Starting phenix.real_space_refine on Sat Aug 23 07:59:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qqu_18605/08_2025/8qqu_18605.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qqu_18605/08_2025/8qqu_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 { model { file = "/net/cci-nas-00/data/ceres_data/8qqu_18605/08_2025/8qqu_18605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qqu_18605/08_2025/8qqu_18605.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qqu_18605/08_2025/8qqu_18605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qqu_18605/08_2025/8qqu_18605.map" } 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-2.0-5787/lib/python3.9/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: 2.82, per 1000 atoms: 0.26 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: 1.05 Conformation dependent library (CDL) restraints added in 540.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.25 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: 2.24 Time building geometry restraints manager: 1.38 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=" C HIS C 78 " pdb=" N PRO C 79 " ideal model delta sigma weight residual 1.334 1.356 -0.022 8.40e-03 1.42e+04 7.00e+00 bond pdb=" C1' DT E 14 " pdb=" N1 DT E 14 " ideal model delta sigma weight residual 1.490 1.556 -0.066 3.00e-02 1.11e+03 4.81e+00 bond pdb=" C3' DT E 14 " pdb=" O3' DT E 14 " ideal model delta sigma weight residual 1.422 1.482 -0.060 3.00e-02 1.11e+03 3.96e+00 bond pdb=" C1' DT E 13 " pdb=" N1 DT E 13 " ideal model delta sigma weight residual 1.490 1.549 -0.059 3.00e-02 1.11e+03 3.84e+00 bond pdb=" C1' DT E 15 " pdb=" N1 DT E 15 " ideal model delta sigma weight residual 1.490 1.548 -0.058 3.00e-02 1.11e+03 3.76e+00 ... (remaining 10954 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 14197 1.31 - 2.62: 604 2.62 - 3.92: 77 3.92 - 5.23: 45 5.23 - 6.54: 15 Bond angle restraints: 14938 Sorted by residual: angle pdb=" C3' DT E 14 " pdb=" O3' DT E 14 " pdb=" P DT E 15 " ideal model delta sigma weight residual 120.20 125.02 -4.82 1.50e+00 4.44e-01 1.03e+01 angle pdb=" C LYS C 140 " pdb=" N GLU C 141 " pdb=" CA GLU C 141 " ideal model delta sigma weight residual 121.54 126.67 -5.13 1.91e+00 2.74e-01 7.22e+00 angle pdb=" C3' DT E 6 " pdb=" C2' DT E 6 " pdb=" C1' DT E 6 " ideal model delta sigma weight residual 101.60 105.52 -3.92 1.50e+00 4.44e-01 6.83e+00 angle pdb=" C3' DA F 9 " pdb=" C2' DA F 9 " pdb=" C1' DA F 9 " ideal model delta sigma weight residual 101.60 105.43 -3.83 1.50e+00 4.44e-01 6.52e+00 angle pdb=" CA GLU C 139 " pdb=" CB GLU C 139 " pdb=" CG GLU C 139 " ideal model delta sigma weight residual 114.10 118.91 -4.81 2.00e+00 2.50e-01 5.77e+00 ... (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 - 0.037: 1102 0.037 - 0.075: 418 0.075 - 0.112: 86 0.112 - 0.150: 61 0.150 - 0.187: 8 Chirality restraints: 1675 Sorted by residual: 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 chirality pdb=" CA ILE C 182 " pdb=" N ILE C 182 " pdb=" C ILE C 182 " pdb=" CB ILE C 182 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.77e-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: 4.570 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.200 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:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 : 0.004 0.066 10959 Z= 0.186 Angle : 0.673 6.541 14938 Z= 0.366 Chirality : 0.046 0.187 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 aren 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 covalent geometry : bond 0.00429 (10959) covalent geometry : angle 0.67265 (14938) hydrogen bonds : bond 0.16858 ( 566) hydrogen bonds : angle 6.65200 ( 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 : 0.455 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: 0.7783 (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: 0.8255 time to fit residues: 233.9111 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 : 0.444 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3795 r_free = 0.3795 target = 0.148025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.121581 restraints weight = 13894.797| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.78 r_work: 0.3349 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10959 Z= 0.122 Angle : 0.524 6.016 14938 Z= 0.285 Chirality : 0.041 0.145 1675 Planarity : 0.004 0.042 1846 Dihedral : 14.751 171.508 1783 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.68 % Favored : 97.24 % Rotamer: Outliers : 1.96 % Allowed : 12.61 % Favored : 85.43 % 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: 0.68 (0.23), residues: 1267 helix: 2.13 (0.21), residues: 594 sheet: -1.19 (0.36), residues: 196 loop : -0.98 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 665 TYR 0.010 0.001 TYR C 321 PHE 0.011 0.001 PHE D 169 TRP 0.011 0.001 TRP D 170 HIS 0.004 0.001 HIS D 237 Details of bonding type rmsd covalent geometry : bond 0.00274 (10959) covalent geometry : angle 0.52425 (14938) hydrogen bonds : bond 0.04046 ( 566) hydrogen bonds : angle 4.62829 ( 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 184 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.418 Fit side-chains REVERT: C 6 ARG cc_start: 0.7192 (mtm-85) cc_final: 0.6927 (ttp-110) REVERT: C 231 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7700 (mp0) REVERT: C 440 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7115 (pt0) REVERT: C 479 LYS cc_start: 0.7981 (mtpp) cc_final: 0.7446 (mttm) REVERT: D 124 ASN cc_start: 0.8059 (p0) cc_final: 0.7599 (t0) REVERT: D 147 HIS cc_start: 0.7511 (m-70) cc_final: 0.7234 (m-70) REVERT: D 205 LEU cc_start: 0.7605 (tt) cc_final: 0.7382 (tp) REVERT: D 247 LYS cc_start: 0.7809 (tttp) cc_final: 0.7446 (ptpt) REVERT: D 399 ASP cc_start: 0.7398 (m-30) cc_final: 0.6979 (t70) REVERT: D 406 LYS cc_start: 0.8230 (mttt) cc_final: 0.7966 (mtmt) REVERT: D 624 GLN cc_start: 0.7385 (mp10) cc_final: 0.7050 (mp10) REVERT: D 731 ARG cc_start: 0.8198 (mtp180) cc_final: 0.7955 (mtp180) REVERT: D 752 GLU cc_start: 0.8205 (pt0) cc_final: 0.7985 (pt0) REVERT: D 758 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8217 (mm-30) outliers start: 21 outliers final: 5 residues processed: 175 average time/residue: 0.6874 time to fit residues: 128.6892 Evaluate side-chains 133 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.0170 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 120 optimal weight: 0.0050 chunk 18 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 overall best weight: 0.5834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 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 = 0.3784 r_free = 0.3784 target = 0.147168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119945 restraints weight = 14029.379| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.76 r_work: 0.3333 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10959 Z= 0.120 Angle : 0.499 6.101 14938 Z= 0.271 Chirality : 0.041 0.186 1675 Planarity : 0.004 0.051 1846 Dihedral : 14.594 179.329 1780 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.43 % Allowed : 14.10 % Favored : 83.47 % 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 (0.24), residues: 1267 helix: 2.39 (0.21), residues: 594 sheet: -0.94 (0.35), residues: 202 loop : -0.91 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 276 TYR 0.008 0.001 TYR C 321 PHE 0.013 0.001 PHE D 243 TRP 0.012 0.001 TRP D 170 HIS 0.005 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00270 (10959) covalent geometry : angle 0.49936 (14938) hydrogen bonds : bond 0.03764 ( 566) hydrogen bonds : angle 4.31789 ( 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 164 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.424 Fit side-chains REVERT: C 231 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7770 (mp0) REVERT: C 440 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7165 (pt0) REVERT: D 124 ASN cc_start: 0.8021 (p0) cc_final: 0.7813 (t0) REVERT: D 205 LEU cc_start: 0.7637 (tt) cc_final: 0.7429 (tp) REVERT: D 247 LYS cc_start: 0.7947 (tttp) cc_final: 0.7514 (ptpt) REVERT: D 262 PHE cc_start: 0.6486 (OUTLIER) cc_final: 0.6093 (p90) REVERT: D 399 ASP cc_start: 0.7436 (m-30) cc_final: 0.7024 (t0) REVERT: D 406 LYS cc_start: 0.8215 (mttt) cc_final: 0.7953 (mtmt) REVERT: D 581 GLU cc_start: 0.8152 (tt0) cc_final: 0.7876 (tt0) REVERT: D 698 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6312 (mpt180) REVERT: D 758 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8209 (mm-30) outliers start: 26 outliers final: 5 residues processed: 153 average time/residue: 0.7134 time to fit residues: 116.4470 Evaluate side-chains 126 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 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 698 ARG 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: 0.4980 chunk 82 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 60 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 33 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 338 HIS C 341 GLN C 471 HIS D 55 HIS D 556 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.148192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.120991 restraints weight = 14100.667| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.78 r_work: 0.3328 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2778 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= 0.119 Angle : 0.493 6.256 14938 Z= 0.267 Chirality : 0.040 0.144 1675 Planarity : 0.003 0.052 1846 Dihedral : 14.406 178.193 1780 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.27 % Allowed : 14.38 % 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 aren not related in a simple way. whole: 1.13 (0.24), residues: 1267 helix: 2.48 (0.21), residues: 593 sheet: -0.71 (0.36), residues: 202 loop : -0.83 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 276 TYR 0.007 0.001 TYR D 145 PHE 0.014 0.001 PHE D 243 TRP 0.010 0.001 TRP D 170 HIS 0.005 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00270 (10959) covalent geometry : angle 0.49277 (14938) hydrogen bonds : bond 0.03670 ( 566) hydrogen bonds : angle 4.16845 ( 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 160 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 0.702 Fit side-chains REVERT: C 231 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7581 (mp0) REVERT: C 416 GLN cc_start: 0.8679 (pp30) cc_final: 0.8477 (pp30) REVERT: C 440 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7150 (pt0) REVERT: D 124 ASN cc_start: 0.8123 (p0) cc_final: 0.7852 (t0) REVERT: D 247 LYS cc_start: 0.7952 (tttp) cc_final: 0.7493 (ptpt) REVERT: D 262 PHE cc_start: 0.6385 (OUTLIER) cc_final: 0.5854 (p90) REVERT: D 399 ASP cc_start: 0.7334 (m-30) cc_final: 0.6939 (t0) REVERT: D 531 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8554 (mt0) REVERT: D 581 GLU cc_start: 0.8126 (tt0) cc_final: 0.7831 (tt0) REVERT: D 596 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7233 (mtp180) REVERT: D 698 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.6253 (mpt180) REVERT: D 720 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7831 (pp20) REVERT: D 758 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8193 (mm-30) outliers start: 35 outliers final: 8 residues processed: 145 average time/residue: 0.7326 time to fit residues: 113.7229 Evaluate side-chains 129 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 210 GLU 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 173 LEU Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 596 ARG Chi-restraints excluded: chain D residue 698 ARG Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 728 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 6 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 ASN D 37 HIS D 55 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 = 0.3781 r_free = 0.3781 target = 0.146726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.119281 restraints weight = 13925.241| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.78 r_work: 0.3302 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10959 Z= 0.134 Angle : 0.510 9.477 14938 Z= 0.274 Chirality : 0.041 0.177 1675 Planarity : 0.004 0.055 1846 Dihedral : 14.360 177.431 1780 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.71 % Allowed : 15.13 % Favored : 82.17 % 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 (0.24), residues: 1267 helix: 2.45 (0.21), residues: 594 sheet: -0.49 (0.36), residues: 202 loop : -0.82 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 6 TYR 0.008 0.001 TYR C 63 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 covalent geometry : bond 0.00311 (10959) covalent geometry : angle 0.51033 (14938) hydrogen bonds : bond 0.03838 ( 566) hydrogen bonds : angle 4.15958 ( 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 163 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.423 Fit side-chains REVERT: C 231 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7615 (mp0) REVERT: C 416 GLN cc_start: 0.8693 (pp30) cc_final: 0.8487 (pp30) REVERT: C 440 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7114 (pt0) REVERT: D 124 ASN cc_start: 0.8156 (p0) cc_final: 0.7893 (t0) REVERT: D 247 LYS cc_start: 0.7968 (tttp) cc_final: 0.7503 (ptpt) REVERT: D 262 PHE cc_start: 0.6449 (OUTLIER) cc_final: 0.5915 (p90) REVERT: D 399 ASP cc_start: 0.7302 (m-30) cc_final: 0.6931 (t0) REVERT: D 531 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8551 (mt0) REVERT: D 581 GLU cc_start: 0.8125 (tt0) cc_final: 0.7841 (tt0) REVERT: D 596 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7229 (mtp180) REVERT: D 698 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6114 (mmt90) REVERT: D 758 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8197 (mm-30) outliers start: 29 outliers final: 7 residues processed: 154 average time/residue: 0.7267 time to fit residues: 119.5794 Evaluate side-chains 132 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 508 LEU Chi-restraints excluded: chain D residue 173 LEU 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 698 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: 1.9990 chunk 41 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 61 optimal weight: 0.0030 chunk 6 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 HIS ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 556 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.143270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115699 restraints weight = 13970.945| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.77 r_work: 0.3255 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10959 Z= 0.195 Angle : 0.566 8.324 14938 Z= 0.302 Chirality : 0.043 0.186 1675 Planarity : 0.004 0.057 1846 Dihedral : 14.624 174.899 1780 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.01 % Allowed : 14.75 % 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 aren not related in a simple way. whole: 1.01 (0.24), residues: 1267 helix: 2.24 (0.21), residues: 592 sheet: -0.42 (0.37), residues: 202 loop : -0.87 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 276 TYR 0.013 0.001 TYR C 63 PHE 0.017 0.002 PHE D 243 TRP 0.012 0.001 TRP D 170 HIS 0.009 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00469 (10959) covalent geometry : angle 0.56634 (14938) hydrogen bonds : bond 0.04526 ( 566) hydrogen bonds : angle 4.37379 ( 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 170 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 0.464 Fit side-chains REVERT: C 231 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7691 (mp0) REVERT: C 416 GLN cc_start: 0.8651 (pp30) cc_final: 0.8449 (pp30) REVERT: C 425 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6977 (mm-30) REVERT: C 440 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7025 (pt0) REVERT: D 124 ASN cc_start: 0.8460 (p0) cc_final: 0.7795 (t0) REVERT: D 170 TRP cc_start: 0.6687 (OUTLIER) cc_final: 0.5578 (m-10) REVERT: D 247 LYS cc_start: 0.7919 (tttp) cc_final: 0.7484 (ptpt) REVERT: D 262 PHE cc_start: 0.6555 (OUTLIER) cc_final: 0.6090 (p90) REVERT: D 399 ASP cc_start: 0.7457 (m-30) cc_final: 0.6993 (t70) REVERT: D 531 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8557 (mt0) REVERT: D 553 ASP cc_start: 0.7946 (m-30) cc_final: 0.7690 (m-30) REVERT: D 596 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7243 (mtp180) REVERT: D 624 GLN cc_start: 0.7370 (mp10) cc_final: 0.7079 (mp10) REVERT: D 730 SER cc_start: 0.9041 (OUTLIER) cc_final: 0.8799 (p) REVERT: D 758 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8301 (mm-30) outliers start: 43 outliers final: 15 residues processed: 159 average time/residue: 0.6970 time to fit residues: 118.7582 Evaluate side-chains 140 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 301 MET Chi-restraints excluded: chain C residue 425 GLU 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 444 LEU Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 596 ARG Chi-restraints excluded: chain D residue 728 LYS Chi-restraints excluded: chain D residue 730 SER 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: 0.6980 chunk 85 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 115 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 318 ASN 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 = 0.3778 r_free = 0.3778 target = 0.146445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120049 restraints weight = 13953.630| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.76 r_work: 0.3308 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3066 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= 0.124 Angle : 0.526 12.248 14938 Z= 0.279 Chirality : 0.041 0.174 1675 Planarity : 0.004 0.058 1846 Dihedral : 14.319 177.301 1780 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.43 % Allowed : 16.71 % 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 aren not related in a simple way. whole: 1.13 (0.24), residues: 1267 helix: 2.34 (0.21), residues: 597 sheet: -0.23 (0.37), residues: 202 loop : -0.92 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 276 TYR 0.007 0.001 TYR D 145 PHE 0.015 0.001 PHE D 243 TRP 0.009 0.001 TRP D 170 HIS 0.004 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00287 (10959) covalent geometry : angle 0.52627 (14938) hydrogen bonds : bond 0.03780 ( 566) hydrogen bonds : angle 4.18853 ( 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 148 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.445 Fit side-chains REVERT: C 231 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7809 (mp0) REVERT: C 440 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7070 (pt0) REVERT: D 399 ASP cc_start: 0.7612 (m-30) cc_final: 0.7212 (t70) REVERT: D 531 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8594 (mt0) REVERT: D 581 GLU cc_start: 0.8169 (tt0) cc_final: 0.7898 (tt0) REVERT: D 596 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7293 (mtp180) REVERT: D 624 GLN cc_start: 0.7400 (mp10) cc_final: 0.7174 (mp10) REVERT: D 758 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8252 (mm-30) outliers start: 26 outliers final: 12 residues processed: 142 average time/residue: 0.7341 time to fit residues: 111.2247 Evaluate side-chains 126 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 301 MET Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 508 LEU 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 444 LEU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 596 ARG 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: 0.7980 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 389 ASN D 37 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 = 0.3748 r_free = 0.3748 target = 0.143909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.116379 restraints weight = 13878.032| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.77 r_work: 0.3263 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10959 Z= 0.171 Angle : 0.555 11.748 14938 Z= 0.295 Chirality : 0.042 0.182 1675 Planarity : 0.004 0.058 1846 Dihedral : 14.529 175.497 1780 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.08 % Allowed : 15.50 % 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 aren not related in a simple way. whole: 1.01 (0.24), residues: 1267 helix: 2.24 (0.21), residues: 596 sheet: -0.25 (0.37), residues: 202 loop : -1.00 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 276 TYR 0.011 0.001 TYR C 63 PHE 0.020 0.002 PHE D 182 TRP 0.010 0.001 TRP C 415 HIS 0.008 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00408 (10959) covalent geometry : angle 0.55532 (14938) hydrogen bonds : bond 0.04289 ( 566) hydrogen bonds : angle 4.31856 ( 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 145 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.410 Fit side-chains REVERT: C 113 ASP cc_start: 0.8129 (t70) cc_final: 0.7880 (t0) REVERT: C 231 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7699 (mp0) REVERT: C 372 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8532 (mtpp) REVERT: C 440 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7023 (pt0) REVERT: D 202 SER cc_start: 0.7823 (OUTLIER) cc_final: 0.7371 (t) REVERT: D 262 PHE cc_start: 0.6492 (OUTLIER) cc_final: 0.5964 (p90) REVERT: D 399 ASP cc_start: 0.7551 (m-30) cc_final: 0.7090 (t70) REVERT: D 531 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8556 (mt0) REVERT: D 581 GLU cc_start: 0.8124 (tt0) cc_final: 0.7813 (tt0) REVERT: D 596 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7234 (mtp180) REVERT: D 624 GLN cc_start: 0.7367 (mp10) cc_final: 0.7095 (mp10) REVERT: D 704 ASP cc_start: 0.7885 (p0) cc_final: 0.7535 (p0) REVERT: D 758 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8282 (mm-30) outliers start: 33 outliers final: 16 residues processed: 138 average time/residue: 0.7399 time to fit residues: 109.2268 Evaluate side-chains 131 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 301 MET 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 21 LYS 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 444 LEU Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 596 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: 5.9990 chunk 102 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 42 optimal weight: 0.0370 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 HIS ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.145945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.118675 restraints weight = 13919.401| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.77 r_work: 0.3296 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10959 Z= 0.125 Angle : 0.526 11.207 14938 Z= 0.279 Chirality : 0.041 0.184 1675 Planarity : 0.004 0.059 1846 Dihedral : 14.380 176.981 1780 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.05 % Allowed : 16.62 % Favored : 81.33 % 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: 1.10 (0.24), residues: 1267 helix: 2.32 (0.21), residues: 596 sheet: -0.22 (0.38), residues: 199 loop : -0.94 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 276 TYR 0.008 0.001 TYR C 86 PHE 0.015 0.001 PHE D 182 TRP 0.008 0.001 TRP C 415 HIS 0.005 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00286 (10959) covalent geometry : angle 0.52601 (14938) hydrogen bonds : bond 0.03837 ( 566) hydrogen bonds : angle 4.21239 ( 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 133 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.433 Fit side-chains REVERT: C 113 ASP cc_start: 0.8105 (t70) cc_final: 0.7824 (t0) REVERT: C 231 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7678 (mp0) REVERT: C 372 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8522 (mtpp) REVERT: C 440 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7035 (pt0) REVERT: D 202 SER cc_start: 0.7772 (OUTLIER) cc_final: 0.7346 (t) REVERT: D 399 ASP cc_start: 0.7540 (m-30) cc_final: 0.7104 (t70) REVERT: D 531 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8587 (mt0) REVERT: D 581 GLU cc_start: 0.8130 (tt0) cc_final: 0.7845 (tt0) REVERT: D 596 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7240 (mtp180) REVERT: D 624 GLN cc_start: 0.7358 (mp10) cc_final: 0.7092 (mp10) REVERT: D 704 ASP cc_start: 0.7844 (p0) cc_final: 0.7525 (p0) REVERT: D 758 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8261 (mm-30) outliers start: 22 outliers final: 12 residues processed: 128 average time/residue: 0.7309 time to fit residues: 100.0902 Evaluate side-chains 126 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR 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 508 LEU 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 444 LEU Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 596 ARG Chi-restraints excluded: chain D residue 728 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 43 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 HIS ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.144857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.117596 restraints weight = 13949.073| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.77 r_work: 0.3280 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10959 Z= 0.149 Angle : 0.544 10.758 14938 Z= 0.287 Chirality : 0.042 0.185 1675 Planarity : 0.004 0.059 1846 Dihedral : 14.423 176.073 1780 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.68 % Allowed : 16.99 % Favored : 81.33 % 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: 1.06 (0.24), residues: 1267 helix: 2.28 (0.21), residues: 596 sheet: -0.23 (0.38), residues: 199 loop : -0.95 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 276 TYR 0.009 0.001 TYR D 184 PHE 0.018 0.002 PHE D 182 TRP 0.010 0.001 TRP D 170 HIS 0.006 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00353 (10959) covalent geometry : angle 0.54364 (14938) hydrogen bonds : bond 0.04052 ( 566) hydrogen bonds : angle 4.25412 ( 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 131 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.366 Fit side-chains REVERT: C 113 ASP cc_start: 0.8104 (t70) cc_final: 0.7832 (t0) REVERT: C 231 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7699 (mp0) REVERT: C 372 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8530 (mtpp) REVERT: C 401 PRO cc_start: 0.8039 (Cg_endo) cc_final: 0.7768 (Cg_exo) REVERT: C 440 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7024 (pt0) REVERT: D 202 SER cc_start: 0.7783 (OUTLIER) cc_final: 0.7350 (t) REVERT: D 399 ASP cc_start: 0.7569 (m-30) cc_final: 0.7127 (t70) REVERT: D 531 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8573 (mt0) REVERT: D 581 GLU cc_start: 0.8135 (tt0) cc_final: 0.7934 (tt0) REVERT: D 596 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7272 (mtp180) REVERT: D 624 GLN cc_start: 0.7358 (mp10) cc_final: 0.7090 (mp10) REVERT: D 704 ASP cc_start: 0.7783 (p0) cc_final: 0.7444 (p0) REVERT: D 758 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8285 (mm-30) outliers start: 18 outliers final: 12 residues processed: 129 average time/residue: 0.6922 time to fit residues: 95.5295 Evaluate side-chains 125 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 301 MET Chi-restraints excluded: chain C residue 372 LYS Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain D residue 78 ILE 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 523 GLU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 596 ARG Chi-restraints excluded: chain D residue 728 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 69 optimal weight: 0.4980 chunk 90 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 HIS ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.146090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.118897 restraints weight = 13982.729| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.78 r_work: 0.3298 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10959 Z= 0.125 Angle : 0.529 10.824 14938 Z= 0.280 Chirality : 0.041 0.181 1675 Planarity : 0.004 0.059 1846 Dihedral : 14.325 176.977 1780 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.96 % Allowed : 16.81 % 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 aren not related in a simple way. whole: 1.12 (0.24), residues: 1267 helix: 2.34 (0.21), residues: 599 sheet: -0.17 (0.38), residues: 199 loop : -0.98 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 276 TYR 0.007 0.001 TYR C 86 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 covalent geometry : bond 0.00289 (10959) covalent geometry : angle 0.52935 (14938) hydrogen bonds : bond 0.03814 ( 566) hydrogen bonds : angle 4.18587 ( 1608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4308.63 seconds wall clock time: 74 minutes 2.33 seconds (4442.33 seconds total)