Starting phenix.real_space_refine on Fri Oct 10 17:41:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u1n_41818/10_2025/8u1n_41818.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u1n_41818/10_2025/8u1n_41818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u1n_41818/10_2025/8u1n_41818.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u1n_41818/10_2025/8u1n_41818.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u1n_41818/10_2025/8u1n_41818.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u1n_41818/10_2025/8u1n_41818.map" } resolution = 3.9 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= 0.002 sd= 0.015 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 6 5.49 5 Mg 2 5.21 5 S 28 5.16 5 C 5158 2.51 5 N 1366 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8164 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4050 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 11, 'TRANS': 485} Chain breaks: 1 Chain: "B" Number of atoms: 4050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4050 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 11, 'TRANS': 485} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.81, per 1000 atoms: 0.22 Number of scatterers: 8164 At special positions: 0 Unit cell: (115.83, 120.978, 103.818, 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 28 16.00 P 6 15.00 Mg 2 11.99 O 1604 8.00 N 1366 7.00 C 5158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 433.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1884 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 37.5% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 21 through 32 removed outlier: 4.051A pdb=" N PHE A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 61 removed outlier: 3.624A pdb=" N LEU A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.647A pdb=" N LEU A 65 " --> pdb=" O PRO A 62 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP A 66 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER A 67 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.654A pdb=" N ALA A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 187 through 193 removed outlier: 4.031A pdb=" N ALA A 190 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU A 191 " --> pdb=" O ASP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 397 through 421 removed outlier: 3.681A pdb=" N GLU A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 443 removed outlier: 6.972A pdb=" N LYS A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS A 437 " --> pdb=" O SER A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 452 removed outlier: 3.834A pdb=" N ASP A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 Processing helix chain 'A' and resid 473 through 475 No H-bonds generated for 'chain 'A' and resid 473 through 475' Processing helix chain 'A' and resid 491 through 496 removed outlier: 3.696A pdb=" N ALA A 494 " --> pdb=" O ASP A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 505 removed outlier: 3.591A pdb=" N LYS A 504 " --> pdb=" O ARG A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 524 Processing helix chain 'B' and resid 20 through 32 removed outlier: 3.699A pdb=" N LEU B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 61 removed outlier: 3.819A pdb=" N THR B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 101 Processing helix chain 'B' and resid 108 through 115 removed outlier: 3.763A pdb=" N ALA B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 138 removed outlier: 3.829A pdb=" N SER B 135 " --> pdb=" O GLY B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 296 through 309 removed outlier: 4.240A pdb=" N TYR B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 396 through 418 Processing helix chain 'B' and resid 421 through 443 removed outlier: 6.937A pdb=" N LYS B 434 " --> pdb=" O GLU B 430 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASN B 435 " --> pdb=" O GLN B 431 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU B 436 " --> pdb=" O PHE B 432 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 437 " --> pdb=" O SER B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 454 Processing helix chain 'B' and resid 468 through 474 removed outlier: 3.615A pdb=" N VAL B 472 " --> pdb=" O LEU B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 495 removed outlier: 3.725A pdb=" N VAL B 493 " --> pdb=" O ASN B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 504 removed outlier: 3.952A pdb=" N ARG B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N VAL B 502 " --> pdb=" O PHE B 498 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 504 " --> pdb=" O GLU B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 521 removed outlier: 3.588A pdb=" N VAL B 521 " --> pdb=" O ASP B 517 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.592A pdb=" N PHE A 15 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE B 165 " --> pdb=" O PHE A 15 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 168 " --> pdb=" O MET B 156 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 159 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 143 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19 removed outlier: 7.040A pdb=" N GLN A 18 " --> pdb=" O ILE B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 215 removed outlier: 7.233A pdb=" N ILE A 73 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP A 88 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 178 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 168 " --> pdb=" O MET A 156 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 314 through 322 removed outlier: 6.641A pdb=" N VAL A 334 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL A 317 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU A 332 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N HIS A 319 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ALA A 330 " --> pdb=" O HIS A 319 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER A 321 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N PHE A 328 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 455 through 456 Processing sheet with id=AA7, first strand: chain 'A' and resid 483 through 485 removed outlier: 7.439A pdb=" N TYR A 483 " --> pdb=" O VAL A 510 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 317 through 322 removed outlier: 3.575A pdb=" N LEU B 332 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE B 320 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET B 362 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL B 356 " --> pdb=" O PHE B 360 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N PHE B 360 " --> pdb=" O VAL B 356 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 455 through 456 Processing sheet with id=AB1, first strand: chain 'B' and resid 482 through 483 removed outlier: 6.015A pdb=" N ILE B 482 " --> pdb=" O VAL B 533 " (cutoff:3.500A) 293 hydrogen bonds defined for protein. 798 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.29 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2661 1.34 - 1.46: 1767 1.46 - 1.58: 3826 1.58 - 1.70: 4 1.70 - 1.82: 48 Bond restraints: 8306 Sorted by residual: bond pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " ideal model delta sigma weight residual 1.443 1.221 0.222 1.00e-02 1.00e+04 4.93e+02 bond pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " ideal model delta sigma weight residual 1.443 1.222 0.221 1.00e-02 1.00e+04 4.90e+02 bond pdb=" C1' ATP B 801 " pdb=" O4' ATP B 801 " ideal model delta sigma weight residual 1.416 1.359 0.057 1.30e-02 5.92e+03 1.94e+01 bond pdb=" C4' ATP B 801 " pdb=" O4' ATP B 801 " ideal model delta sigma weight residual 1.444 1.397 0.047 1.10e-02 8.26e+03 1.86e+01 bond pdb=" C3' ATP B 801 " pdb=" O3' ATP B 801 " ideal model delta sigma weight residual 1.423 1.377 0.046 1.10e-02 8.26e+03 1.73e+01 ... (remaining 8301 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.88: 11152 6.88 - 13.76: 18 13.76 - 20.64: 4 20.64 - 27.53: 1 27.53 - 34.41: 7 Bond angle restraints: 11182 Sorted by residual: angle pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " pdb=" PA ATP A 801 " ideal model delta sigma weight residual 121.27 155.68 -34.41 1.00e+00 1.00e+00 1.18e+03 angle pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " pdb=" PA ATP B 801 " ideal model delta sigma weight residual 121.27 154.53 -33.26 1.00e+00 1.00e+00 1.11e+03 angle pdb=" C3' ATP A 801 " pdb=" C4' ATP A 801 " pdb=" C5' ATP A 801 " ideal model delta sigma weight residual 115.19 82.86 32.33 1.76e+00 3.23e-01 3.37e+02 angle pdb=" C3' ATP B 801 " pdb=" C4' ATP B 801 " pdb=" C5' ATP B 801 " ideal model delta sigma weight residual 115.19 84.99 30.20 1.76e+00 3.23e-01 2.95e+02 angle pdb=" C4' ATP A 801 " pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " ideal model delta sigma weight residual 108.83 138.61 -29.78 2.33e+00 1.85e-01 1.64e+02 ... (remaining 11177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4300 17.84 - 35.67: 613 35.67 - 53.51: 153 53.51 - 71.34: 34 71.34 - 89.18: 16 Dihedral angle restraints: 5116 sinusoidal: 2194 harmonic: 2922 Sorted by residual: dihedral pdb=" CA TYR B 511 " pdb=" C TYR B 511 " pdb=" N MET B 512 " pdb=" CA MET B 512 " ideal model delta harmonic sigma weight residual -180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA TYR A 507 " pdb=" C TYR A 507 " pdb=" N GLU A 508 " pdb=" CA GLU A 508 " ideal model delta harmonic sigma weight residual 180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA GLU B 514 " pdb=" C GLU B 514 " pdb=" N PRO B 515 " pdb=" CA PRO B 515 " ideal model delta harmonic sigma weight residual -180.00 -159.58 -20.42 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 5113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1161 0.096 - 0.192: 55 0.192 - 0.288: 4 0.288 - 0.384: 0 0.384 - 0.480: 2 Chirality restraints: 1222 Sorted by residual: chirality pdb=" C4' ATP B 801 " pdb=" C3' ATP B 801 " pdb=" C5' ATP B 801 " pdb=" O4' ATP B 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.97 0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" C4' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" C5' ATP A 801 " pdb=" O4' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.95 0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" C3' ATP A 801 " pdb=" C2' ATP A 801 " pdb=" C4' ATP A 801 " pdb=" O3' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1219 not shown) Planarity restraints: 1426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 514 " -0.058 5.00e-02 4.00e+02 8.71e-02 1.21e+01 pdb=" N PRO B 515 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO B 515 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 515 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 285 " -0.036 5.00e-02 4.00e+02 5.54e-02 4.92e+00 pdb=" N PRO B 286 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 286 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 286 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 76 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO B 77 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 77 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 77 " -0.024 5.00e-02 4.00e+02 ... (remaining 1423 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 86 2.49 - 3.09: 5771 3.09 - 3.69: 12970 3.69 - 4.30: 17680 4.30 - 4.90: 27978 Nonbonded interactions: 64485 Sorted by model distance: nonbonded pdb=" O2G ATP A 801 " pdb="MG MG A 802 " model vdw 1.883 2.170 nonbonded pdb=" O5' ATP B 801 " pdb="MG MG B 802 " model vdw 1.893 2.170 nonbonded pdb=" O2A ATP B 801 " pdb="MG MG B 802 " model vdw 1.914 2.170 nonbonded pdb=" O2B ATP A 801 " pdb="MG MG A 802 " model vdw 1.915 2.170 nonbonded pdb=" O2G ATP B 801 " pdb="MG MG B 802 " model vdw 1.962 2.170 ... (remaining 64480 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.200 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.140 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 : 0.005 0.222 8306 Z= 0.417 Angle : 1.169 34.407 11182 Z= 0.710 Chirality : 0.048 0.480 1222 Planarity : 0.004 0.087 1426 Dihedral : 17.981 89.180 3232 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 26.00 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.26), residues: 986 helix: -0.15 (0.29), residues: 317 sheet: 0.20 (0.44), residues: 158 loop : -1.53 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 329 TYR 0.023 0.001 TYR B 519 PHE 0.010 0.001 PHE B 165 TRP 0.007 0.001 TRP A 311 HIS 0.004 0.001 HIS A 481 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 8306) covalent geometry : angle 1.16929 (11182) hydrogen bonds : bond 0.21833 ( 293) hydrogen bonds : angle 8.04466 ( 798) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 LEU cc_start: 0.8395 (mt) cc_final: 0.8118 (mt) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0740 time to fit residues: 6.2903 Evaluate side-chains 45 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN A 479 GLN A 492 GLN B 149 HIS ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** 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 = 0.3782 r_free = 0.3782 target = 0.067064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.047315 restraints weight = 42902.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.049336 restraints weight = 23494.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.050618 restraints weight = 16283.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.051428 restraints weight = 12949.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.051940 restraints weight = 11213.762| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8306 Z= 0.171 Angle : 0.629 7.843 11182 Z= 0.330 Chirality : 0.043 0.146 1222 Planarity : 0.004 0.056 1426 Dihedral : 10.380 89.220 1150 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.24 % Allowed : 22.99 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.27), residues: 986 helix: -0.03 (0.28), residues: 318 sheet: 0.07 (0.43), residues: 176 loop : -1.58 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 329 TYR 0.018 0.002 TYR A 527 PHE 0.011 0.001 PHE B 165 TRP 0.008 0.002 TRP A 311 HIS 0.006 0.001 HIS A 481 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8306) covalent geometry : angle 0.62928 (11182) hydrogen bonds : bond 0.04904 ( 293) hydrogen bonds : angle 6.19119 ( 798) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 48 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8222 (mp0) REVERT: A 117 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8500 (mp) REVERT: A 267 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7036 (pptt) REVERT: A 508 GLU cc_start: 0.6092 (OUTLIER) cc_final: 0.5733 (mt-10) REVERT: A 512 MET cc_start: 0.3394 (mmp) cc_final: 0.3125 (mmp) REVERT: B 84 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.6279 (t80) REVERT: B 152 ASP cc_start: 0.9070 (OUTLIER) cc_final: 0.8752 (t70) REVERT: B 512 MET cc_start: 0.5588 (tmm) cc_final: 0.5057 (tmm) outliers start: 38 outliers final: 15 residues processed: 83 average time/residue: 0.0701 time to fit residues: 9.0469 Evaluate side-chains 67 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 28 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.065786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.046119 restraints weight = 43460.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.048104 restraints weight = 23731.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.049342 restraints weight = 16473.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.050152 restraints weight = 13174.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.050642 restraints weight = 11442.961| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 8306 Z= 0.222 Angle : 0.663 8.097 11182 Z= 0.344 Chirality : 0.043 0.175 1222 Planarity : 0.004 0.049 1426 Dihedral : 9.808 84.305 1150 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.25 % Allowed : 24.33 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.26), residues: 986 helix: -0.29 (0.27), residues: 326 sheet: -0.09 (0.43), residues: 174 loop : -1.81 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 391 TYR 0.015 0.002 TYR A 428 PHE 0.011 0.002 PHE B 360 TRP 0.010 0.002 TRP A 157 HIS 0.005 0.002 HIS A 481 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 8306) covalent geometry : angle 0.66328 (11182) hydrogen bonds : bond 0.04771 ( 293) hydrogen bonds : angle 6.04627 ( 798) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 45 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8212 (mp0) REVERT: A 93 MET cc_start: 0.7070 (mmt) cc_final: 0.6390 (mmt) REVERT: A 117 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8511 (mp) REVERT: A 267 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.6873 (pptt) REVERT: A 514 GLU cc_start: 0.5959 (OUTLIER) cc_final: 0.5504 (pm20) REVERT: A 527 TYR cc_start: 0.8107 (t80) cc_final: 0.7625 (t80) REVERT: B 84 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.6340 (t80) REVERT: B 152 ASP cc_start: 0.9092 (OUTLIER) cc_final: 0.8675 (t70) REVERT: B 300 TYR cc_start: 0.5155 (OUTLIER) cc_final: 0.4620 (m-10) REVERT: B 342 LEU cc_start: 0.6440 (OUTLIER) cc_final: 0.5408 (tp) REVERT: B 512 MET cc_start: 0.5803 (tmm) cc_final: 0.5385 (tmm) outliers start: 47 outliers final: 28 residues processed: 87 average time/residue: 0.0700 time to fit residues: 9.5411 Evaluate side-chains 79 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 43 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 58 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.066323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.046747 restraints weight = 43976.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.048757 restraints weight = 23705.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.050022 restraints weight = 16340.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.050844 restraints weight = 12974.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.051304 restraints weight = 11229.866| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8306 Z= 0.164 Angle : 0.604 7.524 11182 Z= 0.315 Chirality : 0.042 0.145 1222 Planarity : 0.004 0.050 1426 Dihedral : 9.609 81.961 1150 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.69 % Allowed : 25.56 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.26), residues: 986 helix: -0.01 (0.28), residues: 314 sheet: -0.05 (0.44), residues: 174 loop : -1.80 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 391 TYR 0.013 0.001 TYR A 428 PHE 0.009 0.001 PHE B 360 TRP 0.008 0.001 TRP A 311 HIS 0.005 0.001 HIS A 441 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8306) covalent geometry : angle 0.60415 (11182) hydrogen bonds : bond 0.04138 ( 293) hydrogen bonds : angle 5.79971 ( 798) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 45 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8171 (mp0) REVERT: A 93 MET cc_start: 0.7118 (mmt) cc_final: 0.6815 (mmt) REVERT: A 117 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8495 (mp) REVERT: A 267 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.6879 (pptt) REVERT: A 514 GLU cc_start: 0.5908 (OUTLIER) cc_final: 0.5547 (pm20) REVERT: A 527 TYR cc_start: 0.8032 (t80) cc_final: 0.7653 (t80) REVERT: B 84 PHE cc_start: 0.6989 (OUTLIER) cc_final: 0.6242 (t80) REVERT: B 152 ASP cc_start: 0.9094 (OUTLIER) cc_final: 0.8741 (t70) REVERT: B 300 TYR cc_start: 0.4982 (OUTLIER) cc_final: 0.4426 (m-10) REVERT: B 512 MET cc_start: 0.5743 (tmm) cc_final: 0.5169 (tmm) outliers start: 42 outliers final: 25 residues processed: 82 average time/residue: 0.0776 time to fit residues: 9.3785 Evaluate side-chains 76 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 44 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 519 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 71 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 44 optimal weight: 0.1980 chunk 93 optimal weight: 30.0000 chunk 53 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.068099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.048445 restraints weight = 42858.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.050569 restraints weight = 22541.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.051935 restraints weight = 15293.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.052810 restraints weight = 11998.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.053396 restraints weight = 10283.942| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8306 Z= 0.102 Angle : 0.555 8.096 11182 Z= 0.289 Chirality : 0.041 0.149 1222 Planarity : 0.004 0.047 1426 Dihedral : 9.295 83.717 1150 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.79 % Allowed : 26.34 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.26), residues: 986 helix: 0.37 (0.30), residues: 309 sheet: 0.08 (0.45), residues: 163 loop : -1.73 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.010 0.001 TYR A 355 PHE 0.009 0.001 PHE B 498 TRP 0.008 0.001 TRP B 157 HIS 0.004 0.001 HIS A 441 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8306) covalent geometry : angle 0.55498 (11182) hydrogen bonds : bond 0.03426 ( 293) hydrogen bonds : angle 5.41682 ( 798) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 50 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.6410 (mmt) cc_final: 0.5621 (mmt) REVERT: A 117 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8430 (mp) REVERT: A 267 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.6767 (pptt) REVERT: A 514 GLU cc_start: 0.5778 (OUTLIER) cc_final: 0.5404 (pm20) REVERT: A 527 TYR cc_start: 0.8017 (t80) cc_final: 0.7701 (t80) REVERT: B 98 LEU cc_start: 0.8411 (mt) cc_final: 0.8168 (mt) REVERT: B 300 TYR cc_start: 0.4740 (OUTLIER) cc_final: 0.4185 (m-10) REVERT: B 342 LEU cc_start: 0.6333 (OUTLIER) cc_final: 0.5265 (tp) outliers start: 34 outliers final: 15 residues processed: 78 average time/residue: 0.0692 time to fit residues: 8.2840 Evaluate side-chains 64 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 380 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 71 optimal weight: 0.0000 chunk 39 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.068795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.049096 restraints weight = 42784.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.051300 restraints weight = 22553.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.052695 restraints weight = 15253.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.053601 restraints weight = 11946.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.054158 restraints weight = 10203.956| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8306 Z= 0.100 Angle : 0.563 9.447 11182 Z= 0.290 Chirality : 0.041 0.145 1222 Planarity : 0.003 0.047 1426 Dihedral : 9.043 80.258 1150 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.90 % Allowed : 27.57 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.26), residues: 986 helix: 0.33 (0.29), residues: 320 sheet: 0.24 (0.45), residues: 163 loop : -1.73 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 455 TYR 0.017 0.001 TYR A 428 PHE 0.008 0.001 PHE A 432 TRP 0.007 0.001 TRP B 157 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8306) covalent geometry : angle 0.56267 (11182) hydrogen bonds : bond 0.03318 ( 293) hydrogen bonds : angle 5.28031 ( 798) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 47 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8435 (mp) REVERT: A 267 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.6759 (pptt) REVERT: A 514 GLU cc_start: 0.5856 (OUTLIER) cc_final: 0.5541 (pm20) REVERT: A 527 TYR cc_start: 0.8076 (t80) cc_final: 0.7722 (t80) REVERT: B 295 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.7841 (mm) REVERT: B 300 TYR cc_start: 0.4710 (OUTLIER) cc_final: 0.4268 (m-10) REVERT: B 342 LEU cc_start: 0.6318 (OUTLIER) cc_final: 0.5256 (tp) REVERT: B 512 MET cc_start: 0.5618 (tmm) cc_final: 0.5155 (tmm) outliers start: 26 outliers final: 15 residues processed: 70 average time/residue: 0.0605 time to fit residues: 6.5193 Evaluate side-chains 65 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 44 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 376 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 68 optimal weight: 0.5980 chunk 17 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 23 optimal weight: 0.0770 chunk 86 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 70 optimal weight: 0.2980 chunk 48 optimal weight: 0.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.068250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.048275 restraints weight = 43535.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.050412 restraints weight = 23185.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.051754 restraints weight = 15819.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.052643 restraints weight = 12487.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.053220 restraints weight = 10712.743| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8306 Z= 0.106 Angle : 0.566 11.196 11182 Z= 0.293 Chirality : 0.041 0.142 1222 Planarity : 0.003 0.046 1426 Dihedral : 9.023 81.188 1150 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.13 % Allowed : 26.90 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.27), residues: 986 helix: 0.57 (0.30), residues: 309 sheet: 0.26 (0.45), residues: 163 loop : -1.66 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 455 TYR 0.016 0.001 TYR A 428 PHE 0.006 0.001 PHE B 39 TRP 0.006 0.001 TRP A 157 HIS 0.005 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8306) covalent geometry : angle 0.56583 (11182) hydrogen bonds : bond 0.03282 ( 293) hydrogen bonds : angle 5.21792 ( 798) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 45 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8435 (mp) REVERT: A 267 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.6851 (pptt) REVERT: A 393 MET cc_start: 0.7536 (mmm) cc_final: 0.7329 (mmm) REVERT: A 514 GLU cc_start: 0.5892 (OUTLIER) cc_final: 0.5532 (pm20) REVERT: A 527 TYR cc_start: 0.8105 (t80) cc_final: 0.7766 (t80) REVERT: B 54 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7584 (mm) REVERT: B 295 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.7792 (mm) REVERT: B 300 TYR cc_start: 0.4810 (OUTLIER) cc_final: 0.4420 (m-10) REVERT: B 342 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.5221 (tp) REVERT: B 512 MET cc_start: 0.5673 (tmm) cc_final: 0.5124 (tmm) outliers start: 37 outliers final: 20 residues processed: 78 average time/residue: 0.0562 time to fit residues: 7.1050 Evaluate side-chains 72 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 45 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 380 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 40 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.071857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.051143 restraints weight = 43964.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.053403 restraints weight = 22809.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.054814 restraints weight = 15296.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.055559 restraints weight = 12030.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.056190 restraints weight = 10500.332| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8306 Z= 0.109 Angle : 0.562 9.933 11182 Z= 0.290 Chirality : 0.041 0.140 1222 Planarity : 0.003 0.046 1426 Dihedral : 9.090 82.280 1150 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.24 % Allowed : 27.57 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.27), residues: 986 helix: 0.60 (0.30), residues: 308 sheet: 0.29 (0.43), residues: 172 loop : -1.63 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 391 TYR 0.015 0.001 TYR A 428 PHE 0.007 0.001 PHE B 165 TRP 0.007 0.001 TRP A 311 HIS 0.004 0.001 HIS A 441 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8306) covalent geometry : angle 0.56222 (11182) hydrogen bonds : bond 0.03341 ( 293) hydrogen bonds : angle 5.19201 ( 798) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 47 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8438 (mp) REVERT: A 267 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.6793 (pptt) REVERT: A 514 GLU cc_start: 0.5869 (OUTLIER) cc_final: 0.5133 (mp0) REVERT: A 527 TYR cc_start: 0.8119 (t80) cc_final: 0.7795 (t80) REVERT: B 93 MET cc_start: 0.7295 (mmt) cc_final: 0.7071 (mmp) REVERT: B 295 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.7755 (mm) REVERT: B 300 TYR cc_start: 0.4851 (OUTLIER) cc_final: 0.4444 (m-10) REVERT: B 342 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.5134 (tp) REVERT: B 512 MET cc_start: 0.5723 (tmm) cc_final: 0.5134 (tmm) outliers start: 29 outliers final: 18 residues processed: 72 average time/residue: 0.0638 time to fit residues: 7.2912 Evaluate side-chains 70 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 46 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 380 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 84 optimal weight: 0.0030 chunk 38 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.066659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.047097 restraints weight = 43857.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.049138 restraints weight = 23661.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.050428 restraints weight = 16273.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.051233 restraints weight = 12891.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.051772 restraints weight = 11141.447| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8306 Z= 0.179 Angle : 0.629 11.906 11182 Z= 0.319 Chirality : 0.042 0.139 1222 Planarity : 0.004 0.044 1426 Dihedral : 9.477 88.427 1150 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.57 % Allowed : 27.46 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.27), residues: 986 helix: 0.43 (0.29), residues: 315 sheet: 0.16 (0.43), residues: 174 loop : -1.69 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 391 TYR 0.023 0.001 TYR A 428 PHE 0.011 0.001 PHE B 360 TRP 0.009 0.002 TRP A 157 HIS 0.006 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 8306) covalent geometry : angle 0.62899 (11182) hydrogen bonds : bond 0.03948 ( 293) hydrogen bonds : angle 5.41809 ( 798) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 44 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 267 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.6636 (pptt) REVERT: A 514 GLU cc_start: 0.6008 (OUTLIER) cc_final: 0.5779 (pm20) REVERT: A 527 TYR cc_start: 0.8068 (t80) cc_final: 0.7739 (t80) REVERT: B 84 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.6184 (t80) REVERT: B 295 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.7869 (mm) REVERT: B 300 TYR cc_start: 0.4844 (OUTLIER) cc_final: 0.4445 (m-10) REVERT: B 342 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.5174 (tp) REVERT: B 512 MET cc_start: 0.5818 (tmm) cc_final: 0.5177 (tmm) outliers start: 32 outliers final: 21 residues processed: 72 average time/residue: 0.0628 time to fit residues: 7.0334 Evaluate side-chains 70 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 43 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 434 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 40 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.065246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.045798 restraints weight = 44181.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.047769 restraints weight = 23587.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.049075 restraints weight = 16206.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.049875 restraints weight = 12842.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.050388 restraints weight = 11085.093| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8306 Z= 0.243 Angle : 0.710 10.071 11182 Z= 0.363 Chirality : 0.044 0.147 1222 Planarity : 0.004 0.044 1426 Dihedral : 9.816 78.045 1150 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.35 % Allowed : 27.57 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.26), residues: 986 helix: 0.02 (0.28), residues: 313 sheet: -0.05 (0.43), residues: 173 loop : -1.75 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 329 TYR 0.030 0.002 TYR A 428 PHE 0.016 0.002 PHE B 303 TRP 0.010 0.002 TRP B 288 HIS 0.006 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 8306) covalent geometry : angle 0.71043 (11182) hydrogen bonds : bond 0.04654 ( 293) hydrogen bonds : angle 5.81832 ( 798) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 41 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 93 MET cc_start: 0.7250 (mmt) cc_final: 0.6385 (mmt) REVERT: A 267 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.6654 (pptt) REVERT: A 514 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.6020 (pm20) REVERT: A 527 TYR cc_start: 0.8176 (t80) cc_final: 0.7774 (t80) REVERT: B 84 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.6221 (t80) REVERT: B 295 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8058 (mm) REVERT: B 300 TYR cc_start: 0.4907 (OUTLIER) cc_final: 0.4504 (m-10) REVERT: B 342 LEU cc_start: 0.6377 (OUTLIER) cc_final: 0.5285 (tp) REVERT: B 512 MET cc_start: 0.5858 (tmm) cc_final: 0.5157 (tmm) outliers start: 30 outliers final: 21 residues processed: 68 average time/residue: 0.0639 time to fit residues: 6.7406 Evaluate side-chains 68 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 41 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 380 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 46 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.065773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.046204 restraints weight = 44298.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.048219 restraints weight = 23798.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.049527 restraints weight = 16400.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.050327 restraints weight = 12988.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.050840 restraints weight = 11224.880| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8306 Z= 0.175 Angle : 0.649 10.223 11182 Z= 0.329 Chirality : 0.042 0.136 1222 Planarity : 0.004 0.047 1426 Dihedral : 9.543 79.299 1150 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.01 % Allowed : 28.24 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.27), residues: 986 helix: 0.17 (0.29), residues: 315 sheet: -0.07 (0.43), residues: 174 loop : -1.80 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 329 TYR 0.025 0.002 TYR A 428 PHE 0.011 0.001 PHE B 360 TRP 0.007 0.001 TRP A 157 HIS 0.004 0.001 HIS A 441 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8306) covalent geometry : angle 0.64895 (11182) hydrogen bonds : bond 0.04133 ( 293) hydrogen bonds : angle 5.61984 ( 798) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1675.74 seconds wall clock time: 29 minutes 42.68 seconds (1782.68 seconds total)