Starting phenix.real_space_refine on Mon Jul 28 22:00:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x67_22072/07_2025/6x67_22072.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x67_22072/07_2025/6x67_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6x67_22072/07_2025/6x67_22072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x67_22072/07_2025/6x67_22072.map" model { file = "/net/cci-nas-00/data/ceres_data/6x67_22072/07_2025/6x67_22072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x67_22072/07_2025/6x67_22072.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.00, per 1000 atoms: 0.64 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: 2.54 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 4.37 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: 4.52 Time building geometry restraints manager: 2.98 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.240 Process input model: 33.500 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.970 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.045 0.011 TRP D 150 HIS 0.010 0.003 HIS D 487 PHE 0.022 0.006 PHE C 502 TYR 0.038 0.008 TYR D 406 ARG 0.006 0.001 ARG C 222 Details of bonding type rmsd hydrogen bonds : bond 0.18651 ( 491) hydrogen bonds : angle 6.47804 ( 1245) metal coordination : bond 0.26802 ( 16) metal coordination : angle 9.99432 ( 18) covalent geometry : bond 0.01458 (11528) covalent geometry : angle 1.84002 (16238) *********************** 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 : 0.915 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: 0.7934 (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: 0.8455 (t) cc_final: 0.8147 (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: 0.3035 time to fit residues: 169.1815 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 : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.140827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.101614 restraints weight = 17653.871| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.76 r_work: 0.3003 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3277 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= 0.179 Angle : 0.770 8.813 16256 Z= 0.425 Chirality : 0.042 0.165 1800 Planarity : 0.004 0.040 1508 Dihedral : 24.165 120.642 2824 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.47 % Favored : 96.11 % Rotamer: Outliers : 3.17 % Allowed : 20.25 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.27), residues: 952 helix: 0.58 (0.27), residues: 379 sheet: 0.77 (0.48), residues: 110 loop : -0.58 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 150 HIS 0.008 0.002 HIS D 487 PHE 0.014 0.002 PHE C 395 TYR 0.021 0.002 TYR C 283 ARG 0.008 0.001 ARG D 277 Details of bonding type rmsd hydrogen bonds : bond 0.05730 ( 491) hydrogen bonds : angle 4.38052 ( 1245) metal coordination : bond 0.00944 ( 16) metal coordination : angle 2.57218 ( 18) covalent geometry : bond 0.00410 (11528) covalent geometry : angle 0.76523 (16238) *********************** 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 346 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 318 time to evaluate : 1.108 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: 0.8527 (pm20) cc_final: 0.8269 (mp0) REVERT: C 238 ASN cc_start: 0.8424 (m-40) cc_final: 0.7414 (t0) REVERT: C 394 MET cc_start: 0.8298 (mtp) cc_final: 0.7843 (ttm) REVERT: C 418 SER cc_start: 0.8844 (t) cc_final: 0.8501 (p) REVERT: C 440 ASN cc_start: 0.8926 (m-40) cc_final: 0.8712 (m110) REVERT: C 467 MET cc_start: 0.9045 (mmm) cc_final: 0.8796 (mmm) REVERT: C 554 LYS cc_start: 0.8899 (mmmm) cc_final: 0.8618 (tptp) REVERT: C 555 LYS cc_start: 0.9225 (mmtm) cc_final: 0.8829 (mptt) REVERT: C 586 ASN cc_start: 0.7678 (OUTLIER) cc_final: 0.7060 (m-40) REVERT: D 154 GLU cc_start: 0.8886 (tp30) cc_final: 0.8466 (tp30) REVERT: D 206 MET cc_start: 0.8820 (mmt) cc_final: 0.8517 (mmp) REVERT: D 227 ASP cc_start: 0.8309 (t0) cc_final: 0.7900 (t0) REVERT: D 305 TYR cc_start: 0.9332 (t80) cc_final: 0.9003 (t80) REVERT: D 342 ASN cc_start: 0.8857 (t0) cc_final: 0.8523 (t0) REVERT: D 417 LEU cc_start: 0.9075 (tp) cc_final: 0.8861 (tp) REVERT: D 438 TYR cc_start: 0.8319 (t80) cc_final: 0.7987 (t80) REVERT: D 441 GLN cc_start: 0.9447 (tt0) cc_final: 0.9164 (tt0) REVERT: D 447 ASP cc_start: 0.8701 (p0) cc_final: 0.8102 (p0) REVERT: D 452 MET cc_start: 0.8825 (mtp) cc_final: 0.8587 (mtp) outliers start: 28 outliers final: 12 residues processed: 332 average time/residue: 0.2497 time to fit residues: 115.8019 Evaluate side-chains 275 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 262 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 289 SER Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 469 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 104 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 D 434 GLN D 487 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.136298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.096084 restraints weight = 18108.531| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.75 r_work: 0.2919 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11544 Z= 0.199 Angle : 0.722 7.748 16256 Z= 0.395 Chirality : 0.041 0.152 1800 Planarity : 0.005 0.045 1508 Dihedral : 24.235 130.625 2824 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.41 % Favored : 95.48 % Rotamer: Outliers : 3.96 % Allowed : 22.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.27), residues: 952 helix: 1.18 (0.27), residues: 371 sheet: 0.54 (0.46), residues: 108 loop : -1.01 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 348 HIS 0.007 0.002 HIS D 487 PHE 0.011 0.002 PHE C 482 TYR 0.020 0.002 TYR C 283 ARG 0.006 0.001 ARG D 277 Details of bonding type rmsd hydrogen bonds : bond 0.05043 ( 491) hydrogen bonds : angle 4.11398 ( 1245) metal coordination : bond 0.00507 ( 16) metal coordination : angle 2.34906 ( 18) covalent geometry : bond 0.00468 (11528) covalent geometry : angle 0.71797 (16238) *********************** 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 317 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 282 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 132 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9010 (tt) REVERT: C 163 MET cc_start: 0.8900 (mtp) cc_final: 0.8682 (ptp) REVERT: C 173 GLU cc_start: 0.8664 (pm20) cc_final: 0.8357 (mp0) REVERT: C 198 ASP cc_start: 0.9131 (m-30) cc_final: 0.8881 (m-30) REVERT: C 225 ARG cc_start: 0.7753 (mmt-90) cc_final: 0.7438 (ttp-170) REVERT: C 227 ASP cc_start: 0.8815 (t0) cc_final: 0.8113 (p0) REVERT: C 238 ASN cc_start: 0.8417 (m-40) cc_final: 0.7374 (t0) REVERT: C 254 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8749 (mm-40) REVERT: C 269 GLU cc_start: 0.8731 (pt0) cc_final: 0.8157 (pm20) REVERT: C 275 ARG cc_start: 0.9101 (mtp-110) cc_final: 0.8638 (mtp-110) REVERT: C 322 VAL cc_start: 0.9114 (m) cc_final: 0.8911 (m) REVERT: C 380 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8772 (mm-30) REVERT: C 406 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.5396 (p90) REVERT: C 418 SER cc_start: 0.8853 (t) cc_final: 0.7642 (p) REVERT: C 437 MET cc_start: 0.9286 (mmm) cc_final: 0.9064 (tpp) REVERT: C 494 GLU cc_start: 0.8588 (mp0) cc_final: 0.8227 (mp0) REVERT: C 503 MET cc_start: 0.9342 (mmm) cc_final: 0.9128 (mtp) REVERT: C 554 LYS cc_start: 0.8909 (mmmm) cc_final: 0.8613 (tptp) REVERT: C 555 LYS cc_start: 0.9206 (mmtm) cc_final: 0.8923 (mptt) REVERT: D 142 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8832 (mm-30) REVERT: D 154 GLU cc_start: 0.8956 (tp30) cc_final: 0.8539 (tp30) REVERT: D 227 ASP cc_start: 0.8614 (t0) cc_final: 0.8080 (t70) REVERT: D 305 TYR cc_start: 0.9420 (t80) cc_final: 0.8776 (t80) REVERT: D 332 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9108 (mm) REVERT: D 376 ARG cc_start: 0.8665 (ptp-170) cc_final: 0.8437 (ptp-110) REVERT: D 406 TYR cc_start: 0.8019 (p90) cc_final: 0.7596 (p90) REVERT: D 447 ASP cc_start: 0.8672 (p0) cc_final: 0.8174 (p0) REVERT: D 452 MET cc_start: 0.8796 (mtp) cc_final: 0.8452 (mtp) outliers start: 35 outliers final: 22 residues processed: 301 average time/residue: 0.2223 time to fit residues: 95.0279 Evaluate side-chains 272 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 247 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 182 ILE 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 367 ILE Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 469 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 10 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 23 optimal weight: 0.0570 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- 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 441 GLN ** C 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.140086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.101040 restraints weight = 17890.196| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.74 r_work: 0.3012 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4468 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= 0.143 Angle : 0.678 8.360 16256 Z= 0.368 Chirality : 0.039 0.161 1800 Planarity : 0.004 0.048 1508 Dihedral : 23.991 126.234 2824 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.62 % Favored : 95.27 % Rotamer: Outliers : 2.60 % Allowed : 23.64 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.27), residues: 952 helix: 1.39 (0.27), residues: 378 sheet: 0.55 (0.46), residues: 105 loop : -1.25 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 465 HIS 0.002 0.000 HIS D 193 PHE 0.011 0.001 PHE C 135 TYR 0.014 0.001 TYR C 283 ARG 0.004 0.000 ARG D 277 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 491) hydrogen bonds : angle 3.84760 ( 1245) metal coordination : bond 0.00335 ( 16) metal coordination : angle 2.29988 ( 18) covalent geometry : bond 0.00330 (11528) covalent geometry : angle 0.67434 (16238) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 283 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 173 GLU cc_start: 0.8572 (pm20) cc_final: 0.8251 (mp0) REVERT: C 198 ASP cc_start: 0.9086 (m-30) cc_final: 0.8818 (m-30) REVERT: C 238 ASN cc_start: 0.8410 (m-40) cc_final: 0.7403 (t0) REVERT: C 269 GLU cc_start: 0.8731 (pt0) cc_final: 0.8285 (pm20) REVERT: C 322 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8878 (p) REVERT: C 406 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.5474 (p90) REVERT: C 418 SER cc_start: 0.8910 (t) cc_final: 0.8425 (p) REVERT: C 437 MET cc_start: 0.9257 (mmm) cc_final: 0.9018 (tpp) REVERT: C 494 GLU cc_start: 0.8574 (mp0) cc_final: 0.8176 (mp0) REVERT: C 554 LYS cc_start: 0.8927 (mmmm) cc_final: 0.8646 (tptp) REVERT: C 555 LYS cc_start: 0.9238 (mmtm) cc_final: 0.8907 (mptt) REVERT: D 142 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8757 (mm-30) REVERT: D 154 GLU cc_start: 0.8941 (tp30) cc_final: 0.8479 (tp30) REVERT: D 269 GLU cc_start: 0.8590 (pp20) cc_final: 0.7884 (pp20) REVERT: D 376 ARG cc_start: 0.8620 (ptp-170) cc_final: 0.8378 (ptp-110) REVERT: D 406 TYR cc_start: 0.7919 (OUTLIER) cc_final: 0.7422 (p90) REVERT: D 414 VAL cc_start: 0.9098 (p) cc_final: 0.8857 (m) REVERT: D 447 ASP cc_start: 0.8508 (p0) cc_final: 0.8038 (p0) REVERT: D 520 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8689 (mp0) REVERT: D 524 LEU cc_start: 0.9518 (tp) cc_final: 0.9257 (tp) REVERT: D 535 ILE cc_start: 0.8902 (tt) cc_final: 0.8564 (tt) outliers start: 23 outliers final: 16 residues processed: 293 average time/residue: 0.2375 time to fit residues: 99.4523 Evaluate side-chains 270 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 251 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 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 404 VAL 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 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 Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 500 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 96 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 534 ASN D 192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.136083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.095476 restraints weight = 17984.343| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.82 r_work: 0.2894 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4673 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= 0.177 Angle : 0.682 7.053 16256 Z= 0.371 Chirality : 0.040 0.151 1800 Planarity : 0.005 0.050 1508 Dihedral : 24.037 126.594 2824 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.04 % Favored : 94.85 % Rotamer: Outliers : 3.96 % Allowed : 23.53 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.28), residues: 952 helix: 1.61 (0.27), residues: 378 sheet: 0.47 (0.48), residues: 103 loop : -1.37 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 465 HIS 0.005 0.001 HIS D 193 PHE 0.011 0.001 PHE C 179 TYR 0.018 0.001 TYR D 305 ARG 0.006 0.001 ARG C 236 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 491) hydrogen bonds : angle 3.83870 ( 1245) metal coordination : bond 0.00336 ( 16) metal coordination : angle 2.03635 ( 18) covalent geometry : bond 0.00417 (11528) covalent geometry : angle 0.67899 (16238) *********************** 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 302 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 267 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 163 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8590 (ptp) REVERT: C 173 GLU cc_start: 0.8685 (pm20) cc_final: 0.8441 (pm20) REVERT: C 237 GLU cc_start: 0.9254 (mm-30) cc_final: 0.9052 (mm-30) REVERT: C 238 ASN cc_start: 0.8420 (m-40) cc_final: 0.7470 (t0) REVERT: C 254 GLN cc_start: 0.9332 (mm-40) cc_final: 0.8937 (mm-40) REVERT: C 269 GLU cc_start: 0.8680 (pt0) cc_final: 0.8230 (pm20) REVERT: C 275 ARG cc_start: 0.9143 (mtp-110) cc_final: 0.8611 (mtp-110) REVERT: C 306 MET cc_start: 0.9263 (tpp) cc_final: 0.8976 (tpt) REVERT: C 322 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8962 (p) REVERT: C 406 TYR cc_start: 0.7733 (OUTLIER) cc_final: 0.5462 (p90) REVERT: C 418 SER cc_start: 0.9057 (t) cc_final: 0.8612 (p) REVERT: C 434 GLN cc_start: 0.9031 (tp40) cc_final: 0.8635 (tp40) REVERT: C 435 MET cc_start: 0.9230 (tpp) cc_final: 0.8941 (tpp) REVERT: C 437 MET cc_start: 0.9278 (mmm) cc_final: 0.9069 (tpp) REVERT: C 475 ASN cc_start: 0.8919 (m-40) cc_final: 0.8684 (m-40) REVERT: C 554 LYS cc_start: 0.8966 (mmmm) cc_final: 0.8677 (tptm) REVERT: C 555 LYS cc_start: 0.9234 (mmtm) cc_final: 0.8993 (mptt) REVERT: C 584 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8380 (tm-30) REVERT: D 142 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8862 (mm-30) REVERT: D 154 GLU cc_start: 0.8982 (tp30) cc_final: 0.8499 (tp30) REVERT: D 194 MET cc_start: 0.7985 (mmm) cc_final: 0.7708 (mmm) REVERT: D 206 MET cc_start: 0.8846 (mmt) cc_final: 0.8427 (mmt) REVERT: D 227 ASP cc_start: 0.8657 (t0) cc_final: 0.7977 (t0) REVERT: D 305 TYR cc_start: 0.9487 (t80) cc_final: 0.8830 (t80) REVERT: D 332 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9026 (mm) REVERT: D 372 ARG cc_start: 0.8879 (ttm110) cc_final: 0.7732 (mtt90) REVERT: D 376 ARG cc_start: 0.8556 (ptp-170) cc_final: 0.8285 (ptp-110) REVERT: D 406 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.7639 (p90) REVERT: D 418 SER cc_start: 0.9243 (t) cc_final: 0.9023 (p) REVERT: D 447 ASP cc_start: 0.8491 (p0) cc_final: 0.8149 (p0) REVERT: D 452 MET cc_start: 0.8627 (mtp) cc_final: 0.8300 (mtp) REVERT: D 520 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8656 (mp0) REVERT: D 524 LEU cc_start: 0.9590 (tp) cc_final: 0.9365 (tp) outliers start: 35 outliers final: 22 residues processed: 283 average time/residue: 0.2246 time to fit residues: 91.1988 Evaluate side-chains 282 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 255 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 163 MET 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 532 ILE 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 303 THR 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 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 Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 500 LYS Chi-restraints excluded: chain D residue 508 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 100 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 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 440 ASN D 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.136506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.096946 restraints weight = 18142.577| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.73 r_work: 0.2941 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11544 Z= 0.176 Angle : 0.673 6.822 16256 Z= 0.366 Chirality : 0.039 0.152 1800 Planarity : 0.005 0.055 1508 Dihedral : 23.977 127.457 2824 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.15 % Favored : 94.75 % Rotamer: Outliers : 4.19 % Allowed : 23.30 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.28), residues: 952 helix: 1.68 (0.28), residues: 378 sheet: 0.32 (0.47), residues: 108 loop : -1.37 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 465 HIS 0.005 0.001 HIS D 193 PHE 0.010 0.001 PHE D 251 TYR 0.015 0.001 TYR D 305 ARG 0.006 0.000 ARG C 236 Details of bonding type rmsd hydrogen bonds : bond 0.04410 ( 491) hydrogen bonds : angle 3.79134 ( 1245) metal coordination : bond 0.00332 ( 16) metal coordination : angle 2.00875 ( 18) covalent geometry : bond 0.00416 (11528) covalent geometry : angle 0.66997 (16238) *********************** 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 296 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 259 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 238 ASN cc_start: 0.8432 (m-40) cc_final: 0.7441 (t0) REVERT: C 254 GLN cc_start: 0.9302 (mm-40) cc_final: 0.8846 (mm-40) REVERT: C 269 GLU cc_start: 0.8721 (pt0) cc_final: 0.8311 (pm20) REVERT: C 275 ARG cc_start: 0.9108 (mtp-110) cc_final: 0.8615 (mtp-110) REVERT: C 306 MET cc_start: 0.9236 (tpp) cc_final: 0.8800 (tpt) REVERT: C 406 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.5508 (p90) REVERT: C 418 SER cc_start: 0.8908 (t) cc_final: 0.8458 (p) REVERT: C 434 GLN cc_start: 0.9053 (tp40) cc_final: 0.8622 (tp40) REVERT: C 494 GLU cc_start: 0.8521 (mp0) cc_final: 0.8161 (mp0) REVERT: C 517 LYS cc_start: 0.9237 (ttpp) cc_final: 0.8800 (tppt) REVERT: C 554 LYS cc_start: 0.8976 (mmmm) cc_final: 0.8732 (tptp) REVERT: C 555 LYS cc_start: 0.9234 (mmtm) cc_final: 0.8882 (mptt) REVERT: C 584 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8255 (tm-30) REVERT: D 154 GLU cc_start: 0.9001 (tp30) cc_final: 0.8524 (tp30) REVERT: D 194 MET cc_start: 0.8073 (mmm) cc_final: 0.7838 (mmm) REVERT: D 227 ASP cc_start: 0.8650 (t0) cc_final: 0.8160 (t70) REVERT: D 332 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.8988 (mm) REVERT: D 372 ARG cc_start: 0.8914 (ttm110) cc_final: 0.7673 (mtt90) REVERT: D 376 ARG cc_start: 0.8559 (ptp-170) cc_final: 0.8231 (ptp-110) REVERT: D 406 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.7605 (p90) REVERT: D 447 ASP cc_start: 0.8482 (p0) cc_final: 0.8164 (p0) REVERT: D 452 MET cc_start: 0.8669 (mtp) cc_final: 0.8339 (mtp) REVERT: D 520 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8681 (mp0) REVERT: D 524 LEU cc_start: 0.9585 (tp) cc_final: 0.9361 (tp) outliers start: 37 outliers final: 24 residues processed: 278 average time/residue: 0.2194 time to fit residues: 87.1587 Evaluate side-chains 264 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 162 SER Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 303 THR 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 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 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 Chi-restraints excluded: chain D residue 500 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 85 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 chunk 92 optimal weight: 50.0000 chunk 18 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.139066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.099732 restraints weight = 18143.972| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.74 r_work: 0.2992 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11544 Z= 0.145 Angle : 0.664 9.366 16256 Z= 0.360 Chirality : 0.038 0.152 1800 Planarity : 0.005 0.094 1508 Dihedral : 23.868 129.273 2824 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.04 % Favored : 94.85 % Rotamer: Outliers : 2.94 % Allowed : 25.68 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.28), residues: 952 helix: 1.75 (0.28), residues: 378 sheet: 0.21 (0.47), residues: 110 loop : -1.46 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 465 HIS 0.003 0.001 HIS D 193 PHE 0.010 0.001 PHE D 251 TYR 0.016 0.001 TYR C 363 ARG 0.010 0.000 ARG C 225 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 491) hydrogen bonds : angle 3.69241 ( 1245) metal coordination : bond 0.00267 ( 16) metal coordination : angle 1.98189 ( 18) covalent geometry : bond 0.00334 (11528) covalent geometry : angle 0.66120 (16238) *********************** 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 281 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 255 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 225 ARG cc_start: 0.7862 (ttm-80) cc_final: 0.7482 (mtp180) REVERT: C 238 ASN cc_start: 0.8423 (m-40) cc_final: 0.7428 (t0) REVERT: C 254 GLN cc_start: 0.9284 (mm-40) cc_final: 0.8812 (mm-40) REVERT: C 269 GLU cc_start: 0.8708 (pt0) cc_final: 0.8194 (pm20) REVERT: C 306 MET cc_start: 0.9242 (tpp) cc_final: 0.8921 (tpt) REVERT: C 418 SER cc_start: 0.8892 (t) cc_final: 0.8465 (p) REVERT: C 456 MET cc_start: 0.8893 (ttm) cc_final: 0.8528 (ttm) REVERT: C 555 LYS cc_start: 0.9241 (mmtm) cc_final: 0.9006 (mptt) REVERT: C 584 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8157 (tm-30) REVERT: D 154 GLU cc_start: 0.8975 (tp30) cc_final: 0.8489 (tp30) REVERT: D 194 MET cc_start: 0.7881 (mmm) cc_final: 0.7592 (mmm) REVERT: D 305 TYR cc_start: 0.9271 (t80) cc_final: 0.9025 (t80) REVERT: D 332 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8964 (mm) REVERT: D 372 ARG cc_start: 0.8891 (ttm110) cc_final: 0.7669 (mtt90) REVERT: D 376 ARG cc_start: 0.8506 (ptp-170) cc_final: 0.8069 (ptp-110) REVERT: D 406 TYR cc_start: 0.8153 (OUTLIER) cc_final: 0.7549 (p90) REVERT: D 447 ASP cc_start: 0.8441 (p0) cc_final: 0.8109 (p0) REVERT: D 452 MET cc_start: 0.8613 (mtp) cc_final: 0.8285 (mtp) REVERT: D 524 LEU cc_start: 0.9552 (tp) cc_final: 0.9278 (tp) outliers start: 26 outliers final: 19 residues processed: 267 average time/residue: 0.2357 time to fit residues: 92.0087 Evaluate side-chains 265 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 244 time to evaluate : 1.387 ------------------------------------------------------------------------------- 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 176 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 370 THR 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 324 LEU 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 Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 500 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 440 ASN C 475 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.137291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.097663 restraints weight = 18519.899| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.76 r_work: 0.2948 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11544 Z= 0.160 Angle : 0.668 9.293 16256 Z= 0.361 Chirality : 0.039 0.146 1800 Planarity : 0.005 0.057 1508 Dihedral : 23.886 131.593 2824 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.15 % Favored : 94.75 % Rotamer: Outliers : 2.94 % Allowed : 26.58 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.28), residues: 952 helix: 1.71 (0.27), residues: 379 sheet: 0.29 (0.48), residues: 110 loop : -1.48 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 465 HIS 0.005 0.001 HIS D 193 PHE 0.017 0.001 PHE D 251 TYR 0.013 0.001 TYR D 305 ARG 0.005 0.000 ARG C 236 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 491) hydrogen bonds : angle 3.70623 ( 1245) metal coordination : bond 0.00304 ( 16) metal coordination : angle 1.94034 ( 18) covalent geometry : bond 0.00374 (11528) covalent geometry : angle 0.66523 (16238) *********************** 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 277 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 251 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 198 ASP cc_start: 0.9208 (m-30) cc_final: 0.8846 (m-30) REVERT: C 238 ASN cc_start: 0.8344 (m-40) cc_final: 0.7475 (t0) REVERT: C 269 GLU cc_start: 0.8698 (pt0) cc_final: 0.8283 (pm20) REVERT: C 306 MET cc_start: 0.9274 (tpp) cc_final: 0.8913 (tpt) REVERT: C 406 TYR cc_start: 0.7662 (OUTLIER) cc_final: 0.6758 (p90) REVERT: C 418 SER cc_start: 0.8825 (t) cc_final: 0.8386 (p) REVERT: C 434 GLN cc_start: 0.9056 (tp40) cc_final: 0.8563 (tp40) REVERT: C 435 MET cc_start: 0.9071 (tpp) cc_final: 0.8765 (ttp) REVERT: C 475 ASN cc_start: 0.8812 (m-40) cc_final: 0.8394 (m110) REVERT: C 584 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8020 (tm-30) REVERT: D 154 GLU cc_start: 0.8959 (tp30) cc_final: 0.8457 (tp30) REVERT: D 194 MET cc_start: 0.7970 (mmm) cc_final: 0.7734 (mmm) REVERT: D 227 ASP cc_start: 0.8602 (t0) cc_final: 0.8099 (t70) REVERT: D 305 TYR cc_start: 0.9338 (t80) cc_final: 0.9030 (t80) REVERT: D 332 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8955 (mm) REVERT: D 368 VAL cc_start: 0.9057 (t) cc_final: 0.8764 (p) REVERT: D 372 ARG cc_start: 0.8906 (ttm110) cc_final: 0.8568 (ttm110) REVERT: D 376 ARG cc_start: 0.8318 (ptp-170) cc_final: 0.7857 (ptp-110) REVERT: D 406 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.7650 (p90) REVERT: D 447 ASP cc_start: 0.8427 (p0) cc_final: 0.8155 (p0) REVERT: D 452 MET cc_start: 0.8564 (mtp) cc_final: 0.8206 (mtp) REVERT: D 524 LEU cc_start: 0.9559 (tp) cc_final: 0.9285 (tp) outliers start: 26 outliers final: 21 residues processed: 266 average time/residue: 0.2535 time to fit residues: 97.0699 Evaluate side-chains 264 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 176 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 422 GLU 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 282 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 418 SER Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 500 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 55 optimal weight: 0.0570 chunk 7 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.135628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.095780 restraints weight = 18697.492| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.76 r_work: 0.2917 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.5218 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= 0.187 Angle : 0.691 8.569 16256 Z= 0.374 Chirality : 0.040 0.157 1800 Planarity : 0.005 0.057 1508 Dihedral : 23.878 133.268 2824 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.46 % Favored : 94.43 % Rotamer: Outliers : 3.62 % Allowed : 25.68 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.28), residues: 952 helix: 1.60 (0.27), residues: 379 sheet: 0.22 (0.48), residues: 115 loop : -1.48 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 465 HIS 0.006 0.001 HIS D 193 PHE 0.011 0.001 PHE D 514 TYR 0.015 0.001 TYR D 305 ARG 0.010 0.001 ARG C 225 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 491) hydrogen bonds : angle 3.78285 ( 1245) metal coordination : bond 0.00400 ( 16) metal coordination : angle 1.98133 ( 18) covalent geometry : bond 0.00439 (11528) covalent geometry : angle 0.68857 (16238) *********************** 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 271 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: C 198 ASP cc_start: 0.9193 (m-30) cc_final: 0.8866 (m-30) REVERT: C 238 ASN cc_start: 0.8371 (m-40) cc_final: 0.7542 (t0) REVERT: C 269 GLU cc_start: 0.8692 (pt0) cc_final: 0.8371 (pm20) REVERT: C 306 MET cc_start: 0.9297 (tpp) cc_final: 0.8868 (tpt) REVERT: C 406 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.7022 (p90) REVERT: C 418 SER cc_start: 0.8849 (t) cc_final: 0.8373 (p) REVERT: C 434 GLN cc_start: 0.9119 (tp40) cc_final: 0.8663 (tp40) REVERT: C 435 MET cc_start: 0.9078 (tpp) cc_final: 0.8760 (ttp) REVERT: C 475 ASN cc_start: 0.8884 (m-40) cc_final: 0.8359 (m110) REVERT: D 154 GLU cc_start: 0.8954 (tp30) cc_final: 0.8302 (tt0) REVERT: D 194 MET cc_start: 0.8028 (mmm) cc_final: 0.7753 (mmm) REVERT: D 227 ASP cc_start: 0.8666 (t0) cc_final: 0.8161 (t70) REVERT: D 305 TYR cc_start: 0.9426 (t80) cc_final: 0.9012 (t80) REVERT: D 332 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8954 (mm) REVERT: D 368 VAL cc_start: 0.9170 (t) cc_final: 0.8900 (p) REVERT: D 406 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.7777 (p90) REVERT: D 447 ASP cc_start: 0.8459 (p0) cc_final: 0.8201 (p0) REVERT: D 452 MET cc_start: 0.8612 (mtp) cc_final: 0.8241 (mtp) REVERT: D 524 LEU cc_start: 0.9559 (tp) cc_final: 0.9319 (tp) outliers start: 32 outliers final: 25 residues processed: 258 average time/residue: 0.1981 time to fit residues: 75.1876 Evaluate side-chains 267 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 156 SER Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 224 LEU 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 363 TYR Chi-restraints excluded: chain C residue 370 THR 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 83 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 8 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.139290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.099570 restraints weight = 18493.481| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.77 r_work: 0.2983 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11544 Z= 0.147 Angle : 0.671 8.622 16256 Z= 0.362 Chirality : 0.038 0.154 1800 Planarity : 0.005 0.058 1508 Dihedral : 23.768 134.022 2824 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.36 % Favored : 94.54 % Rotamer: Outliers : 2.83 % Allowed : 26.81 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.28), residues: 952 helix: 1.61 (0.27), residues: 381 sheet: 0.34 (0.49), residues: 110 loop : -1.58 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 465 HIS 0.003 0.001 HIS D 193 PHE 0.017 0.001 PHE C 139 TYR 0.012 0.001 TYR D 305 ARG 0.006 0.000 ARG C 236 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 491) hydrogen bonds : angle 3.68066 ( 1245) metal coordination : bond 0.00254 ( 16) metal coordination : angle 1.90909 ( 18) covalent geometry : bond 0.00339 (11528) covalent geometry : angle 0.66788 (16238) ********************** 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 271 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 246 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: C 185 MET cc_start: 0.9288 (tpp) cc_final: 0.8630 (tpp) REVERT: C 198 ASP cc_start: 0.9260 (m-30) cc_final: 0.8951 (m-30) REVERT: C 238 ASN cc_start: 0.8302 (m-40) cc_final: 0.7412 (t0) REVERT: C 269 GLU cc_start: 0.8669 (pt0) cc_final: 0.8225 (pm20) REVERT: C 306 MET cc_start: 0.9270 (tpp) cc_final: 0.8964 (tpt) REVERT: C 406 TYR cc_start: 0.7695 (OUTLIER) cc_final: 0.6811 (p90) REVERT: C 418 SER cc_start: 0.8746 (t) cc_final: 0.8301 (p) REVERT: C 435 MET cc_start: 0.9071 (tpp) cc_final: 0.8750 (ttp) REVERT: C 456 MET cc_start: 0.8881 (ttm) cc_final: 0.8513 (ttm) REVERT: C 475 ASN cc_start: 0.8752 (m-40) cc_final: 0.8382 (m110) REVERT: D 154 GLU cc_start: 0.8942 (tp30) cc_final: 0.8445 (tp30) REVERT: D 194 MET cc_start: 0.7823 (mmm) cc_final: 0.7429 (mmm) REVERT: D 259 TYR cc_start: 0.9043 (t80) cc_final: 0.8634 (t80) REVERT: D 305 TYR cc_start: 0.9417 (t80) cc_final: 0.8548 (t80) REVERT: D 332 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8892 (mm) REVERT: D 368 VAL cc_start: 0.8953 (t) cc_final: 0.8656 (p) REVERT: D 376 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7498 (ptp-110) REVERT: D 406 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.7627 (p90) REVERT: D 447 ASP cc_start: 0.8428 (p0) cc_final: 0.8136 (p0) REVERT: D 452 MET cc_start: 0.8561 (mtp) cc_final: 0.8233 (mtp) REVERT: D 524 LEU cc_start: 0.9521 (tp) cc_final: 0.9248 (tp) outliers start: 25 outliers final: 18 residues processed: 259 average time/residue: 0.2172 time to fit residues: 82.1088 Evaluate side-chains 260 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 238 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 486 SER 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 332 LEU Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 376 ARG Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 500 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 91 optimal weight: 30.0000 chunk 90 optimal weight: 0.0470 chunk 11 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.3284 ------------------------------------------------------------------------------- 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 480 ASN D 192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.137871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.098310 restraints weight = 18381.074| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.74 r_work: 0.2959 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.5480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11544 Z= 0.163 Angle : 0.686 8.517 16256 Z= 0.369 Chirality : 0.039 0.149 1800 Planarity : 0.005 0.058 1508 Dihedral : 23.795 135.193 2824 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.46 % Favored : 94.33 % Rotamer: Outliers : 3.05 % Allowed : 26.81 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.28), residues: 952 helix: 1.67 (0.27), residues: 378 sheet: 0.33 (0.50), residues: 111 loop : -1.57 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 465 HIS 0.005 0.001 HIS D 193 PHE 0.016 0.001 PHE C 139 TYR 0.013 0.001 TYR D 305 ARG 0.006 0.000 ARG C 225 Details of bonding type rmsd hydrogen bonds : bond 0.04168 ( 491) hydrogen bonds : angle 3.71312 ( 1245) metal coordination : bond 0.00410 ( 16) metal coordination : angle 1.87196 ( 18) covalent geometry : bond 0.00382 (11528) covalent geometry : angle 0.68359 (16238) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5525.49 seconds wall clock time: 99 minutes 52.12 seconds (5992.12 seconds total)