cc_final: 0.7616 (t0) REVERT: A 294 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7358 (mt-10) REVERT: A 317 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.7620 (mtt) REVERT: A 336 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8422 (ttmt) REVERT: A 348 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7705 (ttp) REVERT: A 402 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: A 659 LYS cc_start: 0.7412 (mttt) cc_final: 0.6960 (mmpt) REVERT: B 52 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7628 (tmtm) REVERT: B 658 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8284 (mt) outliers start: 27 outliers final: 15 residues processed: 176 average time/residue: 0.5930 time to fit residues: 111.8202 Evaluate side-chains 178 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 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 509 GLU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 599 GLU 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 267 ILE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 111 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 135 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS A 44 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.157657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.126797 restraints weight = 11099.281| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.49 r_work: 0.3358 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11689 Z= 0.116 Angle : 0.452 7.089 15774 Z= 0.252 Chirality : 0.040 0.135 1678 Planarity : 0.003 0.037 2012 Dihedral : 6.884 66.342 1671 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.11 % Allowed : 17.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.22), residues: 1382 helix: 1.45 (0.20), residues: 662 sheet: -0.18 (0.42), residues: 134 loop : 0.43 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 331 TYR 0.019 0.001 TYR B 57 PHE 0.018 0.002 PHE A 74 TRP 0.010 0.001 TRP A 9 HIS 0.004 0.001 HIS B 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (11688) covalent geometry : angle 0.45234 / 0.25 (15774) hydrogen bonds : bond 0.03383 / 2.27 ( 538) hydrogen bonds : angle 4.99317 / 3.51 ( 1554) Misc. bond : bond 0.00137 / 0.07 ( 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 191 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.481 Fit side-chains REVERT: A 60 GLU cc_start: 0.6523 (pt0) cc_final: 0.5713 (tp30) REVERT: A 61 ASN cc_start: 0.7654 (m110) cc_final: 0.7047 (m-40) REVERT: A 66 GLU cc_start: 0.7214 (tp30) cc_final: 0.6898 (tp30) REVERT: A 294 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7333 (mt-10) REVERT: A 336 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8402 (ttmt) REVERT: A 402 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: A 599 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8165 (mt-10) REVERT: A 659 LYS cc_start: 0.7381 (mttt) cc_final: 0.6931 (mmpt) REVERT: B 52 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7630 (tmtm) REVERT: B 60 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6671 (mm-30) REVERT: B 190 MET cc_start: 0.8908 (mtm) cc_final: 0.8611 (mtt) REVERT: B 384 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.7177 (pp20) REVERT: B 658 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8247 (mt) outliers start: 26 outliers final: 15 residues processed: 179 average time/residue: 0.6360 time to fit residues: 122.1415 Evaluate side-chains 181 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 336 LYS Chi-restraints excluded: chain A residue 348 MET 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 599 GLU 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 384 GLU 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 20 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS A 44 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.156129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.126439 restraints weight = 11000.662| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.39 r_work: 0.3335 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11689 Z= 0.214 Angle : 0.546 7.633 15774 Z= 0.301 Chirality : 0.044 0.153 1678 Planarity : 0.004 0.051 2012 Dihedral : 7.248 68.859 1671 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.35 % Allowed : 17.29 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.22), residues: 1382 helix: 1.15 (0.20), residues: 660 sheet: -0.10 (0.43), residues: 130 loop : 0.33 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 235 TYR 0.018 0.002 TYR A 612 PHE 0.022 0.002 PHE A 487 TRP 0.008 0.002 TRP A 9 HIS 0.006 0.001 HIS B 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (11688) covalent geometry : angle 0.54592 / 0.30 (15774) hydrogen bonds : bond 0.04204 / 2.84 ( 538) hydrogen bonds : angle 5.31438 / 3.74 ( 1554) Misc. bond : bond 0.00239 / 0.13 ( 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 187 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.467 Fit side-chains REVERT: A 66 GLU cc_start: 0.7291 (tp30) cc_final: 0.6977 (tp30) REVERT: A 294 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7433 (mt-10) REVERT: A 315 ASP cc_start: 0.8110 (p0) cc_final: 0.7842 (p0) REVERT: A 336 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8502 (ttmt) REVERT: A 348 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7967 (ttp) REVERT: A 402 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7973 (mp0) REVERT: A 599 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8214 (mt-10) REVERT: B 52 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7587 (tmtm) REVERT: B 658 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8293 (mt) outliers start: 29 outliers final: 15 residues processed: 177 average time/residue: 0.6553 time to fit residues: 124.6213 Evaluate side-chains 174 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 537 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 GLU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 14 optimal weight: 0.3980 chunk 97 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS A 44 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.159419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.130113 restraints weight = 11074.629| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.40 r_work: 0.3383 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1628 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= 0.122 Angle : 0.468 7.108 15774 Z= 0.260 Chirality : 0.040 0.139 1678 Planarity : 0.003 0.047 2012 Dihedral : 6.896 66.771 1671 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.62 % Allowed : 18.10 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.22), residues: 1382 helix: 1.36 (0.20), residues: 662 sheet: -0.21 (0.43), residues: 134 loop : 0.35 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 235 TYR 0.010 0.001 TYR A 498 PHE 0.020 0.002 PHE A 74 TRP 0.010 0.002 TRP A 9 HIS 0.004 0.001 HIS B 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (11688) covalent geometry : angle 0.46813 / 0.26 (15774) hydrogen bonds : bond 0.03454 / 2.32 ( 538) hydrogen bonds : angle 5.05147 / 3.55 ( 1554) Misc. bond : bond 0.00138 / 0.07 ( 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 186 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.429 Fit side-chains REVERT: A 60 GLU cc_start: 0.6558 (pt0) cc_final: 0.5733 (tp30) REVERT: A 61 ASN cc_start: 0.7650 (m110) cc_final: 0.7039 (m-40) REVERT: A 66 GLU cc_start: 0.7295 (tp30) cc_final: 0.6984 (tp30) REVERT: A 294 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7315 (mt-10) REVERT: A 348 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7664 (ttp) REVERT: A 402 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: A 599 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8222 (mt-10) REVERT: A 659 LYS cc_start: 0.7468 (mttt) cc_final: 0.7005 (mmpt) REVERT: B 52 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7605 (tmtm) REVERT: B 658 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8281 (mt) outliers start: 20 outliers final: 13 residues processed: 176 average time/residue: 0.6179 time to fit residues: 116.8813 Evaluate side-chains 178 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 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 537 SER Chi-restraints excluded: chain A residue 599 GLU 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 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 69 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 2 optimal weight: 0.0870 chunk 60 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS A 44 ASN A 568 HIS ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 232 ASN B 320 ASN B 474 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.158555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.129072 restraints weight = 11068.973| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.40 r_work: 0.3374 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11689 Z= 0.140 Angle : 0.487 8.415 15774 Z= 0.269 Chirality : 0.041 0.139 1678 Planarity : 0.003 0.050 2012 Dihedral : 6.875 67.205 1671 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.79 % Allowed : 18.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.22), residues: 1382 helix: 1.33 (0.20), residues: 662 sheet: -0.23 (0.42), residues: 134 loop : 0.35 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 235 TYR 0.019 0.001 TYR B 57 PHE 0.021 0.002 PHE A 74 TRP 0.010 0.002 TRP A 9 HIS 0.005 0.001 HIS B 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (11688) covalent geometry : angle 0.48678 / 0.27 (15774) hydrogen bonds : bond 0.03619 / 2.43 ( 538) hydrogen bonds : angle 5.09079 / 3.58 ( 1554) Misc. bond : bond 0.00150 / 0.08 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4263.31 seconds wall clock time: 73 minutes 37.29 seconds (4417.29 seconds total)