Starting phenix.real_space_refine on Fri Sep 11 17:52:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x67_22072/09_2026/6x67_22072.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x67_22072/09_2026/6x67_22072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x67_22072/09_2026/6x67_22072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x67_22072/09_2026/6x67_22072.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x67_22072/09_2026/6x67_22072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x67_22072/09_2026/6x67_22072.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6x67_22072/09_2026/6x67_22072.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x67_22072/09_2026/6x67_22072.cif" } resolution = 3.47 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= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 158 5.49 5 S 88 5.16 5 C 6413 2.51 5 N 1953 2.21 5 O 2364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10984 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 3848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3848 Classifications: {'peptide': 478} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 452} Chain: "D" Number of atoms: 3848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3848 Classifications: {'peptide': 478} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 452} Chain: "E" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 762 Classifications: {'DNA': 37} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 36} Chain: "F" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 961 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "G" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 163 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 514 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "K" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 717 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "L" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 163 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3568 SG CYS C 559 44.667 25.532 50.448 1.00 96.71 S ATOM 3593 SG CYS C 562 44.522 22.338 51.255 1.00 99.50 S ATOM 3747 SG CYS C 582 44.160 23.439 47.991 1.00107.27 S ATOM 3684 SG CYS C 574 38.869 35.104 47.373 1.00152.47 S ATOM 3708 SG CYS C 577 39.538 35.442 50.590 1.00153.59 S ATOM 3815 SG CYS C 590 37.374 32.630 49.357 1.00160.83 S ATOM 3836 SG CYS C 593 36.317 35.624 49.163 1.00169.71 S ATOM 7416 SG CYS D 559 37.258 28.178 26.376 1.00261.70 S ATOM 7441 SG CYS D 562 39.984 28.518 24.406 1.00266.25 S ATOM 7595 SG CYS D 582 40.202 28.443 28.046 1.00241.26 S ATOM 7532 SG CYS D 574 30.661 29.621 35.861 1.00239.63 S ATOM 7556 SG CYS D 577 28.278 29.558 33.616 1.00244.66 S ATOM 7663 SG CYS D 590 30.865 32.084 33.669 1.00249.59 S ATOM 7684 SG CYS D 593 28.715 31.926 35.920 1.00249.56 S Time building chain proxies: 2.66, per 1000 atoms: 0.24 Number of scatterers: 10984 At special positions: 0 Unit cell: (91.16, 89.04, 148.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 88 16.00 P 158 15.00 O 2364 8.00 N 1953 7.00 C 6413 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: 0.97 Conformation dependent library (CDL) restraints added in 325.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 562 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 582 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 559 " pdb="ZN ZN C 601 " - pdb=" ND1 HIS C 585 " pdb=" ZN C 602 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 590 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 574 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 593 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 577 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 562 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 585 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 582 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 559 " pdb=" ZN D 602 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 574 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 590 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 593 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 577 " Number of angles added : 18 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1820 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 42.6% alpha, 11.3% beta 69 base pairs and 122 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'C' and resid 123 through 126 Processing helix chain 'C' and resid 132 through 156 removed outlier: 4.457A pdb=" N PHE C 138 " --> pdb=" O CYS C 134 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ASP C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N GLU C 142 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE C 143 " --> pdb=" O PHE C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 189 Processing helix chain 'C' and resid 195 through 200 removed outlier: 3.650A pdb=" N PHE C 200 " --> pdb=" O THR C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 224 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.589A pdb=" N LEU C 235 " --> pdb=" O ILE C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 258 removed outlier: 4.543A pdb=" N LYS C 246 " --> pdb=" O THR C 242 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 333 Processing helix chain 'C' and resid 334 through 337 Processing helix chain 'C' and resid 351 through 358 Processing helix chain 'C' and resid 379 through 383 Processing helix chain 'C' and resid 433 through 443 Processing helix chain 'C' and resid 446 through 456 Processing helix chain 'C' and resid 464 through 493 removed outlier: 3.966A pdb=" N ALA C 468 " --> pdb=" O ARG C 464 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 469 " --> pdb=" O TRP C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 519 removed outlier: 5.088A pdb=" N SER C 513 " --> pdb=" O SER C 509 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N PHE C 514 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 533 Processing helix chain 'C' and resid 563 through 567 Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.695A pdb=" N ARG D 126 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 139 through 156 Processing helix chain 'D' and resid 160 through 164 Processing helix chain 'D' and resid 172 through 190 Processing helix chain 'D' and resid 195 through 200 Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 241 through 258 removed outlier: 4.379A pdb=" N LYS D 246 " --> pdb=" O THR D 242 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 334 through 337 Processing helix chain 'D' and resid 351 through 357 Processing helix chain 'D' and resid 433 through 443 Processing helix chain 'D' and resid 446 through 456 Processing helix chain 'D' and resid 464 through 493 removed outlier: 3.866A pdb=" N ALA D 468 " --> pdb=" O ARG D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 519 removed outlier: 5.091A pdb=" N SER D 513 " --> pdb=" O SER D 509 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N PHE D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 534 Processing sheet with id=AA1, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AA2, first strand: chain 'C' and resid 306 through 311 removed outlier: 6.998A pdb=" N MET C 306 " --> pdb=" O ASP C 300 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASP C 300 " --> pdb=" O MET C 306 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU C 265 " --> pdb=" O THR C 344 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR C 370 " --> pdb=" O CYS C 345 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR C 415 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS C 412 " --> pdb=" O PRO C 408 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 572 through 573 Processing sheet with id=AA4, first strand: chain 'D' and resid 282 through 283 removed outlier: 6.553A pdb=" N ASP D 300 " --> pdb=" O MET D 306 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N MET D 306 " --> pdb=" O ASP D 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 282 through 283 removed outlier: 6.348A pdb=" N LEU D 265 " --> pdb=" O THR D 344 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR D 370 " --> pdb=" O CYS D 345 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR D 415 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LYS D 412 " --> pdb=" O PRO D 408 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 572 through 573 322 hydrogen bonds defined for protein. 903 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 171 hydrogen bonds 342 hydrogen bond angles 0 basepair planarities 69 basepair parallelities 122 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2427 1.33 - 1.45: 3635 1.45 - 1.58: 5026 1.58 - 1.70: 304 1.70 - 1.83: 136 Bond restraints: 11528 Sorted by residual: bond pdb=" C4' DT K -23 " pdb=" C3' DT K -23 " ideal model delta sigma weight residual 1.529 1.631 -0.102 1.00e-02 1.00e+04 1.04e+02 bond pdb=" C3' DT K -23 " pdb=" O3' DT K -23 " ideal model delta sigma weight residual 1.435 1.557 -0.122 1.30e-02 5.92e+03 8.74e+01 bond pdb=" O3' DT J 21 " pdb=" P DA J 22 " ideal model delta sigma weight residual 1.607 1.515 0.092 1.20e-02 6.94e+03 5.92e+01 bond pdb=" C5' DT K -22 " pdb=" C4' DT K -22 " ideal model delta sigma weight residual 1.512 1.561 -0.049 7.00e-03 2.04e+04 4.93e+01 bond pdb=" O3' DT K -23 " pdb=" P DT K -22 " ideal model delta sigma weight residual 1.607 1.691 -0.084 1.20e-02 6.94e+03 4.93e+01 ... (remaining 11523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.02: 15881 5.02 - 10.04: 330 10.04 - 15.06: 24 15.06 - 20.08: 2 20.08 - 25.10: 1 Bond angle restraints: 16238 Sorted by residual: angle pdb=" C3' DT K -23 " pdb=" O3' DT K -23 " pdb=" P DT K -22 " ideal model delta sigma weight residual 119.70 144.80 -25.10 1.20e+00 6.94e-01 4.38e+02 angle pdb=" C3' DT J 21 " pdb=" O3' DT J 21 " pdb=" P DA J 22 " ideal model delta sigma weight residual 119.70 101.85 17.85 1.20e+00 6.94e-01 2.21e+02 angle pdb=" O5' DT K -22 " pdb=" C5' DT K -22 " pdb=" C4' DT K -22 " ideal model delta sigma weight residual 109.40 119.28 -9.88 8.00e-01 1.56e+00 1.52e+02 angle pdb=" C3' DT E 26 " pdb=" O3' DT E 26 " pdb=" P DT E 27 " ideal model delta sigma weight residual 119.70 131.86 -12.16 1.20e+00 6.94e-01 1.03e+02 angle pdb=" CA HIS D 193 " pdb=" CB HIS D 193 " pdb=" CG HIS D 193 " ideal model delta sigma weight residual 113.80 104.11 9.69 1.00e+00 1.00e+00 9.39e+01 ... (remaining 16233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.74: 5411 22.74 - 45.48: 878 45.48 - 68.23: 328 68.23 - 90.97: 12 90.97 - 113.71: 1 Dihedral angle restraints: 6630 sinusoidal: 3814 harmonic: 2816 Sorted by residual: dihedral pdb=" C PRO D 362 " pdb=" N PRO D 362 " pdb=" CA PRO D 362 " pdb=" CB PRO D 362 " ideal model delta harmonic sigma weight residual -120.70 -105.48 -15.22 0 2.50e+00 1.60e-01 3.71e+01 dihedral pdb=" C PRO D 285 " pdb=" N PRO D 285 " pdb=" CA PRO D 285 " pdb=" CB PRO D 285 " ideal model delta harmonic sigma weight residual -120.70 -106.96 -13.74 0 2.50e+00 1.60e-01 3.02e+01 dihedral pdb=" C PRO C 541 " pdb=" N PRO C 541 " pdb=" CA PRO C 541 " pdb=" CB PRO C 541 " ideal model delta harmonic sigma weight residual -120.70 -108.54 -12.16 0 2.50e+00 1.60e-01 2.36e+01 ... (remaining 6627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1483 0.122 - 0.243: 269 0.243 - 0.365: 40 0.365 - 0.487: 7 0.487 - 0.608: 1 Chirality restraints: 1800 Sorted by residual: chirality pdb=" P DT K -22 " pdb=" OP1 DT K -22 " pdb=" OP2 DT K -22 " pdb=" O5' DT K -22 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.61 2.00e-01 2.50e+01 9.25e+00 chirality pdb=" CA PRO D 233 " pdb=" N PRO D 233 " pdb=" C PRO D 233 " pdb=" CB PRO D 233 " both_signs ideal model delta sigma weight residual False 2.72 2.25 0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" CA PRO C 537 " pdb=" N PRO C 537 " pdb=" C PRO C 537 " pdb=" CB PRO C 537 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.42 2.00e-01 2.50e+01 4.40e+00 ... (remaining 1797 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA E 25 " 0.141 2.00e-02 2.50e+03 6.23e-02 1.07e+02 pdb=" N9 DA E 25 " -0.009 2.00e-02 2.50e+03 pdb=" C8 DA E 25 " -0.064 2.00e-02 2.50e+03 pdb=" N7 DA E 25 " -0.060 2.00e-02 2.50e+03 pdb=" C5 DA E 25 " -0.016 2.00e-02 2.50e+03 pdb=" C6 DA E 25 " 0.024 2.00e-02 2.50e+03 pdb=" N6 DA E 25 " 0.094 2.00e-02 2.50e+03 pdb=" N1 DA E 25 " 0.011 2.00e-02 2.50e+03 pdb=" C2 DA E 25 " -0.040 2.00e-02 2.50e+03 pdb=" N3 DA E 25 " -0.057 2.00e-02 2.50e+03 pdb=" C4 DA E 25 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT J 21 " 0.081 2.00e-02 2.50e+03 3.69e-02 3.40e+01 pdb=" N1 DT J 21 " -0.016 2.00e-02 2.50e+03 pdb=" C2 DT J 21 " -0.014 2.00e-02 2.50e+03 pdb=" O2 DT J 21 " -0.042 2.00e-02 2.50e+03 pdb=" N3 DT J 21 " 0.014 2.00e-02 2.50e+03 pdb=" C4 DT J 21 " 0.014 2.00e-02 2.50e+03 pdb=" O4 DT J 21 " 0.038 2.00e-02 2.50e+03 pdb=" C5 DT J 21 " -0.022 2.00e-02 2.50e+03 pdb=" C7 DT J 21 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DT J 21 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT K -23 " 0.041 2.00e-02 2.50e+03 3.26e-02 2.66e+01 pdb=" N1 DT K -23 " 0.022 2.00e-02 2.50e+03 pdb=" C2 DT K -23 " -0.007 2.00e-02 2.50e+03 pdb=" O2 DT K -23 " -0.066 2.00e-02 2.50e+03 pdb=" N3 DT K -23 " 0.016 2.00e-02 2.50e+03 pdb=" C4 DT K -23 " 0.014 2.00e-02 2.50e+03 pdb=" O4 DT K -23 " 0.038 2.00e-02 2.50e+03 pdb=" C5 DT K -23 " -0.011 2.00e-02 2.50e+03 pdb=" C7 DT K -23 " -0.045 2.00e-02 2.50e+03 pdb=" C6 DT K -23 " -0.003 2.00e-02 2.50e+03 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 216 2.60 - 3.18: 9164 3.18 - 3.75: 17872 3.75 - 4.33: 26051 4.33 - 4.90: 38247 Nonbonded interactions: 91550 Sorted by model distance: nonbonded pdb=" OD2 ASP C 346 " pdb="CA CA C 603 " model vdw 2.028 2.510 nonbonded pdb=" OD2 ASP D 346 " pdb="CA CA D 603 " model vdw 2.034 2.510 nonbonded pdb=" OP1 DT K 0 " pdb="CA CA C 603 " model vdw 2.067 2.510 nonbonded pdb=" OP1 DT F 0 " pdb="CA CA D 603 " model vdw 2.074 2.510 nonbonded pdb=" OD2 ASP C 218 " pdb="CA CA C 604 " model vdw 2.126 2.510 ... (remaining 91545 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'L' } 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: 0.840 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.390 Find NCS groups from input model: 0.140 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 0.018 0.413 11544 Z= 1.232 Angle : 1.908 25.103 16256 Z= 1.420 Chirality : 0.098 0.608 1800 Planarity : 0.005 0.062 1508 Dihedral : 21.586 113.710 4810 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.84 % Allowed : 4.62 % Favored : 94.54 % Rotamer: Outliers : 0.23 % Allowed : 7.47 % Favored : 92.31 % Cbeta Deviations : 0.88 % 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: -0.81 (0.26), residues: 952 helix: -0.85 (0.23), residues: 377 sheet: 0.72 (0.50), residues: 116 loop : -0.44 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 222 TYR 0.038 0.008 TYR D 406 PHE 0.022 0.006 PHE C 502 TRP 0.045 0.011 TRP D 150 HIS 0.010 0.003 HIS D 487 Details of bonding type rmsd/Z covalent geometry : bond 0.01446 / 1.18 (11528) covalent geometry : angle 1.88025 / 1.42 (16238) hydrogen bonds : bond 0.18651 / 12.44 ( 491) hydrogen bonds : angle 6.47804 / 4.61 ( 1245) metal coordination : bond 0.26802 / 16.61 ( 16) metal coordination : angle 9.99432 / 6.48 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 416 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 185 MET cc_start: 0.8909 (tpp) cc_final: 0.8665 (tpp) REVERT: C 326 GLU cc_start: 0.6220 (mp0) cc_final: 0.5899 (mp0) REVERT: C 418 SER cc_start: 0.8017 (t) cc_final: 0.6897 (p) REVERT: C 503 MET cc_start: 0.9163 (mmm) cc_final: 0.8896 (mmm) REVERT: C 535 ILE cc_start: 0.8721 (mt) cc_final: 0.8509 (mt) REVERT: D 175 GLU cc_start: 0.7988 (tt0) cc_final: 0.7748 (tt0) REVERT: D 189 ARG cc_start: 0.8285 (mmm-85) cc_final: 0.7928 (mtp85) REVERT: D 255 CYS cc_start: 0.8310 (m) cc_final: 0.7935 (m) REVERT: D 259 TYR cc_start: 0.8072 (t80) cc_final: 0.7850 (t80) REVERT: D 305 TYR cc_start: 0.8723 (t80) cc_final: 0.8190 (t80) REVERT: D 418 SER cc_start: 0.8456 (t) cc_final: 0.8145 (p) REVERT: D 447 ASP cc_start: 0.8274 (p0) cc_final: 0.7984 (p0) REVERT: D 458 CYS cc_start: 0.8919 (t) cc_final: 0.8660 (p) outliers start: 2 outliers final: 0 residues processed: 417 average time/residue: 0.1257 time to fit residues: 70.8016 Evaluate side-chains 271 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 50.0000 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 HIS C 440 ASN C 475 ASN C 487 HIS ** C 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 HIS D 505 ASN D 531 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.139867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.100755 restraints weight = 17641.643| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.73 r_work: 0.2986 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11544 Z= 0.213 Angle : 0.907 10.689 16256 Z= 0.502 Chirality : 0.054 0.497 1800 Planarity : 0.006 0.053 1508 Dihedral : 24.663 124.757 2824 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.53 % Allowed : 3.36 % Favored : 96.11 % Rotamer: Outliers : 3.73 % Allowed : 17.53 % Favored : 78.73 % 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: -0.20 (0.26), residues: 952 helix: 0.38 (0.26), residues: 378 sheet: 0.57 (0.47), residues: 110 loop : -0.67 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 337 TYR 0.025 0.002 TYR C 283 PHE 0.014 0.002 PHE D 179 TRP 0.016 0.002 TRP D 150 HIS 0.009 0.002 HIS D 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 (11528) covalent geometry : angle 0.89804 / 0.50 (16238) hydrogen bonds : bond 0.07951 / 5.31 ( 491) hydrogen bonds : angle 4.76098 / 3.35 ( 1245) metal coordination : bond 0.01653 / 0.83 ( 16) metal coordination : angle 3.90838 / 2.27 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 307 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 173 GLU cc_start: 0.8499 (pm20) cc_final: 0.8228 (mp0) REVERT: C 185 MET cc_start: 0.9232 (tpp) cc_final: 0.8849 (tpp) REVERT: C 206 MET cc_start: 0.9051 (mmm) cc_final: 0.8581 (mmt) REVERT: C 257 GLN cc_start: 0.8800 (tp40) cc_final: 0.8587 (tp40) REVERT: C 269 GLU cc_start: 0.8708 (pt0) cc_final: 0.8003 (pm20) REVERT: C 306 MET cc_start: 0.8726 (ttt) cc_final: 0.8007 (ttt) REVERT: C 326 GLU cc_start: 0.7455 (mp0) cc_final: 0.6747 (mp0) REVERT: C 394 MET cc_start: 0.8310 (mtp) cc_final: 0.7756 (ttm) REVERT: C 418 SER cc_start: 0.9008 (t) cc_final: 0.8587 (p) REVERT: C 554 LYS cc_start: 0.8867 (mmmm) cc_final: 0.8590 (mmtp) REVERT: C 586 ASN cc_start: 0.7604 (OUTLIER) cc_final: 0.7316 (m-40) REVERT: D 227 ASP cc_start: 0.8395 (t0) cc_final: 0.7995 (t0) REVERT: D 250 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9218 (mp) REVERT: D 305 TYR cc_start: 0.9374 (t80) cc_final: 0.8372 (t80) REVERT: D 342 ASN cc_start: 0.8913 (t0) cc_final: 0.8593 (t0) REVERT: D 418 SER cc_start: 0.8876 (t) cc_final: 0.8329 (p) REVERT: D 438 TYR cc_start: 0.8155 (t80) cc_final: 0.7922 (t80) REVERT: D 441 GLN cc_start: 0.9433 (tt0) cc_final: 0.8990 (tt0) REVERT: D 447 ASP cc_start: 0.8797 (p0) cc_final: 0.8215 (p0) REVERT: D 517 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.9134 (ttmt) outliers start: 33 outliers final: 15 residues processed: 319 average time/residue: 0.1031 time to fit residues: 47.0827 Evaluate side-chains 293 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 275 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 586 ASN Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 299 CYS Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 517 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 0.2980 chunk 30 optimal weight: 0.1980 chunk 68 optimal weight: 0.7980 chunk 95 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 193 HIS ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN C 440 ASN C 475 ASN C 487 HIS ** C 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 GLN D 487 HIS D 531 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.140375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.100658 restraints weight = 18010.355| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.77 r_work: 0.2993 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11544 Z= 0.163 Angle : 0.765 11.346 16256 Z= 0.431 Chirality : 0.046 0.241 1800 Planarity : 0.005 0.050 1508 Dihedral : 24.469 121.699 2824 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.10 % Favored : 95.59 % Rotamer: Outliers : 3.17 % Allowed : 21.49 % Favored : 75.34 % 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: -0.19 (0.26), residues: 952 helix: 0.82 (0.26), residues: 374 sheet: 0.36 (0.46), residues: 110 loop : -1.02 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 236 TYR 0.019 0.002 TYR C 363 PHE 0.012 0.001 PHE D 482 TRP 0.010 0.001 TRP C 150 HIS 0.007 0.001 HIS D 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (11528) covalent geometry : angle 0.75478 / 0.43 (16238) hydrogen bonds : bond 0.06181 / 4.08 ( 491) hydrogen bonds : angle 4.38740 / 3.04 ( 1245) metal coordination : bond 0.00626 / 0.35 ( 16) metal coordination : angle 3.78307 / 2.29 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 298 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 173 GLU cc_start: 0.8549 (pm20) cc_final: 0.8287 (mp0) REVERT: C 185 MET cc_start: 0.9201 (tpp) cc_final: 0.8705 (tpp) REVERT: C 238 ASN cc_start: 0.8492 (m-40) cc_final: 0.7360 (t0) REVERT: C 254 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8834 (mm-40) REVERT: C 269 GLU cc_start: 0.8771 (pt0) cc_final: 0.8106 (pm20) REVERT: C 297 MET cc_start: 0.8414 (ttm) cc_final: 0.7585 (ttm) REVERT: C 306 MET cc_start: 0.8619 (ttt) cc_final: 0.8286 (ttt) REVERT: C 376 ARG cc_start: 0.8232 (ttt-90) cc_final: 0.7927 (ttt-90) REVERT: C 394 MET cc_start: 0.8317 (mtp) cc_final: 0.7851 (ttm) REVERT: C 418 SER cc_start: 0.8872 (t) cc_final: 0.7739 (p) REVERT: C 520 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8457 (mt-10) REVERT: C 586 ASN cc_start: 0.7671 (OUTLIER) cc_final: 0.6980 (m-40) REVERT: D 227 ASP cc_start: 0.8298 (t0) cc_final: 0.7947 (t0) REVERT: D 257 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8093 (tm-30) REVERT: D 269 GLU cc_start: 0.8446 (pp20) cc_final: 0.8214 (pp20) REVERT: D 305 TYR cc_start: 0.9343 (t80) cc_final: 0.8374 (t80) REVERT: D 342 ASN cc_start: 0.8875 (t0) cc_final: 0.8549 (t0) REVERT: D 397 PHE cc_start: 0.7693 (m-80) cc_final: 0.7457 (m-80) REVERT: D 434 GLN cc_start: 0.8811 (tp40) cc_final: 0.8565 (tp-100) REVERT: D 437 MET cc_start: 0.9486 (mmt) cc_final: 0.9225 (mmt) REVERT: D 441 GLN cc_start: 0.9432 (tt0) cc_final: 0.9163 (tt0) REVERT: D 447 ASP cc_start: 0.8709 (p0) cc_final: 0.8148 (p0) REVERT: D 535 ILE cc_start: 0.8842 (tt) cc_final: 0.8569 (tt) outliers start: 28 outliers final: 14 residues processed: 313 average time/residue: 0.0971 time to fit residues: 44.5868 Evaluate side-chains 274 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 259 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain C residue 586 ASN Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 469 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 39 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.0070 chunk 3 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 30.0000 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN C 475 ASN ** C 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN D 487 HIS D 531 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.137921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.098184 restraints weight = 18221.186| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.76 r_work: 0.2958 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11544 Z= 0.172 Angle : 0.735 7.825 16256 Z= 0.413 Chirality : 0.045 0.200 1800 Planarity : 0.005 0.073 1508 Dihedral : 24.529 126.103 2824 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.52 % Favored : 95.38 % Rotamer: Outliers : 3.62 % Allowed : 20.70 % Favored : 75.68 % 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: -0.16 (0.27), residues: 952 helix: 0.96 (0.27), residues: 379 sheet: 0.50 (0.47), residues: 107 loop : -1.16 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 169 TYR 0.022 0.002 TYR C 305 PHE 0.012 0.001 PHE D 251 TRP 0.007 0.001 TRP C 465 HIS 0.007 0.001 HIS D 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (11528) covalent geometry : angle 0.72968 / 0.41 (16238) hydrogen bonds : bond 0.05699 / 3.80 ( 491) hydrogen bonds : angle 4.18852 / 2.90 ( 1245) metal coordination : bond 0.00388 / 0.21 ( 16) metal coordination : angle 2.72965 / 1.62 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 274 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 173 GLU cc_start: 0.8577 (pm20) cc_final: 0.8275 (mp0) REVERT: C 238 ASN cc_start: 0.8660 (m-40) cc_final: 0.7454 (t0) REVERT: C 254 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8786 (mm-40) REVERT: C 268 ASP cc_start: 0.7967 (t0) cc_final: 0.6822 (t0) REVERT: C 269 GLU cc_start: 0.8782 (pt0) cc_final: 0.8210 (pm20) REVERT: C 297 MET cc_start: 0.8458 (ttm) cc_final: 0.7391 (ttm) REVERT: C 306 MET cc_start: 0.8794 (ttt) cc_final: 0.8329 (ttt) REVERT: C 380 GLU cc_start: 0.9307 (mp0) cc_final: 0.9102 (mp0) REVERT: C 383 LYS cc_start: 0.8772 (mttp) cc_final: 0.8293 (mttp) REVERT: C 406 TYR cc_start: 0.7503 (OUTLIER) cc_final: 0.5948 (p90) REVERT: C 418 SER cc_start: 0.8958 (t) cc_final: 0.8434 (p) REVERT: C 435 MET cc_start: 0.8790 (mtt) cc_final: 0.8487 (mtt) REVERT: C 520 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8463 (mt-10) REVERT: D 154 GLU cc_start: 0.8957 (tp30) cc_final: 0.8433 (tp30) REVERT: D 175 GLU cc_start: 0.8964 (tt0) cc_final: 0.8609 (tt0) REVERT: D 227 ASP cc_start: 0.8410 (t0) cc_final: 0.7982 (t0) REVERT: D 257 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8128 (tm-30) REVERT: D 269 GLU cc_start: 0.8513 (pp20) cc_final: 0.8217 (pp20) REVERT: D 305 TYR cc_start: 0.9398 (t80) cc_final: 0.9121 (t80) REVERT: D 342 ASN cc_start: 0.8975 (t0) cc_final: 0.8771 (t0) REVERT: D 397 PHE cc_start: 0.7904 (m-80) cc_final: 0.7364 (m-80) REVERT: D 434 GLN cc_start: 0.8852 (tp40) cc_final: 0.8634 (tp-100) REVERT: D 437 MET cc_start: 0.9492 (mmt) cc_final: 0.9290 (mmt) REVERT: D 441 GLN cc_start: 0.9456 (tt0) cc_final: 0.9171 (tt0) REVERT: D 447 ASP cc_start: 0.8720 (p0) cc_final: 0.8178 (p0) REVERT: D 501 LYS cc_start: 0.8813 (ttpt) cc_final: 0.8428 (ttpp) outliers start: 32 outliers final: 21 residues processed: 288 average time/residue: 0.0983 time to fit residues: 41.2135 Evaluate side-chains 275 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 253 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 394 MET Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 589 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 93 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 ASN D 487 HIS D 531 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.137158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.097362 restraints weight = 17973.176| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.76 r_work: 0.2948 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11544 Z= 0.182 Angle : 0.722 7.989 16256 Z= 0.403 Chirality : 0.045 0.190 1800 Planarity : 0.005 0.053 1508 Dihedral : 24.513 125.859 2824 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.73 % Favored : 95.17 % Rotamer: Outliers : 4.52 % Allowed : 20.81 % Favored : 74.66 % 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: -0.10 (0.27), residues: 952 helix: 1.24 (0.27), residues: 379 sheet: 0.35 (0.47), residues: 110 loop : -1.32 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 337 TYR 0.023 0.002 TYR D 363 PHE 0.012 0.001 PHE D 179 TRP 0.008 0.001 TRP C 465 HIS 0.007 0.002 HIS D 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (11528) covalent geometry : angle 0.71765 / 0.40 (16238) hydrogen bonds : bond 0.05450 / 3.64 ( 491) hydrogen bonds : angle 4.12688 / 2.84 ( 1245) metal coordination : bond 0.00698 / 0.39 ( 16) metal coordination : angle 2.47304 / 1.44 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 261 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 225 ARG cc_start: 0.7664 (mmt-90) cc_final: 0.7278 (ttp-170) REVERT: C 238 ASN cc_start: 0.8507 (m-40) cc_final: 0.7349 (t0) REVERT: C 268 ASP cc_start: 0.7986 (t0) cc_final: 0.6786 (t0) REVERT: C 269 GLU cc_start: 0.8701 (pt0) cc_final: 0.8346 (pm20) REVERT: C 383 LYS cc_start: 0.8722 (mttp) cc_final: 0.8342 (mttp) REVERT: C 406 TYR cc_start: 0.7625 (OUTLIER) cc_final: 0.5630 (p90) REVERT: C 418 SER cc_start: 0.8943 (t) cc_final: 0.8472 (p) REVERT: D 124 MET cc_start: 0.9068 (mmm) cc_final: 0.8828 (mmm) REVERT: D 132 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9087 (tt) REVERT: D 154 GLU cc_start: 0.8979 (tp30) cc_final: 0.8454 (tp30) REVERT: D 227 ASP cc_start: 0.8535 (t0) cc_final: 0.8066 (t70) REVERT: D 257 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8118 (tm-30) REVERT: D 269 GLU cc_start: 0.8607 (pp20) cc_final: 0.8067 (pp20) REVERT: D 305 TYR cc_start: 0.9446 (t80) cc_final: 0.9204 (t80) REVERT: D 363 TYR cc_start: 0.6945 (m-80) cc_final: 0.6658 (m-80) REVERT: D 376 ARG cc_start: 0.8579 (ptp-110) cc_final: 0.8348 (ptp-110) REVERT: D 406 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.7520 (p90) REVERT: D 437 MET cc_start: 0.9508 (mmt) cc_final: 0.9306 (mmt) REVERT: D 441 GLN cc_start: 0.9461 (tt0) cc_final: 0.9249 (tt0) REVERT: D 447 ASP cc_start: 0.8646 (p0) cc_final: 0.8107 (p0) outliers start: 40 outliers final: 27 residues processed: 280 average time/residue: 0.0941 time to fit residues: 38.8180 Evaluate side-chains 276 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 589 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 21 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 69 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 86 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 342 ASN D 434 GLN D 487 HIS D 531 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.139164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.099487 restraints weight = 18029.176| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.78 r_work: 0.2982 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11544 Z= 0.147 Angle : 0.690 6.843 16256 Z= 0.390 Chirality : 0.043 0.182 1800 Planarity : 0.005 0.054 1508 Dihedral : 24.462 125.233 2824 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.83 % Favored : 95.06 % Rotamer: Outliers : 3.85 % Allowed : 20.48 % Favored : 75.68 % 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: -0.02 (0.27), residues: 952 helix: 1.44 (0.27), residues: 372 sheet: 0.45 (0.47), residues: 107 loop : -1.37 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 169 TYR 0.017 0.001 TYR D 438 PHE 0.010 0.001 PHE D 179 TRP 0.007 0.001 TRP C 465 HIS 0.006 0.001 HIS D 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (11528) covalent geometry : angle 0.68712 / 0.39 (16238) hydrogen bonds : bond 0.04957 / 3.28 ( 491) hydrogen bonds : angle 3.97168 / 2.72 ( 1245) metal coordination : bond 0.00407 / 0.21 ( 16) metal coordination : angle 2.12188 / 1.22 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 269 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 223 CYS cc_start: 0.9148 (m) cc_final: 0.8718 (m) REVERT: C 225 ARG cc_start: 0.7611 (mmt-90) cc_final: 0.7217 (ttp-170) REVERT: C 238 ASN cc_start: 0.8462 (m-40) cc_final: 0.7339 (t0) REVERT: C 268 ASP cc_start: 0.7957 (t0) cc_final: 0.6777 (t0) REVERT: C 269 GLU cc_start: 0.8712 (pt0) cc_final: 0.8435 (pm20) REVERT: C 322 VAL cc_start: 0.9163 (OUTLIER) cc_final: 0.8940 (p) REVERT: C 337 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7835 (ttm-80) REVERT: C 383 LYS cc_start: 0.8727 (mttp) cc_final: 0.8364 (mtpt) REVERT: C 406 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.5585 (p90) REVERT: C 418 SER cc_start: 0.8881 (t) cc_final: 0.8445 (p) REVERT: C 554 LYS cc_start: 0.8831 (mmmm) cc_final: 0.8566 (tptp) REVERT: D 132 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9004 (tt) REVERT: D 154 GLU cc_start: 0.8978 (tp30) cc_final: 0.8515 (tp30) REVERT: D 206 MET cc_start: 0.8768 (mmt) cc_final: 0.8422 (mmt) REVERT: D 257 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8126 (tm-30) REVERT: D 269 GLU cc_start: 0.8623 (pp20) cc_final: 0.8249 (pp20) REVERT: D 305 TYR cc_start: 0.9429 (t80) cc_final: 0.8370 (t80) REVERT: D 406 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.7505 (p90) REVERT: D 437 MET cc_start: 0.9458 (mmt) cc_final: 0.9251 (mmt) REVERT: D 441 GLN cc_start: 0.9432 (tt0) cc_final: 0.9217 (tt0) REVERT: D 447 ASP cc_start: 0.8640 (p0) cc_final: 0.8129 (p0) REVERT: D 501 LYS cc_start: 0.8719 (ttpt) cc_final: 0.8377 (tttm) outliers start: 34 outliers final: 22 residues processed: 285 average time/residue: 0.0951 time to fit residues: 39.2544 Evaluate side-chains 278 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 251 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 500 LYS Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 589 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 98 optimal weight: 30.0000 chunk 45 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN D 192 ASN D 434 GLN D 531 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.134595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.093780 restraints weight = 18098.180| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.80 r_work: 0.2870 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 11544 Z= 0.215 Angle : 0.740 8.115 16256 Z= 0.408 Chirality : 0.045 0.193 1800 Planarity : 0.006 0.056 1508 Dihedral : 24.584 124.685 2824 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.94 % Favored : 94.96 % Rotamer: Outliers : 4.07 % Allowed : 22.06 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.27), residues: 952 helix: 1.55 (0.27), residues: 379 sheet: -0.20 (0.45), residues: 122 loop : -1.31 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 337 TYR 0.018 0.002 TYR D 259 PHE 0.015 0.002 PHE C 139 TRP 0.010 0.001 TRP D 348 HIS 0.010 0.002 HIS D 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 (11528) covalent geometry : angle 0.73735 / 0.41 (16238) hydrogen bonds : bond 0.05640 / 3.81 ( 491) hydrogen bonds : angle 4.02993 / 2.78 ( 1245) metal coordination : bond 0.00634 / 0.33 ( 16) metal coordination : angle 2.12256 / 1.20 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 252 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 185 MET cc_start: 0.9284 (tpp) cc_final: 0.8356 (tpp) REVERT: C 223 CYS cc_start: 0.9203 (m) cc_final: 0.8768 (m) REVERT: C 225 ARG cc_start: 0.7820 (mmt-90) cc_final: 0.7533 (ttp-170) REVERT: C 238 ASN cc_start: 0.8521 (m-40) cc_final: 0.7422 (t0) REVERT: C 257 GLN cc_start: 0.8775 (tp-100) cc_final: 0.8374 (tp-100) REVERT: C 269 GLU cc_start: 0.8731 (pt0) cc_final: 0.8387 (pm20) REVERT: C 322 VAL cc_start: 0.9204 (OUTLIER) cc_final: 0.8980 (p) REVERT: C 337 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7971 (ttm-80) REVERT: C 383 LYS cc_start: 0.8806 (mttp) cc_final: 0.8085 (mtmt) REVERT: C 406 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.5627 (p90) REVERT: C 418 SER cc_start: 0.8923 (t) cc_final: 0.8424 (p) REVERT: D 124 MET cc_start: 0.9007 (mmm) cc_final: 0.8756 (mmm) REVERT: D 132 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9029 (tt) REVERT: D 154 GLU cc_start: 0.8949 (tp30) cc_final: 0.8426 (tp30) REVERT: D 227 ASP cc_start: 0.8719 (t0) cc_final: 0.8006 (t0) REVERT: D 257 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8202 (tm-30) REVERT: D 269 GLU cc_start: 0.8760 (pp20) cc_final: 0.7854 (pp20) REVERT: D 305 TYR cc_start: 0.9491 (t80) cc_final: 0.9248 (t80) REVERT: D 406 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7789 (p90) REVERT: D 437 MET cc_start: 0.9436 (mmt) cc_final: 0.9220 (mmt) REVERT: D 447 ASP cc_start: 0.8596 (p0) cc_final: 0.8213 (p0) outliers start: 36 outliers final: 27 residues processed: 270 average time/residue: 0.0926 time to fit residues: 36.9299 Evaluate side-chains 272 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 240 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 500 LYS Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 589 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 GLN D 531 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.135859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.095210 restraints weight = 18097.564| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.83 r_work: 0.2894 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11544 Z= 0.169 Angle : 0.707 7.055 16256 Z= 0.396 Chirality : 0.043 0.181 1800 Planarity : 0.005 0.060 1508 Dihedral : 24.509 123.047 2824 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.94 % Favored : 94.96 % Rotamer: Outliers : 3.85 % Allowed : 22.96 % Favored : 73.19 % 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: 0.08 (0.27), residues: 952 helix: 1.64 (0.27), residues: 378 sheet: 0.09 (0.46), residues: 117 loop : -1.38 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D 337 TYR 0.027 0.002 TYR D 438 PHE 0.011 0.001 PHE D 179 TRP 0.007 0.001 TRP C 465 HIS 0.005 0.001 HIS D 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (11528) covalent geometry : angle 0.70419 / 0.40 (16238) hydrogen bonds : bond 0.05085 / 3.39 ( 491) hydrogen bonds : angle 3.95771 / 2.72 ( 1245) metal coordination : bond 0.00340 / 0.17 ( 16) metal coordination : angle 2.02912 / 1.15 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 254 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 223 CYS cc_start: 0.9185 (m) cc_final: 0.8764 (m) REVERT: C 225 ARG cc_start: 0.7800 (mmt-90) cc_final: 0.7566 (ttp-170) REVERT: C 238 ASN cc_start: 0.8507 (m-40) cc_final: 0.7393 (t0) REVERT: C 254 GLN cc_start: 0.9371 (tp40) cc_final: 0.9145 (tp40) REVERT: C 269 GLU cc_start: 0.8676 (pt0) cc_final: 0.8348 (pm20) REVERT: C 337 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7888 (ttm-80) REVERT: C 383 LYS cc_start: 0.8768 (mttp) cc_final: 0.8260 (mtmt) REVERT: C 406 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.5616 (p90) REVERT: C 418 SER cc_start: 0.8849 (t) cc_final: 0.8349 (p) REVERT: D 124 MET cc_start: 0.9019 (mmm) cc_final: 0.8749 (mmm) REVERT: D 132 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9020 (tt) REVERT: D 154 GLU cc_start: 0.8941 (tp30) cc_final: 0.8459 (tp30) REVERT: D 227 ASP cc_start: 0.8670 (t0) cc_final: 0.8101 (t70) REVERT: D 257 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8198 (tm-30) REVERT: D 269 GLU cc_start: 0.8774 (pp20) cc_final: 0.7934 (pp20) REVERT: D 305 TYR cc_start: 0.9463 (t80) cc_final: 0.9259 (t80) REVERT: D 386 ARG cc_start: 0.8254 (tpt90) cc_final: 0.7931 (tpp80) REVERT: D 406 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7727 (p90) REVERT: D 437 MET cc_start: 0.9414 (mmt) cc_final: 0.9197 (mmt) REVERT: D 447 ASP cc_start: 0.8521 (p0) cc_final: 0.8136 (p0) outliers start: 34 outliers final: 25 residues processed: 270 average time/residue: 0.0896 time to fit residues: 36.1662 Evaluate side-chains 271 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 242 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 500 LYS Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 589 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 43 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 GLN D 531 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.136804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.096311 restraints weight = 18101.958| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.85 r_work: 0.2916 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11544 Z= 0.156 Angle : 0.700 6.825 16256 Z= 0.392 Chirality : 0.043 0.235 1800 Planarity : 0.005 0.060 1508 Dihedral : 24.491 122.100 2824 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.46 % Favored : 94.43 % Rotamer: Outliers : 3.39 % Allowed : 23.64 % Favored : 72.96 % 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: 0.04 (0.27), residues: 952 helix: 1.71 (0.27), residues: 371 sheet: 0.20 (0.50), residues: 101 loop : -1.44 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 337 TYR 0.020 0.001 TYR C 415 PHE 0.012 0.001 PHE C 135 TRP 0.007 0.001 TRP C 465 HIS 0.004 0.001 HIS D 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (11528) covalent geometry : angle 0.69747 / 0.39 (16238) hydrogen bonds : bond 0.04914 / 3.28 ( 491) hydrogen bonds : angle 3.95408 / 2.71 ( 1245) metal coordination : bond 0.00314 / 0.16 ( 16) metal coordination : angle 1.89368 / 1.07 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 258 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 223 CYS cc_start: 0.9183 (m) cc_final: 0.8779 (m) REVERT: C 238 ASN cc_start: 0.8489 (m-40) cc_final: 0.7438 (t0) REVERT: C 269 GLU cc_start: 0.8648 (pt0) cc_final: 0.8347 (pm20) REVERT: C 406 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.5537 (p90) REVERT: C 418 SER cc_start: 0.8797 (t) cc_final: 0.8312 (p) REVERT: C 456 MET cc_start: 0.8865 (ttm) cc_final: 0.8514 (ttm) REVERT: C 517 LYS cc_start: 0.9391 (ttpp) cc_final: 0.9181 (tppt) REVERT: D 124 MET cc_start: 0.9035 (mmm) cc_final: 0.8762 (mmm) REVERT: D 132 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9027 (tt) REVERT: D 154 GLU cc_start: 0.8947 (tp30) cc_final: 0.8452 (tp30) REVERT: D 227 ASP cc_start: 0.8632 (t0) cc_final: 0.8088 (t70) REVERT: D 257 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8217 (tm-30) REVERT: D 269 GLU cc_start: 0.8775 (pp20) cc_final: 0.7975 (pp20) REVERT: D 376 ARG cc_start: 0.8063 (ptp-110) cc_final: 0.7807 (ptp-110) REVERT: D 406 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.7725 (p90) REVERT: D 447 ASP cc_start: 0.8507 (p0) cc_final: 0.8136 (p0) outliers start: 30 outliers final: 23 residues processed: 273 average time/residue: 0.0948 time to fit residues: 37.8185 Evaluate side-chains 272 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 500 LYS Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain D residue 589 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 40 optimal weight: 3.9990 chunk 97 optimal weight: 50.0000 chunk 54 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.134581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.093878 restraints weight = 18168.384| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.86 r_work: 0.2874 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11544 Z= 0.205 Angle : 0.733 9.173 16256 Z= 0.404 Chirality : 0.044 0.186 1800 Planarity : 0.006 0.063 1508 Dihedral : 24.504 121.850 2824 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.67 % Favored : 94.12 % Rotamer: Outliers : 3.17 % Allowed : 24.10 % Favored : 72.74 % 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 (0.28), residues: 952 helix: 1.64 (0.27), residues: 379 sheet: -0.07 (0.48), residues: 113 loop : -1.40 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG D 337 TYR 0.023 0.002 TYR D 305 PHE 0.012 0.001 PHE C 179 TRP 0.008 0.001 TRP C 348 HIS 0.008 0.002 HIS D 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.21 (11528) covalent geometry : angle 0.73041 / 0.40 (16238) hydrogen bonds : bond 0.05289 / 3.56 ( 491) hydrogen bonds : angle 3.98801 / 2.75 ( 1245) metal coordination : bond 0.00480 / 0.25 ( 16) metal coordination : angle 1.97723 / 1.11 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 247 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 185 MET cc_start: 0.9332 (tpp) cc_final: 0.8385 (tpp) REVERT: C 223 CYS cc_start: 0.9104 (m) cc_final: 0.8782 (m) REVERT: C 238 ASN cc_start: 0.8527 (m-40) cc_final: 0.7528 (t0) REVERT: C 269 GLU cc_start: 0.8669 (pt0) cc_final: 0.8329 (pm20) REVERT: C 406 TYR cc_start: 0.7970 (OUTLIER) cc_final: 0.5816 (p90) REVERT: C 418 SER cc_start: 0.8869 (t) cc_final: 0.8351 (p) REVERT: C 456 MET cc_start: 0.8909 (ttm) cc_final: 0.8530 (ttm) REVERT: C 517 LYS cc_start: 0.9382 (ttpp) cc_final: 0.9171 (tppt) REVERT: D 132 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9039 (tt) REVERT: D 142 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8672 (mm-30) REVERT: D 154 GLU cc_start: 0.8954 (tp30) cc_final: 0.8461 (tp30) REVERT: D 227 ASP cc_start: 0.8716 (t0) cc_final: 0.8072 (t0) REVERT: D 257 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8188 (tm-30) REVERT: D 305 TYR cc_start: 0.9472 (t80) cc_final: 0.8986 (t80) REVERT: D 386 ARG cc_start: 0.8231 (tpt90) cc_final: 0.7963 (tpt90) REVERT: D 406 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7856 (p90) REVERT: D 447 ASP cc_start: 0.8514 (p0) cc_final: 0.8211 (p0) outliers start: 28 outliers final: 22 residues processed: 258 average time/residue: 0.0894 time to fit residues: 34.3073 Evaluate side-chains 265 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 240 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 500 LYS Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain D residue 589 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 16 optimal weight: 0.0670 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.136930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.096585 restraints weight = 18110.380| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.86 r_work: 0.2917 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11544 Z= 0.151 Angle : 0.695 8.356 16256 Z= 0.390 Chirality : 0.042 0.172 1800 Planarity : 0.005 0.062 1508 Dihedral : 24.407 121.246 2824 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.46 % Favored : 94.33 % Rotamer: Outliers : 2.71 % Allowed : 24.43 % Favored : 72.85 % 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: 0.02 (0.28), residues: 952 helix: 1.66 (0.27), residues: 378 sheet: 0.29 (0.51), residues: 101 loop : -1.51 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 236 TYR 0.022 0.001 TYR D 305 PHE 0.013 0.001 PHE C 135 TRP 0.008 0.001 TRP C 465 HIS 0.003 0.001 HIS D 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (11528) covalent geometry : angle 0.69315 / 0.39 (16238) hydrogen bonds : bond 0.04718 / 3.14 ( 491) hydrogen bonds : angle 3.91920 / 2.69 ( 1245) metal coordination : bond 0.00329 / 0.16 ( 16) metal coordination : angle 1.84494 / 1.03 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2481.02 seconds wall clock time: 43 minutes 23.22 seconds (2603.22 seconds total)