Starting phenix.real_space_refine on Wed Aug 5 16:30:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qqu_18605/08_2026/8qqu_18605.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qqu_18605/08_2026/8qqu_18605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qqu_18605/08_2026/8qqu_18605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qqu_18605/08_2026/8qqu_18605.map" model { file = "/net/cci-nas-00/data/ceres_data/8qqu_18605/08_2026/8qqu_18605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qqu_18605/08_2026/8qqu_18605.cif" } resolution = 2.9 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= 0.006 sd= 0.204 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: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 38 5.16 5 C 6634 2.51 5 N 1904 2.21 5 O 2107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10715 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 4096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4096 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 21, 'TRANS': 497} Chain: "D" Number of atoms: 5963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5963 Classifications: {'peptide': 754} Link IDs: {'PTRANS': 26, 'TRANS': 727} Chain breaks: 1 Chain: "E" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 320 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "F" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 336 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 2.59, per 1000 atoms: 0.24 Number of scatterers: 10715 At special positions: 0 Unit cell: (137.058, 101.716, 119.818, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 32 15.00 O 2107 8.00 N 1904 7.00 C 6634 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: 0.89 Conformation dependent library (CDL) restraints added in 439.3 milliseconds 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 14 sheets defined 49.6% alpha, 14.4% beta 15 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'C' and resid 13 through 31 Processing helix chain 'C' and resid 42 through 56 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 128 through 134 removed outlier: 3.694A pdb=" N HIS C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU C 133 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 136 No H-bonds generated for 'chain 'C' and resid 135 through 136' Processing helix chain 'C' and resid 137 through 141 removed outlier: 3.503A pdb=" N LYS C 140 " --> pdb=" O ASP C 137 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 137 through 141' Processing helix chain 'C' and resid 164 through 170 Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 204 through 212 Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 269 through 283 Processing helix chain 'C' and resid 313 through 324 Processing helix chain 'C' and resid 346 through 389 Processing helix chain 'C' and resid 389 through 400 Processing helix chain 'C' and resid 402 through 413 Processing helix chain 'C' and resid 418 through 429 Processing helix chain 'C' and resid 451 through 460 Processing helix chain 'C' and resid 462 through 466 Processing helix chain 'C' and resid 467 through 494 removed outlier: 3.921A pdb=" N HIS C 471 " --> pdb=" O THR C 467 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 513 removed outlier: 3.657A pdb=" N LEU C 498 " --> pdb=" O SER C 494 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 22 removed outlier: 3.919A pdb=" N ARG D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 27 removed outlier: 3.951A pdb=" N TYR D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 52 removed outlier: 3.848A pdb=" N HIS D 37 " --> pdb=" O GLY D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 127 removed outlier: 3.580A pdb=" N ALA D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 198 removed outlier: 3.724A pdb=" N LEU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 231 Processing helix chain 'D' and resid 279 through 301 Processing helix chain 'D' and resid 301 through 307 removed outlier: 3.628A pdb=" N LYS D 305 " --> pdb=" O GLY D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 364 removed outlier: 4.590A pdb=" N SER D 347 " --> pdb=" O SER D 343 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA D 358 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 385 Processing helix chain 'D' and resid 425 through 435 removed outlier: 3.601A pdb=" N GLY D 435 " --> pdb=" O SER D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 474 Processing helix chain 'D' and resid 484 through 488 Processing helix chain 'D' and resid 500 through 518 Processing helix chain 'D' and resid 518 through 524 removed outlier: 3.617A pdb=" N VAL D 522 " --> pdb=" O MET D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 Processing helix chain 'D' and resid 576 through 597 Processing helix chain 'D' and resid 602 through 612 removed outlier: 3.670A pdb=" N ILE D 610 " --> pdb=" O LEU D 606 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR D 611 " --> pdb=" O LYS D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 622 removed outlier: 3.607A pdb=" N LEU D 620 " --> pdb=" O THR D 616 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER D 621 " --> pdb=" O GLU D 617 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 616 through 622' Processing helix chain 'D' and resid 622 through 640 removed outlier: 3.631A pdb=" N VAL D 626 " --> pdb=" O ASP D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 683 removed outlier: 3.600A pdb=" N THR D 683 " --> pdb=" O HIS D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 697 Processing helix chain 'D' and resid 718 through 731 Processing helix chain 'D' and resid 746 through 755 removed outlier: 3.579A pdb=" N MET D 755 " --> pdb=" O TRP D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 782 Processing helix chain 'D' and resid 785 through 801 Processing sheet with id=AA1, first strand: chain 'C' and resid 11 through 12 removed outlier: 5.676A pdb=" N VAL D 527 " --> pdb=" O VAL D 765 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE D 493 " --> pdb=" O TYR D 528 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU D 420 " --> pdb=" O ILE D 494 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLU D 419 " --> pdb=" O ALA D 442 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU D 444 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR D 421 " --> pdb=" O LEU D 444 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AA3, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AA4, first strand: chain 'C' and resid 171 through 174 Processing sheet with id=AA5, first strand: chain 'C' and resid 327 through 333 Processing sheet with id=AA6, first strand: chain 'C' and resid 245 through 250 removed outlier: 6.603A pdb=" N ARG C 245 " --> pdb=" O HIS C 262 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU C 257 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 303 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 304 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU C 292 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU C 306 " --> pdb=" O SER C 290 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AA8, first strand: chain 'C' and resid 415 through 416 Processing sheet with id=AA9, first strand: chain 'D' and resid 149 through 150 removed outlier: 3.545A pdb=" N ARG D 136 " --> pdb=" O LYS D 139 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR D 145 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS D 129 " --> pdb=" O TRP D 170 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG D 168 " --> pdb=" O GLU D 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 241 through 243 removed outlier: 3.506A pdb=" N LYS D 247 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 241 through 243 removed outlier: 3.536A pdb=" N GLY D 251 " --> pdb=" O LYS D 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 542 through 546 Processing sheet with id=AB4, first strand: chain 'D' and resid 565 through 567 removed outlier: 4.203A pdb=" N ARG D 712 " --> pdb=" O ARG D 709 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 647 through 654 removed outlier: 3.574A pdb=" N LEU D 659 " --> pdb=" O ASN D 654 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL D 664 " --> pdb=" O TYR D 675 " (cutoff:3.500A) 540 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2463 1.33 - 1.45: 2243 1.45 - 1.57: 6121 1.57 - 1.69: 62 1.69 - 1.81: 70 Bond restraints: 10959 Sorted by residual: bond pdb=" C1' DT E 14 " pdb=" N1 DT E 14 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.93e+01 bond pdb=" C1' DT E 13 " pdb=" N1 DT E 13 " ideal model delta sigma weight residual 1.468 1.549 -0.081 1.40e-02 5.10e+03 3.33e+01 bond pdb=" C1' DT E 15 " pdb=" N1 DT E 15 " ideal model delta sigma weight residual 1.468 1.548 -0.080 1.40e-02 5.10e+03 3.28e+01 bond pdb=" C1' DT E 8 " pdb=" N1 DT E 8 " ideal model delta sigma weight residual 1.468 1.547 -0.079 1.40e-02 5.10e+03 3.17e+01 bond pdb=" C1' DT E 12 " pdb=" N1 DT E 12 " ideal model delta sigma weight residual 1.468 1.533 -0.065 1.40e-02 5.10e+03 2.14e+01 ... (remaining 10954 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 14071 1.31 - 2.62: 707 2.62 - 3.92: 95 3.92 - 5.23: 49 5.23 - 6.54: 16 Bond angle restraints: 14938 Sorted by residual: angle pdb=" O5' DA F 3 " pdb=" C5' DA F 3 " pdb=" C4' DA F 3 " ideal model delta sigma weight residual 109.40 113.62 -4.22 8.00e-01 1.56e+00 2.78e+01 angle pdb=" O5' DT E 14 " pdb=" C5' DT E 14 " pdb=" C4' DT E 14 " ideal model delta sigma weight residual 109.40 113.52 -4.12 8.00e-01 1.56e+00 2.66e+01 angle pdb=" C3' DT E 14 " pdb=" O3' DT E 14 " pdb=" P DT E 15 " ideal model delta sigma weight residual 119.70 125.02 -5.32 1.20e+00 6.94e-01 1.96e+01 angle pdb=" O5' DA F 8 " pdb=" C5' DA F 8 " pdb=" C4' DA F 8 " ideal model delta sigma weight residual 109.40 112.92 -3.52 8.00e-01 1.56e+00 1.93e+01 angle pdb=" N3 DT E 5 " pdb=" C4 DT E 5 " pdb=" O4 DT E 5 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.84e+01 ... (remaining 14933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.52: 6456 31.52 - 63.04: 191 63.04 - 94.57: 4 94.57 - 126.09: 0 126.09 - 157.61: 2 Dihedral angle restraints: 6653 sinusoidal: 2973 harmonic: 3680 Sorted by residual: dihedral pdb=" CA GLY C 31 " pdb=" C GLY C 31 " pdb=" N ARG C 32 " pdb=" CA ARG C 32 " ideal model delta harmonic sigma weight residual -180.00 -150.95 -29.05 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA GLU D 355 " pdb=" C GLU D 355 " pdb=" N LEU D 356 " pdb=" CA LEU D 356 " ideal model delta harmonic sigma weight residual 180.00 -159.93 -20.07 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" C4' DT E 14 " pdb=" C3' DT E 14 " pdb=" O3' DT E 14 " pdb=" P DT E 15 " ideal model delta sinusoidal sigma weight residual 220.00 62.39 157.61 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 6650 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1116 0.040 - 0.079: 393 0.079 - 0.119: 88 0.119 - 0.158: 68 0.158 - 0.198: 10 Chirality restraints: 1675 Sorted by residual: chirality pdb=" C3' DT E 6 " pdb=" C4' DT E 6 " pdb=" O3' DT E 6 " pdb=" C2' DT E 6 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" CA ILE C 155 " pdb=" N ILE C 155 " pdb=" C ILE C 155 " pdb=" CB ILE C 155 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CA ILE D 273 " pdb=" N ILE D 273 " pdb=" C ILE D 273 " pdb=" CB ILE D 273 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.59e-01 ... (remaining 1672 not shown) Planarity restraints: 1846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 163 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO C 164 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 31 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C GLY C 31 " 0.035 2.00e-02 2.50e+03 pdb=" O GLY C 31 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG C 32 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 786 " -0.028 5.00e-02 4.00e+02 4.13e-02 2.74e+00 pdb=" N PRO D 787 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 787 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 787 " -0.023 5.00e-02 4.00e+02 ... (remaining 1843 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 156 2.67 - 3.23: 9606 3.23 - 3.78: 16084 3.78 - 4.34: 22447 4.34 - 4.90: 37372 Nonbonded interactions: 85665 Sorted by model distance: nonbonded pdb=" O LEU C 320 " pdb=" OG1 THR C 324 " model vdw 2.111 3.040 nonbonded pdb=" O LEU D 509 " pdb=" OG1 THR D 512 " model vdw 2.226 3.040 nonbonded pdb=" NH1 ARG D 394 " pdb=" O GLU D 412 " model vdw 2.244 3.120 nonbonded pdb=" OH TYR D 184 " pdb=" OD2 ASP D 214 " model vdw 2.262 3.040 nonbonded pdb=" O HIS D 505 " pdb=" OG1 THR D 508 " model vdw 2.269 3.040 ... (remaining 85660 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.870 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.920 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 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 0.088 10959 Z= 0.301 Angle : 0.703 6.541 14938 Z= 0.454 Chirality : 0.049 0.198 1675 Planarity : 0.004 0.054 1846 Dihedral : 13.967 157.611 4283 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % 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 are not related in a simple way. whole: 0.03 (0.23), residues: 1267 helix: 1.56 (0.20), residues: 582 sheet: -1.61 (0.36), residues: 189 loop : -1.13 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 32 TYR 0.011 0.001 TYR C 321 PHE 0.016 0.002 PHE D 243 TRP 0.013 0.001 TRP D 170 HIS 0.004 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.30 (10959) covalent geometry : angle 0.70294 / 0.45 (14938) hydrogen bonds : bond 0.16858 / 11.25 ( 566) hydrogen bonds : angle 6.65200 / 4.66 ( 1608) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.422 Fit side-chains REVERT: C 231 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7531 (mp0) REVERT: C 341 GLN cc_start: 0.8005 (mt0) cc_final: 0.7782 (mt0) REVERT: C 479 LYS cc_start: 0.8000 (mtpp) cc_final: 0.7446 (mttm) REVERT: D 45 ASP cc_start: 0.7508 (t0) cc_final: 0.7266 (t0) REVERT: D 124 ASN cc_start: 0.8112 (p0) cc_final: 0.7834 (t0) REVERT: D 247 LYS cc_start: 0.7619 (tttp) cc_final: 0.7391 (ptpt) REVERT: D 406 LYS cc_start: 0.8142 (mttt) cc_final: 0.7885 (mtmt) REVERT: D 731 ARG cc_start: 0.7966 (mtp180) cc_final: 0.7707 (mtp180) REVERT: D 754 THR cc_start: 0.8333 (p) cc_final: 0.8064 (p) REVERT: D 771 ILE cc_start: 0.8480 (mt) cc_final: 0.8073 (pp) outliers start: 0 outliers final: 1 residues processed: 268 average time/residue: 0.7218 time to fit residues: 205.2158 Evaluate side-chains 141 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 465 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 0.0020 chunk 66 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.4980 chunk 55 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 78 HIS C 94 GLN C 269 ASN C 327 GLN C 413 ASN D 141 HIS D 215 HIS D 237 HIS D 556 GLN D 654 ASN D 669 HIS D 721 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.147822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.121521 restraints weight = 13847.563| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.67 r_work: 0.3322 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10959 Z= 0.132 Angle : 0.561 8.231 14938 Z= 0.312 Chirality : 0.044 0.340 1675 Planarity : 0.004 0.042 1846 Dihedral : 14.785 168.357 1783 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.84 % Favored : 97.00 % Rotamer: Outliers : 2.43 % Allowed : 12.42 % Favored : 85.15 % 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 are not related in a simple way. whole: 0.60 (0.23), residues: 1267 helix: 2.04 (0.21), residues: 590 sheet: -1.16 (0.35), residues: 196 loop : -0.98 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 732 TYR 0.011 0.001 TYR C 321 PHE 0.015 0.001 PHE D 169 TRP 0.009 0.001 TRP D 170 HIS 0.004 0.001 HIS D 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (10959) covalent geometry : angle 0.56143 / 0.31 (14938) hydrogen bonds : bond 0.04608 / 3.15 ( 566) hydrogen bonds : angle 4.83752 / 3.49 ( 1608) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.420 Fit side-chains REVERT: C 231 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7688 (mp0) REVERT: C 389 ASN cc_start: 0.8143 (m110) cc_final: 0.7465 (m-40) REVERT: C 440 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7089 (pt0) REVERT: C 479 LYS cc_start: 0.7996 (mtpp) cc_final: 0.7466 (mttm) REVERT: C 487 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7637 (mm-30) REVERT: D 124 ASN cc_start: 0.8102 (p0) cc_final: 0.7638 (t0) REVERT: D 147 HIS cc_start: 0.7590 (m-70) cc_final: 0.7273 (m-70) REVERT: D 247 LYS cc_start: 0.7843 (tttp) cc_final: 0.7461 (ptpt) REVERT: D 406 LYS cc_start: 0.8254 (mttt) cc_final: 0.7984 (mtmt) REVERT: D 538 LYS cc_start: 0.8951 (tttt) cc_final: 0.8747 (tttp) REVERT: D 624 GLN cc_start: 0.7347 (mp10) cc_final: 0.7021 (mp10) REVERT: D 731 ARG cc_start: 0.8202 (mtp180) cc_final: 0.7959 (mtp180) REVERT: D 752 GLU cc_start: 0.8241 (pt0) cc_final: 0.7993 (pt0) outliers start: 26 outliers final: 7 residues processed: 171 average time/residue: 0.6140 time to fit residues: 112.0794 Evaluate side-chains 140 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 723 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.0050 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 341 GLN D 141 HIS D 556 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.146236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.119037 restraints weight = 13976.264| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.75 r_work: 0.3319 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10959 Z= 0.132 Angle : 0.523 6.449 14938 Z= 0.290 Chirality : 0.043 0.351 1675 Planarity : 0.004 0.050 1846 Dihedral : 14.794 179.143 1780 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.37 % Favored : 97.47 % Rotamer: Outliers : 2.52 % Allowed : 13.82 % Favored : 83.66 % 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 are not related in a simple way. whole: 0.80 (0.24), residues: 1267 helix: 2.21 (0.21), residues: 591 sheet: -0.91 (0.36), residues: 196 loop : -0.98 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 285 TYR 0.009 0.001 TYR C 478 PHE 0.019 0.002 PHE D 660 TRP 0.012 0.001 TRP D 170 HIS 0.005 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (10959) covalent geometry : angle 0.52259 / 0.29 (14938) hydrogen bonds : bond 0.04204 / 2.89 ( 566) hydrogen bonds : angle 4.55353 / 3.30 ( 1608) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.393 Fit side-chains REVERT: C 231 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7774 (mp0) REVERT: C 389 ASN cc_start: 0.8175 (m110) cc_final: 0.7605 (m-40) REVERT: C 440 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7098 (pt0) REVERT: D 124 ASN cc_start: 0.8096 (p0) cc_final: 0.7702 (t0) REVERT: D 247 LYS cc_start: 0.7831 (tttp) cc_final: 0.7526 (ptpt) REVERT: D 399 ASP cc_start: 0.7463 (m-30) cc_final: 0.7059 (t70) REVERT: D 406 LYS cc_start: 0.8289 (mttt) cc_final: 0.8028 (mtmt) REVERT: D 538 LYS cc_start: 0.9036 (tttt) cc_final: 0.8835 (tttp) REVERT: D 624 GLN cc_start: 0.7420 (mp10) cc_final: 0.7098 (mp10) REVERT: D 752 GLU cc_start: 0.8251 (pt0) cc_final: 0.8012 (pt0) outliers start: 27 outliers final: 8 residues processed: 155 average time/residue: 0.5579 time to fit residues: 92.7348 Evaluate side-chains 128 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 728 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 54 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 0.0870 chunk 60 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 471 HIS D 55 HIS D 141 HIS D 556 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.146265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.119190 restraints weight = 14101.681| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.74 r_work: 0.3323 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10959 Z= 0.124 Angle : 0.511 7.511 14938 Z= 0.283 Chirality : 0.043 0.360 1675 Planarity : 0.004 0.053 1846 Dihedral : 14.655 178.594 1780 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.63 % Rotamer: Outliers : 2.99 % Allowed : 13.82 % Favored : 83.19 % 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 are not related in a simple way. whole: 0.96 (0.24), residues: 1267 helix: 2.30 (0.21), residues: 592 sheet: -0.79 (0.35), residues: 201 loop : -0.87 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 382 TYR 0.008 0.001 TYR C 63 PHE 0.018 0.001 PHE D 660 TRP 0.011 0.001 TRP D 170 HIS 0.005 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (10959) covalent geometry : angle 0.51074 / 0.28 (14938) hydrogen bonds : bond 0.03963 / 2.72 ( 566) hydrogen bonds : angle 4.39505 / 3.20 ( 1608) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.328 Fit side-chains REVERT: C 6 ARG cc_start: 0.7197 (mtm-85) cc_final: 0.6938 (ttp-110) REVERT: C 231 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7766 (mp0) REVERT: C 425 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6427 (mp0) REVERT: C 440 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7098 (pt0) REVERT: D 124 ASN cc_start: 0.8191 (p0) cc_final: 0.7849 (t0) REVERT: D 202 SER cc_start: 0.7863 (OUTLIER) cc_final: 0.7501 (t) REVERT: D 247 LYS cc_start: 0.7889 (tttp) cc_final: 0.7514 (ptpt) REVERT: D 399 ASP cc_start: 0.7418 (m-30) cc_final: 0.7033 (t0) REVERT: D 406 LYS cc_start: 0.8256 (mttt) cc_final: 0.7986 (mtmt) REVERT: D 531 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8607 (mt0) REVERT: D 538 LYS cc_start: 0.9049 (tttt) cc_final: 0.8825 (tttp) REVERT: D 581 GLU cc_start: 0.8197 (tt0) cc_final: 0.7987 (tt0) REVERT: D 752 GLU cc_start: 0.8242 (pt0) cc_final: 0.8000 (pt0) outliers start: 32 outliers final: 11 residues processed: 151 average time/residue: 0.5623 time to fit residues: 91.0047 Evaluate side-chains 139 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 728 LYS Chi-restraints excluded: chain D residue 735 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 6 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 338 HIS D 55 HIS D 141 HIS D 556 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.144776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.117384 restraints weight = 13870.680| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.76 r_work: 0.3279 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10959 Z= 0.168 Angle : 0.539 7.300 14938 Z= 0.296 Chirality : 0.044 0.363 1675 Planarity : 0.004 0.054 1846 Dihedral : 14.703 178.347 1780 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.64 % Allowed : 14.01 % Favored : 82.35 % 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 are not related in a simple way. whole: 0.96 (0.24), residues: 1267 helix: 2.22 (0.21), residues: 593 sheet: -0.66 (0.36), residues: 202 loop : -0.81 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 276 TYR 0.010 0.001 TYR C 63 PHE 0.016 0.002 PHE D 243 TRP 0.012 0.001 TRP D 170 HIS 0.007 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (10959) covalent geometry : angle 0.53933 / 0.30 (14938) hydrogen bonds : bond 0.04365 / 2.99 ( 566) hydrogen bonds : angle 4.41515 / 3.23 ( 1608) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.301 Fit side-chains REVERT: C 6 ARG cc_start: 0.7065 (mtm-85) cc_final: 0.6864 (ttp-110) REVERT: C 231 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7654 (mp0) REVERT: C 440 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7042 (pt0) REVERT: D 124 ASN cc_start: 0.8313 (p0) cc_final: 0.7869 (t0) REVERT: D 202 SER cc_start: 0.7837 (OUTLIER) cc_final: 0.7391 (t) REVERT: D 247 LYS cc_start: 0.7943 (tttp) cc_final: 0.7484 (ptpt) REVERT: D 275 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8374 (mp10) REVERT: D 399 ASP cc_start: 0.7431 (m-30) cc_final: 0.6951 (t70) REVERT: D 531 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8590 (mt0) REVERT: D 538 LYS cc_start: 0.9052 (tttt) cc_final: 0.8773 (tttp) REVERT: D 553 ASP cc_start: 0.7914 (m-30) cc_final: 0.7666 (m-30) REVERT: D 624 GLN cc_start: 0.7429 (mp10) cc_final: 0.7203 (mp10) REVERT: D 758 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8269 (mm-30) outliers start: 39 outliers final: 15 residues processed: 153 average time/residue: 0.5790 time to fit residues: 94.9109 Evaluate side-chains 140 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 598 GLU Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 728 LYS Chi-restraints excluded: chain D residue 735 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 102 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 61 optimal weight: 0.0270 chunk 6 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 57 ASN D 55 HIS D 232 ASN D 556 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.146327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.119848 restraints weight = 13953.657| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.77 r_work: 0.3299 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10959 Z= 0.130 Angle : 0.521 10.771 14938 Z= 0.285 Chirality : 0.043 0.366 1675 Planarity : 0.004 0.056 1846 Dihedral : 14.649 179.507 1780 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.36 % Allowed : 14.75 % Favored : 81.89 % 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 are not related in a simple way. whole: 1.06 (0.24), residues: 1267 helix: 2.29 (0.21), residues: 593 sheet: -0.51 (0.36), residues: 201 loop : -0.81 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 276 TYR 0.009 0.001 TYR D 145 PHE 0.015 0.001 PHE D 243 TRP 0.009 0.001 TRP D 170 HIS 0.005 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (10959) covalent geometry : angle 0.52143 / 0.28 (14938) hydrogen bonds : bond 0.04002 / 2.73 ( 566) hydrogen bonds : angle 4.34503 / 3.18 ( 1608) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.321 Fit side-chains REVERT: C 6 ARG cc_start: 0.7086 (mtm-85) cc_final: 0.6833 (ttp-110) REVERT: C 231 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7743 (mp0) REVERT: C 440 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7064 (pt0) REVERT: D 124 ASN cc_start: 0.8283 (p0) cc_final: 0.8008 (t0) REVERT: D 170 TRP cc_start: 0.6638 (OUTLIER) cc_final: 0.5603 (m-10) REVERT: D 202 SER cc_start: 0.7837 (OUTLIER) cc_final: 0.7449 (t) REVERT: D 247 LYS cc_start: 0.7977 (tttp) cc_final: 0.7564 (ptpt) REVERT: D 275 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8387 (mp10) REVERT: D 399 ASP cc_start: 0.7434 (m-30) cc_final: 0.7009 (t0) REVERT: D 531 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8569 (mt0) REVERT: D 538 LYS cc_start: 0.9023 (tttt) cc_final: 0.8780 (tttp) REVERT: D 553 ASP cc_start: 0.7921 (m-30) cc_final: 0.7681 (m-30) REVERT: D 596 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7289 (mtp180) REVERT: D 624 GLN cc_start: 0.7431 (mp10) cc_final: 0.7196 (mp10) REVERT: D 758 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8282 (mm-30) outliers start: 36 outliers final: 16 residues processed: 152 average time/residue: 0.5720 time to fit residues: 93.2894 Evaluate side-chains 143 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 170 TRP Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 596 ARG Chi-restraints excluded: chain D residue 598 GLU Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 728 LYS Chi-restraints excluded: chain D residue 735 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 55 HIS D 141 HIS D 556 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.146290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.119134 restraints weight = 13891.961| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.77 r_work: 0.3299 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10959 Z= 0.134 Angle : 0.523 9.448 14938 Z= 0.285 Chirality : 0.043 0.369 1675 Planarity : 0.004 0.058 1846 Dihedral : 14.594 179.097 1780 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.27 % Allowed : 15.31 % Favored : 81.42 % 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 are not related in a simple way. whole: 1.09 (0.24), residues: 1267 helix: 2.28 (0.21), residues: 593 sheet: -0.37 (0.36), residues: 201 loop : -0.80 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 382 TYR 0.009 0.001 TYR D 145 PHE 0.015 0.001 PHE D 243 TRP 0.009 0.001 TRP D 170 HIS 0.006 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (10959) covalent geometry : angle 0.52306 / 0.28 (14938) hydrogen bonds : bond 0.03991 / 2.71 ( 566) hydrogen bonds : angle 4.30627 / 3.15 ( 1608) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: C 6 ARG cc_start: 0.7053 (mtm-85) cc_final: 0.6839 (ttp-110) REVERT: C 231 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7656 (mp0) REVERT: C 372 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8507 (mtpp) REVERT: C 440 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7042 (pt0) REVERT: D 124 ASN cc_start: 0.8411 (p0) cc_final: 0.7837 (t0) REVERT: D 170 TRP cc_start: 0.6581 (OUTLIER) cc_final: 0.5516 (m-10) REVERT: D 202 SER cc_start: 0.7822 (OUTLIER) cc_final: 0.7393 (t) REVERT: D 262 PHE cc_start: 0.6436 (OUTLIER) cc_final: 0.5898 (p90) REVERT: D 275 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8367 (mp10) REVERT: D 399 ASP cc_start: 0.7402 (m-30) cc_final: 0.6949 (t0) REVERT: D 531 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8594 (mt0) REVERT: D 538 LYS cc_start: 0.9049 (tttt) cc_final: 0.8772 (tttp) REVERT: D 553 ASP cc_start: 0.7869 (m-30) cc_final: 0.7619 (m-30) REVERT: D 581 GLU cc_start: 0.8132 (tt0) cc_final: 0.7809 (tt0) REVERT: D 596 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7230 (mtp180) REVERT: D 624 GLN cc_start: 0.7398 (mp10) cc_final: 0.7197 (mp10) REVERT: D 758 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8254 (mm-30) outliers start: 35 outliers final: 16 residues processed: 152 average time/residue: 0.5994 time to fit residues: 97.7553 Evaluate side-chains 143 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 372 LYS Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 170 TRP Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 596 ARG Chi-restraints excluded: chain D residue 598 GLU Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 728 LYS Chi-restraints excluded: chain D residue 735 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 127 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 37 HIS D 55 HIS D 232 ASN D 556 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.146202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.118959 restraints weight = 13873.343| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.76 r_work: 0.3297 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10959 Z= 0.135 Angle : 0.519 9.235 14938 Z= 0.283 Chirality : 0.043 0.371 1675 Planarity : 0.004 0.057 1846 Dihedral : 14.590 178.932 1780 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.17 % Allowed : 15.59 % Favored : 81.23 % 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 are not related in a simple way. whole: 1.07 (0.24), residues: 1267 helix: 2.23 (0.21), residues: 599 sheet: -0.26 (0.37), residues: 202 loop : -0.86 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 276 TYR 0.009 0.001 TYR D 145 PHE 0.017 0.001 PHE D 660 TRP 0.009 0.001 TRP D 170 HIS 0.006 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (10959) covalent geometry : angle 0.51946 / 0.28 (14938) hydrogen bonds : bond 0.03981 / 2.70 ( 566) hydrogen bonds : angle 4.28231 / 3.15 ( 1608) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: C 231 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7664 (mp0) REVERT: C 372 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8538 (mtpp) REVERT: C 440 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7037 (pt0) REVERT: D 170 TRP cc_start: 0.6643 (OUTLIER) cc_final: 0.5557 (m-10) REVERT: D 202 SER cc_start: 0.7777 (OUTLIER) cc_final: 0.7342 (t) REVERT: D 262 PHE cc_start: 0.6410 (OUTLIER) cc_final: 0.5765 (p90) REVERT: D 275 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8408 (mp10) REVERT: D 399 ASP cc_start: 0.7393 (m-30) cc_final: 0.6945 (t0) REVERT: D 531 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8597 (mt0) REVERT: D 538 LYS cc_start: 0.9052 (tttt) cc_final: 0.8758 (tttp) REVERT: D 581 GLU cc_start: 0.8153 (tt0) cc_final: 0.7832 (tt0) REVERT: D 596 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7236 (mtp180) REVERT: D 659 LEU cc_start: 0.6716 (mt) cc_final: 0.6307 (mt) REVERT: D 758 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8285 (mm-30) outliers start: 34 outliers final: 15 residues processed: 151 average time/residue: 0.5955 time to fit residues: 96.0414 Evaluate side-chains 142 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 372 LYS Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 170 TRP Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 596 ARG Chi-restraints excluded: chain D residue 598 GLU Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 728 LYS Chi-restraints excluded: chain D residue 735 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 57 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 37 HIS D 55 HIS D 556 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.144577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.117129 restraints weight = 13895.056| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.76 r_work: 0.3250 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10959 Z= 0.169 Angle : 0.558 8.875 14938 Z= 0.302 Chirality : 0.044 0.372 1675 Planarity : 0.004 0.058 1846 Dihedral : 14.706 177.673 1780 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.99 % Allowed : 16.15 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.24), residues: 1267 helix: 2.18 (0.21), residues: 597 sheet: -0.25 (0.36), residues: 202 loop : -0.89 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 276 TYR 0.012 0.001 TYR C 63 PHE 0.017 0.002 PHE D 243 TRP 0.011 0.001 TRP D 170 HIS 0.007 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (10959) covalent geometry : angle 0.55841 / 0.30 (14938) hydrogen bonds : bond 0.04313 / 2.93 ( 566) hydrogen bonds : angle 4.35292 / 3.22 ( 1608) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.421 Fit side-chains REVERT: C 231 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7845 (mp0) REVERT: C 372 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8520 (mtpp) REVERT: C 440 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7047 (pt0) REVERT: D 170 TRP cc_start: 0.6763 (OUTLIER) cc_final: 0.5618 (m-10) REVERT: D 202 SER cc_start: 0.7821 (OUTLIER) cc_final: 0.7413 (t) REVERT: D 275 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8447 (mp10) REVERT: D 399 ASP cc_start: 0.7514 (m-30) cc_final: 0.7069 (t70) REVERT: D 531 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8590 (mt0) REVERT: D 553 ASP cc_start: 0.8011 (m-30) cc_final: 0.7764 (m-30) REVERT: D 581 GLU cc_start: 0.8163 (tt0) cc_final: 0.7960 (tt0) REVERT: D 596 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7291 (mtp180) REVERT: D 659 LEU cc_start: 0.6867 (mt) cc_final: 0.6465 (mt) REVERT: D 758 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8317 (mm-30) outliers start: 32 outliers final: 14 residues processed: 145 average time/residue: 0.5830 time to fit residues: 90.7669 Evaluate side-chains 138 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 372 LYS Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 170 TRP Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 596 ARG Chi-restraints excluded: chain D residue 598 GLU Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 728 LYS Chi-restraints excluded: chain D residue 735 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 37 HIS D 55 HIS D 556 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.144321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.117812 restraints weight = 13911.713| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.75 r_work: 0.3273 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10959 Z= 0.164 Angle : 0.561 11.407 14938 Z= 0.300 Chirality : 0.044 0.371 1675 Planarity : 0.004 0.065 1846 Dihedral : 14.748 177.770 1780 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.05 % Allowed : 17.18 % Favored : 80.77 % 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 are not related in a simple way. whole: 0.99 (0.24), residues: 1267 helix: 2.14 (0.21), residues: 597 sheet: -0.19 (0.37), residues: 202 loop : -0.92 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 6 TYR 0.011 0.001 TYR C 63 PHE 0.029 0.002 PHE D 660 TRP 0.011 0.001 TRP D 170 HIS 0.007 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (10959) covalent geometry : angle 0.56061 / 0.30 (14938) hydrogen bonds : bond 0.04288 / 2.92 ( 566) hydrogen bonds : angle 4.39152 / 3.25 ( 1608) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.402 Fit side-chains REVERT: C 231 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7817 (mp0) REVERT: C 372 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8552 (mtpp) REVERT: C 440 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7023 (pt0) REVERT: D 170 TRP cc_start: 0.6763 (OUTLIER) cc_final: 0.5617 (m-10) REVERT: D 202 SER cc_start: 0.7825 (OUTLIER) cc_final: 0.7410 (t) REVERT: D 262 PHE cc_start: 0.6537 (OUTLIER) cc_final: 0.5974 (p90) REVERT: D 399 ASP cc_start: 0.7517 (m-30) cc_final: 0.7084 (t70) REVERT: D 531 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8592 (mt0) REVERT: D 553 ASP cc_start: 0.8020 (m-30) cc_final: 0.7770 (m-30) REVERT: D 596 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7279 (mtp180) REVERT: D 652 HIS cc_start: 0.7565 (t-90) cc_final: 0.7339 (t-90) REVERT: D 659 LEU cc_start: 0.6792 (mt) cc_final: 0.6391 (mt) REVERT: D 758 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8288 (mm-30) outliers start: 22 outliers final: 13 residues processed: 131 average time/residue: 0.6440 time to fit residues: 90.4178 Evaluate side-chains 132 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 372 LYS Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 170 TRP Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 596 ARG Chi-restraints excluded: chain D residue 598 GLU Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 728 LYS Chi-restraints excluded: chain D residue 735 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 69 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 75 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 37 HIS D 556 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.145458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.119043 restraints weight = 13943.938| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.74 r_work: 0.3292 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10959 Z= 0.134 Angle : 0.543 10.615 14938 Z= 0.291 Chirality : 0.043 0.371 1675 Planarity : 0.004 0.059 1846 Dihedral : 14.665 178.522 1780 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.15 % Allowed : 16.71 % Favored : 81.14 % 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 are not related in a simple way. whole: 1.07 (0.24), residues: 1267 helix: 2.19 (0.21), residues: 597 sheet: -0.15 (0.38), residues: 199 loop : -0.85 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 6 TYR 0.009 0.001 TYR D 145 PHE 0.027 0.002 PHE D 660 TRP 0.009 0.001 TRP D 170 HIS 0.005 0.001 HIS C 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (10959) covalent geometry : angle 0.54314 / 0.29 (14938) hydrogen bonds : bond 0.04019 / 2.72 ( 566) hydrogen bonds : angle 4.33150 / 3.20 ( 1608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3638.74 seconds wall clock time: 62 minutes 34.02 seconds (3754.02 seconds total)