Starting phenix.real_space_refine on Wed Mar 4 04:08:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x67_22072/03_2026/6x67_22072.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x67_22072/03_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_22072/03_2026/6x67_22072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x67_22072/03_2026/6x67_22072.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x67_22072/03_2026/6x67_22072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x67_22072/03_2026/6x67_22072.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 2.21, per 1000 atoms: 0.20 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: 0.77 Conformation dependent library (CDL) restraints added in 393.3 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: 1.36 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: 1.45 Time building geometry restraints manager: 1.08 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=" C PRO C 288 " pdb=" N SER C 289 " ideal model delta sigma weight residual 1.331 1.239 0.093 1.38e-02 5.25e+03 4.51e+01 bond pdb=" O3' DT J 21 " pdb=" P DA J 22 " ideal model delta sigma weight residual 1.607 1.515 0.092 1.50e-02 4.44e+03 3.79e+01 bond pdb=" O3' DT K -23 " pdb=" P DT K -22 " ideal model delta sigma weight residual 1.607 1.691 -0.084 1.50e-02 4.44e+03 3.15e+01 bond pdb=" N SER D 289 " pdb=" CA SER D 289 " ideal model delta sigma weight residual 1.459 1.391 0.067 1.22e-02 6.72e+03 3.05e+01 bond pdb=" N TRP D 248 " pdb=" CA TRP D 248 " ideal model delta sigma weight residual 1.459 1.394 0.065 1.19e-02 7.06e+03 2.98e+01 ... (remaining 11523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.92: 15893 4.92 - 9.84: 310 9.84 - 14.76: 31 14.76 - 19.68: 3 19.68 - 24.60: 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 120.20 144.80 -24.60 1.50e+00 4.44e-01 2.69e+02 angle pdb=" C3' DT J 21 " pdb=" O3' DT J 21 " pdb=" P DA J 22 " ideal model delta sigma weight residual 120.20 101.85 18.35 1.50e+00 4.44e-01 1.50e+02 angle pdb=" O3' DT K -23 " pdb=" P DT K -22 " pdb=" O5' DT K -22 " ideal model delta sigma weight residual 104.00 118.83 -14.83 1.50e+00 4.44e-01 9.78e+01 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 angle pdb=" N ARG D 556 " pdb=" CA ARG D 556 " pdb=" C ARG D 556 " ideal model delta sigma weight residual 110.80 91.26 19.54 2.13e+00 2.20e-01 8.41e+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 - 0.120: 1487 0.120 - 0.239: 265 0.239 - 0.359: 42 0.359 - 0.478: 5 0.478 - 0.598: 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 2.35 -2.94 -0.60 2.00e-01 2.50e+01 8.94e+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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.830 Find NCS groups from input model: 0.100 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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= 0.974 Angle : 1.869 24.603 16256 Z= 1.225 Chirality : 0.096 0.598 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 covalent geometry : bond 0.01458 (11528) covalent geometry : angle 1.84002 (16238) hydrogen bonds : bond 0.18651 ( 491) hydrogen bonds : angle 6.47804 ( 1245) metal coordination : bond 0.26802 ( 16) metal coordination : angle 9.99432 ( 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 : 0.221 Fit side-chains 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: 0.8663 (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: 0.8511 (mt) REVERT: D 175 GLU cc_start: 0.7988 (tt0) cc_final: 0.7740 (tt0) REVERT: D 189 ARG cc_start: 0.8285 (mmm-85) cc_final: 0.7923 (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: 0.7849 (t80) REVERT: D 305 TYR cc_start: 0.8723 (t80) cc_final: 0.8192 (t80) REVERT: D 418 SER cc_start: 0.8456 (t) cc_final: 0.8148 (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: 0.8664 (p) outliers start: 2 outliers final: 0 residues processed: 417 average time/residue: 0.1136 time to fit residues: 63.5112 Evaluate side-chains 269 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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: 10.0000 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: 0.7980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 HIS D 505 ASN ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.140932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.102008 restraints weight = 17754.891| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.76 r_work: 0.3007 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11544 Z= 0.177 Angle : 0.770 8.772 16256 Z= 0.425 Chirality : 0.042 0.163 1800 Planarity : 0.004 0.041 1508 Dihedral : 24.164 121.739 2824 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.47 % Favored : 96.11 % Rotamer: Outliers : 2.83 % Allowed : 20.70 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.27), residues: 952 helix: 0.57 (0.27), residues: 379 sheet: 0.81 (0.48), residues: 108 loop : -0.60 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 277 TYR 0.020 0.002 TYR C 283 PHE 0.015 0.002 PHE C 395 TRP 0.017 0.002 TRP C 150 HIS 0.007 0.002 HIS D 487 Details of bonding type rmsd covalent geometry : bond 0.00408 (11528) covalent geometry : angle 0.76485 (16238) hydrogen bonds : bond 0.05841 ( 491) hydrogen bonds : angle 4.38589 ( 1245) metal coordination : bond 0.00677 ( 16) metal coordination : angle 2.81072 ( 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 343 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 318 time to evaluate : 0.295 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: symmetry clash REVERT: C 173 GLU cc_start: 0.8534 (pm20) cc_final: 0.8281 (mp0) REVERT: C 238 ASN cc_start: 0.8431 (m-40) cc_final: 0.7376 (t0) REVERT: C 376 ARG cc_start: 0.8061 (tmt170) cc_final: 0.7622 (ttt-90) REVERT: C 394 MET cc_start: 0.8294 (mtp) cc_final: 0.7857 (ttm) REVERT: C 418 SER cc_start: 0.8809 (t) cc_final: 0.8495 (p) REVERT: C 467 MET cc_start: 0.9021 (mmm) cc_final: 0.8771 (mmm) REVERT: C 554 LYS cc_start: 0.8898 (mmmm) cc_final: 0.8618 (tptp) REVERT: C 555 LYS cc_start: 0.9222 (mmtm) cc_final: 0.8822 (mptt) REVERT: C 586 ASN cc_start: 0.7664 (OUTLIER) cc_final: 0.7078 (m-40) REVERT: D 154 GLU cc_start: 0.8898 (tp30) cc_final: 0.8522 (tp30) REVERT: D 206 MET cc_start: 0.8834 (mmt) cc_final: 0.8550 (mmp) REVERT: D 227 ASP cc_start: 0.8305 (t0) cc_final: 0.7895 (t0) REVERT: D 305 TYR cc_start: 0.9331 (t80) cc_final: 0.9007 (t80) REVERT: D 342 ASN cc_start: 0.8865 (t0) cc_final: 0.8585 (t0) REVERT: D 409 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8311 (mttp) REVERT: D 417 LEU cc_start: 0.9095 (tp) cc_final: 0.8884 (tp) REVERT: D 438 TYR cc_start: 0.8303 (t80) cc_final: 0.7976 (t80) REVERT: D 441 GLN cc_start: 0.9440 (tt0) cc_final: 0.9158 (tt0) REVERT: D 447 ASP cc_start: 0.8691 (p0) cc_final: 0.8113 (p0) REVERT: D 452 MET cc_start: 0.8822 (mtp) cc_final: 0.8583 (mtp) outliers start: 25 outliers final: 11 residues processed: 330 average time/residue: 0.0986 time to fit residues: 46.1326 Evaluate side-chains 280 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 267 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 586 ASN Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 409 LYS Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 469 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN C 475 ASN ** C 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 GLN 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 = 0.3670 r_free = 0.3670 target = 0.137004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.096872 restraints weight = 18140.375| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.77 r_work: 0.2933 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11544 Z= 0.187 Angle : 0.716 7.675 16256 Z= 0.391 Chirality : 0.041 0.154 1800 Planarity : 0.004 0.041 1508 Dihedral : 24.228 131.982 2824 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.41 % Favored : 95.48 % Rotamer: Outliers : 4.30 % Allowed : 21.83 % 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: 0.09 (0.27), residues: 952 helix: 1.19 (0.27), residues: 371 sheet: 0.59 (0.46), residues: 108 loop : -1.00 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 277 TYR 0.019 0.002 TYR C 283 PHE 0.018 0.002 PHE C 251 TRP 0.009 0.001 TRP D 348 HIS 0.007 0.001 HIS D 487 Details of bonding type rmsd covalent geometry : bond 0.00442 (11528) covalent geometry : angle 0.71200 (16238) hydrogen bonds : bond 0.04939 ( 491) hydrogen bonds : angle 4.09645 ( 1245) metal coordination : bond 0.00486 ( 16) metal coordination : angle 2.34495 ( 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 323 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 285 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 132 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8999 (tt) REVERT: C 163 MET cc_start: 0.8912 (mtp) cc_final: 0.8689 (ptp) REVERT: C 173 GLU cc_start: 0.8681 (pm20) cc_final: 0.8375 (mp0) REVERT: C 225 ARG cc_start: 0.7704 (mmt-90) cc_final: 0.7371 (ttp-170) REVERT: C 227 ASP cc_start: 0.8785 (t0) cc_final: 0.8102 (p0) REVERT: C 238 ASN cc_start: 0.8404 (m-40) cc_final: 0.7356 (t0) REVERT: C 254 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8794 (mm-40) REVERT: C 269 GLU cc_start: 0.8712 (pt0) cc_final: 0.8056 (pm20) REVERT: C 376 ARG cc_start: 0.8177 (tmt170) cc_final: 0.7810 (ttt-90) REVERT: C 406 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.5464 (p90) REVERT: C 418 SER cc_start: 0.8851 (t) cc_final: 0.7684 (p) REVERT: C 434 GLN cc_start: 0.9091 (tp40) cc_final: 0.8689 (tp40) REVERT: C 437 MET cc_start: 0.9252 (mmm) cc_final: 0.9043 (tpp) REVERT: C 494 GLU cc_start: 0.8523 (mp0) cc_final: 0.8142 (mp0) REVERT: C 554 LYS cc_start: 0.8898 (mmmm) cc_final: 0.8610 (tptp) REVERT: C 555 LYS cc_start: 0.9212 (mmtm) cc_final: 0.8934 (mptt) REVERT: D 154 GLU cc_start: 0.8949 (tp30) cc_final: 0.8536 (tp30) REVERT: D 227 ASP cc_start: 0.8523 (t0) cc_final: 0.8071 (t70) REVERT: D 305 TYR cc_start: 0.9392 (t80) cc_final: 0.8831 (t80) REVERT: D 332 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9103 (mm) REVERT: D 337 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8044 (tpp80) REVERT: D 406 TYR cc_start: 0.7977 (p90) cc_final: 0.7497 (p90) REVERT: D 438 TYR cc_start: 0.8764 (t80) cc_final: 0.8377 (t80) REVERT: D 447 ASP cc_start: 0.8664 (p0) cc_final: 0.8137 (p0) REVERT: D 452 MET cc_start: 0.8812 (mtp) cc_final: 0.8468 (mtp) outliers start: 38 outliers final: 21 residues processed: 304 average time/residue: 0.0967 time to fit residues: 42.0880 Evaluate side-chains 278 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 253 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 303 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 532 ILE Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain D residue 137 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 297 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 337 ARG 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 Chi-restraints excluded: chain D residue 498 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.0370 chunk 3 optimal weight: 0.5980 chunk 73 optimal weight: 0.0970 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN ** C 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.141251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.101600 restraints weight = 18237.226| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.85 r_work: 0.3014 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11544 Z= 0.144 Angle : 0.674 8.756 16256 Z= 0.365 Chirality : 0.038 0.158 1800 Planarity : 0.004 0.044 1508 Dihedral : 23.977 126.761 2824 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.31 % Favored : 95.59 % Rotamer: Outliers : 2.49 % Allowed : 23.42 % Favored : 74.10 % 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: 0.06 (0.27), residues: 952 helix: 1.37 (0.27), residues: 377 sheet: 0.51 (0.45), residues: 106 loop : -1.21 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 277 TYR 0.014 0.001 TYR C 283 PHE 0.012 0.001 PHE C 482 TRP 0.009 0.001 TRP C 465 HIS 0.001 0.000 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00330 (11528) covalent geometry : angle 0.67043 (16238) hydrogen bonds : bond 0.04102 ( 491) hydrogen bonds : angle 3.84951 ( 1245) metal coordination : bond 0.00362 ( 16) metal coordination : angle 2.31805 ( 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 299 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 277 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 154 GLU cc_start: 0.8922 (tp30) cc_final: 0.8428 (tp30) REVERT: C 173 GLU cc_start: 0.8582 (pm20) cc_final: 0.8262 (mp0) REVERT: C 238 ASN cc_start: 0.8384 (m-40) cc_final: 0.7393 (t0) REVERT: C 254 GLN cc_start: 0.9197 (mm-40) cc_final: 0.8760 (mm-40) REVERT: C 269 GLU cc_start: 0.8743 (pt0) cc_final: 0.8306 (pm20) REVERT: C 376 ARG cc_start: 0.8134 (tmt170) cc_final: 0.7789 (ttt-90) REVERT: C 406 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.5535 (p90) REVERT: C 418 SER cc_start: 0.8895 (t) cc_final: 0.8450 (p) REVERT: C 437 MET cc_start: 0.9267 (mmm) cc_final: 0.9039 (tpp) REVERT: C 554 LYS cc_start: 0.8937 (mmmm) cc_final: 0.8650 (tptp) REVERT: C 555 LYS cc_start: 0.9232 (mmtm) cc_final: 0.8899 (mptt) REVERT: D 142 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8762 (mm-30) REVERT: D 154 GLU cc_start: 0.8987 (tp30) cc_final: 0.8543 (tp30) REVERT: D 227 ASP cc_start: 0.8374 (t0) cc_final: 0.7926 (t70) REVERT: D 269 GLU cc_start: 0.8601 (pp20) cc_final: 0.7937 (pp20) REVERT: D 406 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.7495 (p90) REVERT: D 414 VAL cc_start: 0.9085 (p) cc_final: 0.8837 (m) REVERT: D 447 ASP cc_start: 0.8521 (p0) cc_final: 0.8042 (p0) REVERT: D 524 LEU cc_start: 0.9489 (tp) cc_final: 0.9213 (tp) outliers start: 22 outliers final: 16 residues processed: 286 average time/residue: 0.0878 time to fit residues: 36.6100 Evaluate side-chains 283 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 265 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 176 ILE 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 383 LYS Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 535 ILE 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 297 MET 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 426 ILE Chi-restraints excluded: chain D residue 469 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 93 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 76 optimal weight: 0.0570 chunk 85 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN D 118 GLN D 531 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.140009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.099865 restraints weight = 18052.736| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.84 r_work: 0.2992 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11544 Z= 0.150 Angle : 0.661 6.207 16256 Z= 0.360 Chirality : 0.038 0.151 1800 Planarity : 0.004 0.049 1508 Dihedral : 23.952 127.742 2824 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.52 % Favored : 95.38 % Rotamer: Outliers : 3.51 % Allowed : 23.08 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.27), residues: 952 helix: 1.63 (0.27), residues: 378 sheet: 0.44 (0.46), residues: 108 loop : -1.29 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 236 TYR 0.019 0.001 TYR D 305 PHE 0.012 0.001 PHE D 514 TRP 0.007 0.001 TRP C 465 HIS 0.004 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00349 (11528) covalent geometry : angle 0.65762 (16238) hydrogen bonds : bond 0.04086 ( 491) hydrogen bonds : angle 3.75947 ( 1245) metal coordination : bond 0.00241 ( 16) metal coordination : angle 2.01859 ( 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 308 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 277 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 173 GLU cc_start: 0.8666 (pm20) cc_final: 0.8334 (mp0) REVERT: C 198 ASP cc_start: 0.9218 (m-30) cc_final: 0.8968 (m-30) REVERT: C 225 ARG cc_start: 0.7737 (ttm-80) cc_final: 0.7044 (ttp-170) REVERT: C 227 ASP cc_start: 0.8714 (t0) cc_final: 0.8500 (t0) REVERT: C 238 ASN cc_start: 0.8420 (m-40) cc_final: 0.7464 (t0) REVERT: C 254 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8865 (mm-40) REVERT: C 269 GLU cc_start: 0.8726 (pt0) cc_final: 0.8299 (pm20) REVERT: C 380 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8730 (mm-30) REVERT: C 383 LYS cc_start: 0.8860 (mttt) cc_final: 0.8578 (mtmm) REVERT: C 406 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.5577 (p90) REVERT: C 418 SER cc_start: 0.9009 (t) cc_final: 0.8566 (p) REVERT: C 428 GLU cc_start: 0.8982 (pm20) cc_final: 0.8715 (pm20) REVERT: C 435 MET cc_start: 0.9236 (tpp) cc_final: 0.8963 (tpp) REVERT: C 437 MET cc_start: 0.9258 (mmm) cc_final: 0.9004 (tpp) REVERT: C 440 ASN cc_start: 0.8993 (m-40) cc_final: 0.8780 (m110) REVERT: C 494 GLU cc_start: 0.8542 (mp0) cc_final: 0.8110 (mp0) REVERT: C 554 LYS cc_start: 0.8922 (mmmm) cc_final: 0.8648 (tptp) REVERT: C 555 LYS cc_start: 0.9234 (mmtm) cc_final: 0.8877 (mptt) REVERT: C 584 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8347 (tm-30) REVERT: D 154 GLU cc_start: 0.8999 (tp30) cc_final: 0.8541 (tp30) REVERT: D 305 TYR cc_start: 0.9404 (t80) cc_final: 0.9128 (t80) REVERT: D 332 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9011 (mm) REVERT: D 376 ARG cc_start: 0.8327 (ptp-110) cc_final: 0.7964 (ptp-110) REVERT: D 406 TYR cc_start: 0.8135 (OUTLIER) cc_final: 0.7509 (p90) REVERT: D 447 ASP cc_start: 0.8550 (p0) cc_final: 0.8108 (p0) REVERT: D 524 LEU cc_start: 0.9530 (tp) cc_final: 0.9218 (tp) REVERT: D 535 ILE cc_start: 0.8859 (tt) cc_final: 0.8608 (tt) outliers start: 31 outliers final: 21 residues processed: 290 average time/residue: 0.0860 time to fit residues: 36.7457 Evaluate side-chains 277 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 253 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 176 ILE 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 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 469 LEU Chi-restraints excluded: chain C residue 535 ILE 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 297 MET Chi-restraints excluded: chain D residue 332 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 426 ILE Chi-restraints excluded: chain D residue 469 LEU 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: 0.7980 chunk 45 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 6 optimal weight: 0.0870 chunk 7 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 480 ASN C 534 ASN ** C 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.141127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.102339 restraints weight = 17991.032| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.73 r_work: 0.3028 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11544 Z= 0.140 Angle : 0.642 5.867 16256 Z= 0.351 Chirality : 0.037 0.152 1800 Planarity : 0.005 0.059 1508 Dihedral : 23.861 129.401 2824 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.41 % Favored : 95.48 % Rotamer: Outliers : 3.62 % Allowed : 23.76 % Favored : 72.62 % 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: 0.18 (0.28), residues: 952 helix: 1.68 (0.27), residues: 379 sheet: 0.42 (0.46), residues: 108 loop : -1.33 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 236 TYR 0.016 0.001 TYR D 305 PHE 0.011 0.001 PHE C 482 TRP 0.007 0.001 TRP C 465 HIS 0.003 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00321 (11528) covalent geometry : angle 0.63929 (16238) hydrogen bonds : bond 0.03831 ( 491) hydrogen bonds : angle 3.68457 ( 1245) metal coordination : bond 0.00224 ( 16) metal coordination : angle 1.97443 ( 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 318 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 286 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 185 MET cc_start: 0.9225 (tpp) cc_final: 0.8532 (tpp) REVERT: C 198 ASP cc_start: 0.9198 (m-30) cc_final: 0.8968 (m-30) REVERT: C 238 ASN cc_start: 0.8359 (m-40) cc_final: 0.7466 (t0) REVERT: C 254 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8883 (mm-40) REVERT: C 269 GLU cc_start: 0.8682 (pt0) cc_final: 0.7954 (pm20) REVERT: C 380 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8609 (mm-30) REVERT: C 383 LYS cc_start: 0.8949 (mttt) cc_final: 0.8662 (mttp) REVERT: C 406 TYR cc_start: 0.7827 (OUTLIER) cc_final: 0.5819 (p90) REVERT: C 418 SER cc_start: 0.8881 (t) cc_final: 0.8414 (p) REVERT: C 428 GLU cc_start: 0.8968 (pm20) cc_final: 0.8712 (pm20) REVERT: C 435 MET cc_start: 0.9167 (tpp) cc_final: 0.8915 (tpp) REVERT: C 494 GLU cc_start: 0.8453 (mp0) cc_final: 0.8055 (mp0) REVERT: C 517 LYS cc_start: 0.9243 (ttpp) cc_final: 0.8890 (tppt) REVERT: C 555 LYS cc_start: 0.9239 (mmtm) cc_final: 0.8997 (mptt) REVERT: C 584 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8223 (tm-30) REVERT: D 154 GLU cc_start: 0.8969 (tp30) cc_final: 0.8511 (tp30) REVERT: D 305 TYR cc_start: 0.9326 (t80) cc_final: 0.8746 (t80) REVERT: D 332 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8951 (mm) REVERT: D 372 ARG cc_start: 0.8875 (ttm110) cc_final: 0.7614 (mtt90) REVERT: D 376 ARG cc_start: 0.8317 (ptp-110) cc_final: 0.7913 (ptp-110) REVERT: D 406 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.7550 (p90) REVERT: D 501 LYS cc_start: 0.8570 (tttm) cc_final: 0.8363 (tttm) REVERT: D 524 LEU cc_start: 0.9525 (tp) cc_final: 0.9174 (tp) outliers start: 32 outliers final: 19 residues processed: 300 average time/residue: 0.0922 time to fit residues: 40.0129 Evaluate side-chains 277 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 255 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 322 VAL 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 469 LEU Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 469 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 98 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 440 ASN ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 ASN D 192 ASN D 440 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.136432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.096573 restraints weight = 18254.002| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.71 r_work: 0.2943 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11544 Z= 0.202 Angle : 0.705 8.469 16256 Z= 0.380 Chirality : 0.041 0.154 1800 Planarity : 0.005 0.072 1508 Dihedral : 23.954 131.170 2824 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.57 % Favored : 94.33 % Rotamer: Outliers : 3.73 % Allowed : 25.00 % Favored : 71.27 % 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: 0.17 (0.28), residues: 952 helix: 1.73 (0.28), residues: 378 sheet: 0.10 (0.46), residues: 111 loop : -1.31 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 236 TYR 0.014 0.002 TYR D 305 PHE 0.012 0.001 PHE C 179 TRP 0.006 0.001 TRP C 465 HIS 0.006 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00476 (11528) covalent geometry : angle 0.70219 (16238) hydrogen bonds : bond 0.04609 ( 491) hydrogen bonds : angle 3.80447 ( 1245) metal coordination : bond 0.00458 ( 16) metal coordination : angle 1.95731 ( 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 290 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 257 time to evaluate : 0.339 Fit side-chains REVERT: C 198 ASP cc_start: 0.9193 (m-30) cc_final: 0.8939 (m-30) REVERT: C 238 ASN cc_start: 0.8397 (m-40) cc_final: 0.7566 (t0) REVERT: C 269 GLU cc_start: 0.8725 (pt0) cc_final: 0.8157 (pm20) REVERT: C 283 TYR cc_start: 0.9398 (t80) cc_final: 0.9137 (t80) REVERT: C 406 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.5913 (p90) REVERT: C 418 SER cc_start: 0.8873 (t) cc_final: 0.8395 (p) REVERT: C 434 GLN cc_start: 0.9111 (tp40) cc_final: 0.8680 (tp40) REVERT: C 435 MET cc_start: 0.9197 (tpp) cc_final: 0.8965 (tpp) REVERT: C 456 MET cc_start: 0.8916 (ttm) cc_final: 0.8537 (ttm) REVERT: C 584 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8095 (tm-30) REVERT: D 154 GLU cc_start: 0.8944 (tp30) cc_final: 0.8446 (tp30) REVERT: D 194 MET cc_start: 0.8101 (mmm) cc_final: 0.7855 (mmm) REVERT: D 227 ASP cc_start: 0.8632 (t0) cc_final: 0.7991 (t0) REVERT: D 332 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.8980 (mm) REVERT: D 368 VAL cc_start: 0.9172 (t) cc_final: 0.8921 (p) REVERT: D 376 ARG cc_start: 0.8404 (ptp-110) cc_final: 0.8017 (ptp-110) REVERT: D 406 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7789 (p90) REVERT: D 501 LYS cc_start: 0.8657 (tttm) cc_final: 0.8428 (tttm) REVERT: D 524 LEU cc_start: 0.9569 (tp) cc_final: 0.9332 (tp) outliers start: 33 outliers final: 26 residues processed: 274 average time/residue: 0.0850 time to fit residues: 34.4608 Evaluate side-chains 280 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 251 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 210 SER 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 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 469 LEU Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 332 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 426 ILE Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 498 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 54 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 92 optimal weight: 40.0000 chunk 91 optimal weight: 50.0000 chunk 65 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 440 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.139062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.100255 restraints weight = 18351.225| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.74 r_work: 0.3001 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11544 Z= 0.152 Angle : 0.676 8.017 16256 Z= 0.367 Chirality : 0.039 0.155 1800 Planarity : 0.005 0.056 1508 Dihedral : 23.847 132.023 2824 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.94 % Favored : 94.96 % Rotamer: Outliers : 2.94 % Allowed : 26.47 % Favored : 70.59 % 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: 0.11 (0.28), residues: 952 helix: 1.69 (0.27), residues: 379 sheet: 0.41 (0.48), residues: 102 loop : -1.43 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 372 TYR 0.014 0.001 TYR D 305 PHE 0.010 0.001 PHE D 514 TRP 0.007 0.001 TRP C 465 HIS 0.004 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00354 (11528) covalent geometry : angle 0.67321 (16238) hydrogen bonds : bond 0.04053 ( 491) hydrogen bonds : angle 3.68921 ( 1245) metal coordination : bond 0.00278 ( 16) metal coordination : angle 1.91834 ( 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 302 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 276 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: C 185 MET cc_start: 0.9310 (tpp) cc_final: 0.8631 (tpp) REVERT: C 198 ASP cc_start: 0.9164 (m-30) cc_final: 0.8928 (m-30) REVERT: C 238 ASN cc_start: 0.8277 (m-40) cc_final: 0.7444 (t0) REVERT: C 269 GLU cc_start: 0.8674 (pt0) cc_final: 0.8170 (pm20) REVERT: C 283 TYR cc_start: 0.9340 (t80) cc_final: 0.9079 (t80) REVERT: C 406 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.6700 (p90) REVERT: C 413 MET cc_start: 0.8022 (pmm) cc_final: 0.7131 (ptp) REVERT: C 418 SER cc_start: 0.8759 (t) cc_final: 0.8405 (p) REVERT: C 428 GLU cc_start: 0.8970 (pm20) cc_final: 0.8734 (pm20) REVERT: C 435 MET cc_start: 0.9173 (tpp) cc_final: 0.8831 (ttp) REVERT: C 456 MET cc_start: 0.8930 (ttm) cc_final: 0.8619 (ttm) REVERT: C 494 GLU cc_start: 0.8505 (mp0) cc_final: 0.8187 (mp0) REVERT: C 517 LYS cc_start: 0.9237 (ttpp) cc_final: 0.8851 (tppt) REVERT: C 584 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8189 (tm-30) REVERT: D 154 GLU cc_start: 0.8960 (tp30) cc_final: 0.8472 (tp30) REVERT: D 194 MET cc_start: 0.7883 (mmm) cc_final: 0.7583 (mmm) REVERT: D 259 TYR cc_start: 0.9000 (t80) cc_final: 0.8774 (t80) REVERT: D 332 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9005 (mm) REVERT: D 376 ARG cc_start: 0.8279 (ptp-110) cc_final: 0.7791 (ptp-110) REVERT: D 406 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7373 (p90) REVERT: D 458 CYS cc_start: 0.9096 (t) cc_final: 0.8682 (p) REVERT: D 501 LYS cc_start: 0.8627 (tttm) cc_final: 0.8410 (tttm) REVERT: D 516 ARG cc_start: 0.8737 (ttm-80) cc_final: 0.8189 (ttm-80) REVERT: D 524 LEU cc_start: 0.9508 (tp) cc_final: 0.9159 (tp) REVERT: D 535 ILE cc_start: 0.8944 (tt) cc_final: 0.8737 (tt) outliers start: 26 outliers final: 19 residues processed: 288 average time/residue: 0.0855 time to fit residues: 36.5716 Evaluate side-chains 279 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 257 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 220 LEU 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 404 VAL Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 367 ILE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 43 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 20 optimal weight: 0.4980 chunk 94 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 91 optimal weight: 30.0000 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 440 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.136743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.096951 restraints weight = 18505.599| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.74 r_work: 0.2938 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.5269 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= 0.175 Angle : 0.703 7.745 16256 Z= 0.379 Chirality : 0.040 0.144 1800 Planarity : 0.005 0.055 1508 Dihedral : 23.868 133.448 2824 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.99 % Favored : 93.91 % Rotamer: Outliers : 3.96 % Allowed : 26.70 % Favored : 69.34 % 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: 0.01 (0.28), residues: 952 helix: 1.68 (0.27), residues: 380 sheet: 0.45 (0.50), residues: 96 loop : -1.58 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 372 TYR 0.015 0.001 TYR C 259 PHE 0.011 0.001 PHE D 514 TRP 0.007 0.001 TRP D 348 HIS 0.006 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00413 (11528) covalent geometry : angle 0.70077 (16238) hydrogen bonds : bond 0.04359 ( 491) hydrogen bonds : angle 3.73076 ( 1245) metal coordination : bond 0.00347 ( 16) metal coordination : angle 1.91936 ( 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 289 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 254 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: C 198 ASP cc_start: 0.9202 (m-30) cc_final: 0.8960 (m-30) REVERT: C 238 ASN cc_start: 0.8334 (m-40) cc_final: 0.7553 (t0) REVERT: C 269 GLU cc_start: 0.8742 (pt0) cc_final: 0.8304 (pm20) REVERT: C 283 TYR cc_start: 0.9375 (t80) cc_final: 0.9134 (t80) REVERT: C 401 LEU cc_start: 0.9545 (mt) cc_final: 0.9248 (mt) REVERT: C 406 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.6351 (p90) REVERT: C 413 MET cc_start: 0.7951 (pmm) cc_final: 0.7275 (ptt) REVERT: C 418 SER cc_start: 0.8835 (t) cc_final: 0.8424 (p) REVERT: C 434 GLN cc_start: 0.9102 (tp40) cc_final: 0.8650 (tp40) REVERT: C 435 MET cc_start: 0.9066 (tpp) cc_final: 0.8730 (ttp) REVERT: C 584 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8152 (tm-30) REVERT: D 154 GLU cc_start: 0.8956 (tp30) cc_final: 0.8319 (tt0) REVERT: D 194 MET cc_start: 0.7983 (mmm) cc_final: 0.7732 (mmm) REVERT: D 227 ASP cc_start: 0.8661 (t0) cc_final: 0.8178 (t70) REVERT: D 259 TYR cc_start: 0.9022 (t80) cc_final: 0.8782 (t80) REVERT: D 332 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.8999 (mm) REVERT: D 368 VAL cc_start: 0.9160 (t) cc_final: 0.8827 (p) REVERT: D 376 ARG cc_start: 0.7780 (ptp-110) cc_final: 0.7384 (ptp-110) REVERT: D 406 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.7470 (p90) REVERT: D 501 LYS cc_start: 0.8648 (tttm) cc_final: 0.8411 (tttm) REVERT: D 516 ARG cc_start: 0.8719 (ttm-80) cc_final: 0.8241 (ttm-80) REVERT: D 524 LEU cc_start: 0.9543 (tp) cc_final: 0.9239 (tp) outliers start: 35 outliers final: 26 residues processed: 274 average time/residue: 0.0890 time to fit residues: 35.8960 Evaluate side-chains 273 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 244 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 231 ILE 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 404 VAL Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 401 LEU 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 519 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 40 optimal weight: 0.5980 chunk 97 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 58 optimal weight: 0.0270 overall best weight: 1.1240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.138467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.098920 restraints weight = 18510.826| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.77 r_work: 0.2971 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11544 Z= 0.158 Angle : 0.699 8.556 16256 Z= 0.376 Chirality : 0.039 0.147 1800 Planarity : 0.005 0.057 1508 Dihedral : 23.801 134.258 2824 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.46 % Favored : 94.33 % Rotamer: Outliers : 3.51 % Allowed : 26.92 % Favored : 69.57 % 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 (0.28), residues: 952 helix: 1.62 (0.27), residues: 381 sheet: 0.61 (0.54), residues: 87 loop : -1.60 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 337 TYR 0.014 0.001 TYR C 259 PHE 0.013 0.001 PHE C 139 TRP 0.008 0.001 TRP D 348 HIS 0.004 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00370 (11528) covalent geometry : angle 0.69632 (16238) hydrogen bonds : bond 0.04085 ( 491) hydrogen bonds : angle 3.69515 ( 1245) metal coordination : bond 0.00278 ( 16) metal coordination : angle 1.87632 ( 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 296 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 265 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: C 154 GLU cc_start: 0.9008 (tp30) cc_final: 0.8701 (tp30) REVERT: C 185 MET cc_start: 0.9288 (tpp) cc_final: 0.8591 (tpp) REVERT: C 225 ARG cc_start: 0.7655 (ttm-80) cc_final: 0.7257 (mtm110) REVERT: C 237 GLU cc_start: 0.9295 (mm-30) cc_final: 0.9086 (tp30) REVERT: C 238 ASN cc_start: 0.8316 (m-40) cc_final: 0.7563 (t0) REVERT: C 269 GLU cc_start: 0.8743 (pt0) cc_final: 0.8313 (pm20) REVERT: C 283 TYR cc_start: 0.9324 (t80) cc_final: 0.9114 (t80) REVERT: C 394 MET cc_start: 0.8075 (ttm) cc_final: 0.7616 (ttp) REVERT: C 401 LEU cc_start: 0.9539 (mt) cc_final: 0.9237 (mt) REVERT: C 406 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.6529 (p90) REVERT: C 413 MET cc_start: 0.8146 (pmm) cc_final: 0.7665 (ptp) REVERT: C 418 SER cc_start: 0.8798 (t) cc_final: 0.8383 (p) REVERT: C 428 GLU cc_start: 0.8940 (pm20) cc_final: 0.8705 (pm20) REVERT: C 435 MET cc_start: 0.9062 (tpp) cc_final: 0.8714 (ttp) REVERT: C 494 GLU cc_start: 0.8565 (mp0) cc_final: 0.8245 (mp0) REVERT: C 517 LYS cc_start: 0.9253 (ttpp) cc_final: 0.8862 (tppt) REVERT: C 584 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8383 (tm-30) REVERT: D 142 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8804 (mm-30) REVERT: D 154 GLU cc_start: 0.8951 (tp30) cc_final: 0.8456 (tp30) REVERT: D 194 MET cc_start: 0.7835 (mmm) cc_final: 0.7571 (mmm) REVERT: D 259 TYR cc_start: 0.8974 (t80) cc_final: 0.8761 (t80) REVERT: D 332 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9032 (mm) REVERT: D 368 VAL cc_start: 0.9074 (t) cc_final: 0.8762 (p) REVERT: D 376 ARG cc_start: 0.7787 (ptp-110) cc_final: 0.7246 (ptp-110) REVERT: D 406 TYR cc_start: 0.8303 (OUTLIER) cc_final: 0.7421 (p90) REVERT: D 458 CYS cc_start: 0.9076 (t) cc_final: 0.8609 (p) REVERT: D 501 LYS cc_start: 0.8591 (tttm) cc_final: 0.8379 (tttm) REVERT: D 516 ARG cc_start: 0.8728 (ttm-80) cc_final: 0.8222 (ttm-80) REVERT: D 524 LEU cc_start: 0.9531 (tp) cc_final: 0.9219 (tp) outliers start: 31 outliers final: 25 residues processed: 282 average time/residue: 0.0826 time to fit residues: 34.7920 Evaluate side-chains 283 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 231 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 358 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 469 LEU Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 401 LEU 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 519 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.138892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.099049 restraints weight = 18617.362| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.79 r_work: 0.2974 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11544 Z= 0.156 Angle : 0.694 7.890 16256 Z= 0.374 Chirality : 0.039 0.139 1800 Planarity : 0.005 0.057 1508 Dihedral : 23.772 135.340 2824 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.67 % Favored : 94.12 % Rotamer: Outliers : 3.39 % Allowed : 27.49 % Favored : 69.12 % 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: -0.12 (0.28), residues: 952 helix: 1.58 (0.27), residues: 385 sheet: 0.40 (0.55), residues: 89 loop : -1.67 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 225 TYR 0.012 0.001 TYR C 259 PHE 0.012 0.001 PHE C 482 TRP 0.009 0.001 TRP D 348 HIS 0.004 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00365 (11528) covalent geometry : angle 0.69187 (16238) hydrogen bonds : bond 0.04005 ( 491) hydrogen bonds : angle 3.68384 ( 1245) metal coordination : bond 0.00259 ( 16) metal coordination : angle 1.86767 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2253.39 seconds wall clock time: 39 minutes 23.97 seconds (2363.97 seconds total)