Starting phenix.real_space_refine on Wed Feb 4 13:50:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vkw_65145/02_2026/9vkw_65145.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vkw_65145/02_2026/9vkw_65145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vkw_65145/02_2026/9vkw_65145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vkw_65145/02_2026/9vkw_65145.map" model { file = "/net/cci-nas-00/data/ceres_data/9vkw_65145/02_2026/9vkw_65145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vkw_65145/02_2026/9vkw_65145.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.047 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 3 5.49 5 S 59 5.16 5 C 6831 2.51 5 N 1821 2.21 5 O 2017 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10735 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 4169 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 21, 'TRANS': 476} Chain breaks: 4 Chain: "B" Number of atoms: 4385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4385 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 20, 'TRANS': 519} Chain breaks: 2 Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 795 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 568 Classifications: {'peptide': 72} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "D" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 763 Classifications: {'peptide': 93} Link IDs: {'TRANS': 92} Chain breaks: 1 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {' ZN': 1, 'ACO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1462 SG CYS A 303 30.746 45.692 67.965 1.00 91.05 S ATOM 1488 SG CYS A 306 33.751 47.955 67.871 1.00 90.63 S ATOM 1644 SG CYS A 323 31.169 50.215 68.997 1.00105.29 S ATOM 5984 SG CYS B 266 71.447 40.604 73.217 1.00151.56 S ATOM 6002 SG CYS B 269 74.078 38.942 71.683 1.00154.78 S ATOM 6186 SG CYS B 294 70.504 37.953 69.447 1.00135.79 S ATOM 6850 SG CYS B 376 67.557 28.698 92.936 1.00146.57 S ATOM 7059 SG CYS B 402 67.306 32.371 90.615 1.00132.31 S ATOM 6106 SG CYS B 283 61.122 49.086 75.859 1.00138.03 S ATOM 6124 SG CYS B 286 61.503 47.573 79.029 1.00149.01 S ATOM 6322 SG CYS B 310 58.052 48.132 78.013 1.00130.54 S Time building chain proxies: 2.66, per 1000 atoms: 0.25 Number of scatterers: 10735 At special positions: 0 Unit cell: (97.3943, 92.5728, 118.609, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 59 16.00 P 3 15.00 O 2017 8.00 N 1821 7.00 C 6831 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS B 94 " distance=2.07 Simple disulfide: pdb=" SG CYS B 320 " - pdb=" SG CYS B 323 " distance=2.04 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 343 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 657.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 306 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 319 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 323 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 303 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 291 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 294 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 269 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 266 " pdb=" ZN B 802 " pdb="ZN ZN B 802 " - pdb=" ND1 HIS B 399 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 376 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 402 " pdb=" ZN B 803 " pdb="ZN ZN B 803 " - pdb=" SG CYS B 310 " pdb="ZN ZN B 803 " - pdb=" SG CYS B 283 " pdb="ZN ZN B 803 " - pdb=" SG CYS B 286 " Number of angles added : 6 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2498 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 9 sheets defined 49.3% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 127 through 142 removed outlier: 3.577A pdb=" N LEU A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 153 through 167 Processing helix chain 'A' and resid 189 through 199 Proline residue: A 195 - end of helix Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 218 through 228 Processing helix chain 'A' and resid 228 through 237 Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 312 through 321 Processing helix chain 'A' and resid 351 through 361 Processing helix chain 'A' and resid 423 through 426 removed outlier: 4.275A pdb=" N GLN A 426 " --> pdb=" O PRO A 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 423 through 426' Processing helix chain 'A' and resid 429 through 445 Processing helix chain 'A' and resid 456 through 486 removed outlier: 3.975A pdb=" N THR A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG A 484 " --> pdb=" O ASP A 480 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 507 Processing helix chain 'A' and resid 509 through 521 Processing helix chain 'A' and resid 545 through 558 removed outlier: 4.407A pdb=" N ILE A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU A 550 " --> pdb=" O TRP A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 removed outlier: 3.668A pdb=" N LEU A 569 " --> pdb=" O TYR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 594 removed outlier: 4.259A pdb=" N ALA A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 690 removed outlier: 4.379A pdb=" N LYS A 684 " --> pdb=" O TYR A 680 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A 685 " --> pdb=" O GLN A 681 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE A 690 " --> pdb=" O VAL A 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.600A pdb=" N SER B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 140 Processing helix chain 'B' and resid 161 through 173 Processing helix chain 'B' and resid 174 through 179 removed outlier: 7.009A pdb=" N ASN B 177 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL B 179 " --> pdb=" O PRO B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 202 removed outlier: 3.806A pdb=" N TYR B 194 " --> pdb=" O GLN B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 228 removed outlier: 3.624A pdb=" N ILE B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 252 Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 307 through 313 Processing helix chain 'B' and resid 342 through 347 Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 399 through 407 Processing helix chain 'B' and resid 416 through 423 removed outlier: 4.325A pdb=" N ASN B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 465 Processing helix chain 'B' and resid 496 through 511 removed outlier: 3.698A pdb=" N ALA B 500 " --> pdb=" O PRO B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 534 removed outlier: 4.295A pdb=" N ALA B 519 " --> pdb=" O PRO B 515 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY B 534 " --> pdb=" O ARG B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 602 removed outlier: 3.813A pdb=" N ARG B 571 " --> pdb=" O GLU B 567 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL B 600 " --> pdb=" O VAL B 596 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS B 601 " --> pdb=" O PHE B 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 16 Processing helix chain 'C' and resid 17 through 22 removed outlier: 3.567A pdb=" N ASP C 22 " --> pdb=" O LEU C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 42 removed outlier: 3.548A pdb=" N CYS C 26 " --> pdb=" O ASP C 22 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU C 27 " --> pdb=" O HIS C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 98 removed outlier: 3.569A pdb=" N ARG C 55 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 72 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 187 removed outlier: 3.620A pdb=" N THR E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 204 removed outlier: 3.751A pdb=" N ASN E 204 " --> pdb=" O MET E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 227 No H-bonds generated for 'chain 'E' and resid 225 through 227' Processing helix chain 'E' and resid 228 through 244 removed outlier: 4.381A pdb=" N GLU E 244 " --> pdb=" O LYS E 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 46 removed outlier: 3.729A pdb=" N ASP D 21 " --> pdb=" O LYS D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 53 removed outlier: 4.438A pdb=" N ASN D 50 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 110 removed outlier: 3.615A pdb=" N VAL D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 119 removed outlier: 3.571A pdb=" N ILE E 222 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE E 220 " --> pdb=" O ILE A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 275 through 276 removed outlier: 6.124A pdb=" N VAL A 276 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 331 through 336 removed outlier: 7.149A pdb=" N VAL A 341 " --> pdb=" O ILE A 333 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG A 335 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLU A 383 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N PHE A 400 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLU A 385 " --> pdb=" O PHE A 398 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N PHE A 398 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N CYS A 418 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 523 through 524 Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.785A pdb=" N THR B 68 " --> pdb=" O THR B 78 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR B 78 " --> pdb=" O THR B 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 280 through 282 Processing sheet with id=AA7, first strand: chain 'B' and resid 330 through 331 Processing sheet with id=AA8, first strand: chain 'B' and resid 351 through 352 Processing sheet with id=AA9, first strand: chain 'B' and resid 409 through 411 removed outlier: 4.025A pdb=" N TYR B 409 " --> pdb=" O PHE B 434 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.27: 1759 1.27 - 1.41: 2832 1.41 - 1.55: 6289 1.55 - 1.70: 9 1.70 - 1.84: 83 Bond restraints: 10972 Sorted by residual: bond pdb=" C2B ACO A 902 " pdb=" C3B ACO A 902 " ideal model delta sigma weight residual 1.527 1.316 0.211 1.20e-02 6.94e+03 3.10e+02 bond pdb=" C1B ACO A 902 " pdb=" N9A ACO A 902 " ideal model delta sigma weight residual 1.459 1.306 0.153 1.00e-02 1.00e+04 2.35e+02 bond pdb=" C1B ACO A 902 " pdb=" O4B ACO A 902 " ideal model delta sigma weight residual 1.416 1.575 -0.159 1.40e-02 5.10e+03 1.30e+02 bond pdb=" C5A ACO A 902 " pdb=" N7A ACO A 902 " ideal model delta sigma weight residual 1.387 1.274 0.113 1.00e-02 1.00e+04 1.28e+02 bond pdb=" CAP ACO A 902 " pdb=" OAP ACO A 902 " ideal model delta sigma weight residual 1.418 1.316 0.102 1.00e-02 1.00e+04 1.03e+02 ... (remaining 10967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.15: 14750 5.15 - 10.31: 38 10.31 - 15.46: 11 15.46 - 20.62: 3 20.62 - 25.77: 1 Bond angle restraints: 14803 Sorted by residual: angle pdb=" C9P ACO A 902 " pdb=" CAP ACO A 902 " pdb=" CBP ACO A 902 " ideal model delta sigma weight residual 114.53 129.42 -14.89 1.00e+00 1.00e+00 2.22e+02 angle pdb=" C ACO A 902 " pdb=" S1P ACO A 902 " pdb=" C2P ACO A 902 " ideal model delta sigma weight residual 101.25 114.03 -12.78 1.00e+00 1.00e+00 1.63e+02 angle pdb=" P1A ACO A 902 " pdb=" O3A ACO A 902 " pdb=" P2A ACO A 902 " ideal model delta sigma weight residual 136.83 125.38 11.45 1.00e+00 1.00e+00 1.31e+02 angle pdb=" C1B ACO A 902 " pdb=" N9A ACO A 902 " pdb=" C4A ACO A 902 " ideal model delta sigma weight residual 126.88 147.36 -20.48 1.80e+00 3.09e-01 1.30e+02 angle pdb=" N9A ACO A 902 " pdb=" C1B ACO A 902 " pdb=" O4B ACO A 902 " ideal model delta sigma weight residual 108.36 121.74 -13.38 1.26e+00 6.30e-01 1.13e+02 ... (remaining 14798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5609 17.96 - 35.92: 773 35.92 - 53.89: 205 53.89 - 71.85: 45 71.85 - 89.81: 22 Dihedral angle restraints: 6654 sinusoidal: 2807 harmonic: 3847 Sorted by residual: dihedral pdb=" CA GLU B 359 " pdb=" C GLU B 359 " pdb=" N PRO B 360 " pdb=" CA PRO B 360 " ideal model delta harmonic sigma weight residual -180.00 -135.27 -44.73 0 5.00e+00 4.00e-02 8.00e+01 dihedral pdb=" CA TYR A 120 " pdb=" C TYR A 120 " pdb=" N ASP A 121 " pdb=" CA ASP A 121 " ideal model delta harmonic sigma weight residual -180.00 -147.06 -32.94 0 5.00e+00 4.00e-02 4.34e+01 dihedral pdb=" CB CYS B 323 " pdb=" SG CYS B 323 " pdb=" SG CYS B 343 " pdb=" CB CYS B 343 " ideal model delta sinusoidal sigma weight residual 93.00 137.78 -44.78 1 1.00e+01 1.00e-02 2.79e+01 ... (remaining 6651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1394 0.062 - 0.125: 182 0.125 - 0.187: 14 0.187 - 0.250: 0 0.250 - 0.312: 3 Chirality restraints: 1593 Sorted by residual: chirality pdb=" CA CYS A 241 " pdb=" N CYS A 241 " pdb=" C CYS A 241 " pdb=" CB CYS A 241 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C3B ACO A 902 " pdb=" C2B ACO A 902 " pdb=" C4B ACO A 902 " pdb=" O3B ACO A 902 " both_signs ideal model delta sigma weight residual False -2.76 -2.46 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C2B ACO A 902 " pdb=" C1B ACO A 902 " pdb=" C3B ACO A 902 " pdb=" O2B ACO A 902 " both_signs ideal model delta sigma weight residual False -2.72 -2.44 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1590 not shown) Planarity restraints: 1881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 359 " -0.062 5.00e-02 4.00e+02 9.50e-02 1.44e+01 pdb=" N PRO B 360 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 360 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 360 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C7P ACO A 902 " -0.011 2.00e-02 2.50e+03 1.76e-02 3.88e+00 pdb=" C9P ACO A 902 " 0.033 2.00e-02 2.50e+03 pdb=" CAP ACO A 902 " -0.017 2.00e-02 2.50e+03 pdb=" N8P ACO A 902 " 0.003 2.00e-02 2.50e+03 pdb=" O9P ACO A 902 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B ACO A 902 " -0.026 2.00e-02 2.50e+03 1.16e-02 3.73e+00 pdb=" C2A ACO A 902 " 0.004 2.00e-02 2.50e+03 pdb=" C4A ACO A 902 " 0.011 2.00e-02 2.50e+03 pdb=" C5A ACO A 902 " 0.007 2.00e-02 2.50e+03 pdb=" C6A ACO A 902 " -0.011 2.00e-02 2.50e+03 pdb=" C8A ACO A 902 " 0.011 2.00e-02 2.50e+03 pdb=" N1A ACO A 902 " -0.003 2.00e-02 2.50e+03 pdb=" N3A ACO A 902 " 0.009 2.00e-02 2.50e+03 pdb=" N6A ACO A 902 " -0.013 2.00e-02 2.50e+03 pdb=" N7A ACO A 902 " 0.012 2.00e-02 2.50e+03 pdb=" N9A ACO A 902 " -0.001 2.00e-02 2.50e+03 ... (remaining 1878 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 238 2.66 - 3.22: 10392 3.22 - 3.78: 15645 3.78 - 4.34: 20332 4.34 - 4.90: 33466 Nonbonded interactions: 80073 Sorted by model distance: nonbonded pdb=" OD1 ASN A 297 " pdb=" OG1 THR A 311 " model vdw 2.104 3.040 nonbonded pdb=" OE2 GLU C 27 " pdb=" OH TYR C 63 " model vdw 2.170 3.040 nonbonded pdb=" N ASN A 331 " pdb=" OD1 ASN A 331 " model vdw 2.191 3.120 nonbonded pdb=" OD1 ASP B 191 " pdb=" OH TYR B 525 " model vdw 2.194 3.040 nonbonded pdb=" OG1 THR B 68 " pdb=" O GLU B 70 " model vdw 2.194 3.040 ... (remaining 80068 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.740 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4679 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 : 0.008 0.286 10989 Z= 0.496 Angle : 0.992 34.219 14815 Z= 0.546 Chirality : 0.043 0.312 1593 Planarity : 0.004 0.095 1881 Dihedral : 18.140 89.811 4147 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 8.31 % Allowed : 23.42 % Favored : 68.27 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.21), residues: 1276 helix: -0.16 (0.20), residues: 562 sheet: -2.33 (0.60), residues: 71 loop : -3.14 (0.21), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 427 TYR 0.010 0.001 TYR A 334 PHE 0.019 0.001 PHE A 400 TRP 0.011 0.001 TRP B 223 HIS 0.010 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00673 (10972) covalent geometry : angle 0.86463 (14803) SS BOND : bond 0.02262 ( 3) SS BOND : angle 6.23029 ( 6) hydrogen bonds : bond 0.10495 ( 448) hydrogen bonds : angle 4.46468 ( 1284) metal coordination : bond 0.13763 ( 14) metal coordination : angle 23.38063 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 188 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.4582 (tmm) cc_final: 0.4332 (tpt) REVERT: A 339 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.6331 (mp) REVERT: A 409 PHE cc_start: 0.4450 (t80) cc_final: 0.2821 (t80) REVERT: A 425 TYR cc_start: 0.4552 (OUTLIER) cc_final: 0.3181 (p90) REVERT: A 427 ARG cc_start: 0.6628 (OUTLIER) cc_final: 0.6409 (mmm-85) REVERT: A 524 TYR cc_start: 0.6367 (m-80) cc_final: 0.5731 (m-80) REVERT: A 574 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6890 (tt) REVERT: A 664 THR cc_start: 0.1796 (OUTLIER) cc_final: 0.0409 (p) REVERT: A 665 GLU cc_start: 0.5963 (OUTLIER) cc_final: 0.5737 (pm20) REVERT: B 190 GLN cc_start: 0.5166 (OUTLIER) cc_final: 0.3863 (tt0) REVERT: B 192 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6635 (tt0) REVERT: B 322 MET cc_start: 0.5786 (mmm) cc_final: 0.5368 (mmm) REVERT: B 436 HIS cc_start: 0.5228 (OUTLIER) cc_final: 0.4976 (t-90) REVERT: B 588 SER cc_start: 0.4697 (t) cc_final: 0.4302 (p) REVERT: D 103 VAL cc_start: 0.5558 (m) cc_final: 0.5312 (m) outliers start: 100 outliers final: 20 residues processed: 271 average time/residue: 0.1044 time to fit residues: 40.4716 Evaluate side-chains 145 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 436 HIS Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain D residue 68 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 35 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 415 ASN A 674 ASN A 681 GLN A 691 HIS B 122 HIS ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 ASN B 393 ASN C 77 GLN D 31 ASN D 33 GLN D 46 HIS D 47 ASN D 68 ASN D 81 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.209315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.165861 restraints weight = 11490.921| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.68 r_work: 0.3700 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 10989 Z= 0.161 Angle : 0.659 12.520 14815 Z= 0.344 Chirality : 0.043 0.191 1593 Planarity : 0.005 0.071 1881 Dihedral : 10.813 77.837 1511 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 5.98 % Allowed : 23.26 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.23), residues: 1276 helix: 1.12 (0.22), residues: 577 sheet: -1.30 (0.69), residues: 67 loop : -2.31 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 239 TYR 0.018 0.001 TYR A 196 PHE 0.028 0.002 PHE B 390 TRP 0.016 0.002 TRP B 338 HIS 0.018 0.002 HIS B 291 Details of bonding type rmsd covalent geometry : bond 0.00334 (10972) covalent geometry : angle 0.64378 (14803) SS BOND : bond 0.01289 ( 3) SS BOND : angle 3.28694 ( 6) hydrogen bonds : bond 0.05303 ( 448) hydrogen bonds : angle 3.92503 ( 1284) metal coordination : bond 0.03877 ( 14) metal coordination : angle 6.25746 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 145 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ARG cc_start: 0.6854 (mtt180) cc_final: 0.6249 (mtp-110) REVERT: A 204 LYS cc_start: 0.7318 (ptmt) cc_final: 0.7063 (ptpt) REVERT: A 371 TYR cc_start: 0.6917 (m-80) cc_final: 0.6571 (m-80) REVERT: A 425 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.4949 (p90) REVERT: A 508 MET cc_start: 0.7591 (mtm) cc_final: 0.7325 (mtm) REVERT: A 524 TYR cc_start: 0.7187 (m-80) cc_final: 0.6558 (m-80) REVERT: A 664 THR cc_start: 0.2451 (OUTLIER) cc_final: 0.1112 (p) REVERT: A 665 GLU cc_start: 0.5989 (OUTLIER) cc_final: 0.5758 (pm20) REVERT: B 192 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7018 (mt-10) REVERT: B 436 HIS cc_start: 0.5907 (OUTLIER) cc_final: 0.5125 (t-90) REVERT: B 598 ASP cc_start: 0.4504 (OUTLIER) cc_final: 0.4272 (p0) REVERT: E 219 GLU cc_start: 0.6715 (mm-30) cc_final: 0.6163 (tt0) outliers start: 72 outliers final: 28 residues processed: 203 average time/residue: 0.0894 time to fit residues: 27.3310 Evaluate side-chains 149 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 434 PHE Chi-restraints excluded: chain B residue 436 HIS Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 99 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 7 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 88 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 96 optimal weight: 0.0020 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN A 583 ASN ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN B 209 HIS ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 ASN D 64 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.204754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.157640 restraints weight = 11300.127| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 3.04 r_work: 0.3582 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 10989 Z= 0.159 Angle : 0.588 10.309 14815 Z= 0.308 Chirality : 0.041 0.146 1593 Planarity : 0.005 0.070 1881 Dihedral : 9.913 67.852 1485 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.56 % Allowed : 24.00 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.24), residues: 1276 helix: 1.67 (0.22), residues: 569 sheet: -0.71 (0.72), residues: 67 loop : -1.92 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 52 TYR 0.014 0.001 TYR A 334 PHE 0.017 0.001 PHE A 580 TRP 0.018 0.001 TRP B 346 HIS 0.009 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00328 (10972) covalent geometry : angle 0.57652 (14803) SS BOND : bond 0.00838 ( 3) SS BOND : angle 2.60311 ( 6) hydrogen bonds : bond 0.05695 ( 448) hydrogen bonds : angle 3.77782 ( 1284) metal coordination : bond 0.05484 ( 14) metal coordination : angle 5.26399 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 134 time to evaluate : 0.414 Fit side-chains REVERT: A 117 ARG cc_start: 0.7094 (mtt180) cc_final: 0.6316 (mtp-110) REVERT: A 131 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8015 (mp) REVERT: A 204 LYS cc_start: 0.7758 (ptmt) cc_final: 0.7409 (pttm) REVERT: A 310 MET cc_start: 0.8070 (mtm) cc_final: 0.7735 (mtm) REVERT: A 371 TYR cc_start: 0.7678 (m-80) cc_final: 0.7427 (m-80) REVERT: A 425 TYR cc_start: 0.7998 (OUTLIER) cc_final: 0.5312 (p90) REVERT: A 524 TYR cc_start: 0.7347 (m-80) cc_final: 0.6602 (m-80) REVERT: A 550 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6737 (pt0) REVERT: A 665 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.5737 (pm20) REVERT: B 18 PHE cc_start: 0.5540 (OUTLIER) cc_final: 0.4453 (m-10) REVERT: B 95 LYS cc_start: 0.7183 (mmmt) cc_final: 0.6798 (mmtt) REVERT: B 100 GLU cc_start: 0.7438 (tt0) cc_final: 0.7167 (mt-10) REVERT: B 280 ILE cc_start: 0.7396 (OUTLIER) cc_final: 0.7083 (mt) REVERT: B 436 HIS cc_start: 0.6211 (OUTLIER) cc_final: 0.5180 (t-90) REVERT: C 69 ASP cc_start: 0.7894 (t70) cc_final: 0.7550 (t0) REVERT: C 83 GLU cc_start: 0.7002 (tp30) cc_final: 0.6380 (mt-10) REVERT: D 64 HIS cc_start: 0.4266 (OUTLIER) cc_final: 0.4045 (m90) outliers start: 67 outliers final: 32 residues processed: 190 average time/residue: 0.1043 time to fit residues: 28.3010 Evaluate side-chains 149 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 436 HIS Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 561 PHE Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 103 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 121 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 ASN B 106 ASN B 113 ASN ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 ASN B 423 ASN B 490 ASN C 77 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.198251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.149896 restraints weight = 11355.471| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.71 r_work: 0.3489 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.7858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 10989 Z= 0.159 Angle : 0.595 8.677 14815 Z= 0.315 Chirality : 0.042 0.283 1593 Planarity : 0.005 0.076 1881 Dihedral : 10.119 71.799 1484 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.49 % Allowed : 24.75 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.24), residues: 1276 helix: 1.78 (0.22), residues: 564 sheet: -0.42 (0.73), residues: 66 loop : -1.80 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 244 TYR 0.017 0.002 TYR D 43 PHE 0.020 0.002 PHE A 404 TRP 0.010 0.001 TRP E 236 HIS 0.031 0.002 HIS D 64 Details of bonding type rmsd covalent geometry : bond 0.00358 (10972) covalent geometry : angle 0.58538 (14803) SS BOND : bond 0.00922 ( 3) SS BOND : angle 2.75604 ( 6) hydrogen bonds : bond 0.06092 ( 448) hydrogen bonds : angle 3.88805 ( 1284) metal coordination : bond 0.02394 ( 14) metal coordination : angle 4.66363 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 139 time to evaluate : 0.316 Fit side-chains REVERT: A 117 ARG cc_start: 0.7081 (mtt180) cc_final: 0.6635 (mtp-110) REVERT: A 167 ASP cc_start: 0.6201 (t70) cc_final: 0.5910 (t0) REVERT: A 191 GLN cc_start: 0.7494 (mm-40) cc_final: 0.7290 (mp10) REVERT: A 216 GLU cc_start: 0.7816 (tp30) cc_final: 0.7098 (mp0) REVERT: A 371 TYR cc_start: 0.7885 (m-80) cc_final: 0.7539 (m-80) REVERT: A 425 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.5026 (p90) REVERT: A 508 MET cc_start: 0.8665 (mtm) cc_final: 0.8379 (mtt) REVERT: A 524 TYR cc_start: 0.7102 (m-80) cc_final: 0.6621 (m-80) REVERT: A 550 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6783 (pt0) REVERT: A 574 ILE cc_start: 0.8481 (tt) cc_final: 0.8230 (tt) REVERT: A 665 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.5972 (pm20) REVERT: A 698 ARG cc_start: 0.6608 (OUTLIER) cc_final: 0.5629 (ptt90) REVERT: B 95 LYS cc_start: 0.8055 (mmmt) cc_final: 0.7635 (mmtt) REVERT: B 101 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7424 (pp) REVERT: B 390 PHE cc_start: 0.7493 (t80) cc_final: 0.6860 (t80) REVERT: B 436 HIS cc_start: 0.6105 (OUTLIER) cc_final: 0.5046 (t-90) REVERT: B 455 LYS cc_start: 0.7722 (ttmm) cc_final: 0.7505 (ttpt) REVERT: B 554 GLN cc_start: 0.6357 (OUTLIER) cc_final: 0.5427 (mt0) REVERT: B 598 ASP cc_start: 0.4208 (OUTLIER) cc_final: 0.3974 (p0) REVERT: C 65 ASN cc_start: 0.7026 (t0) cc_final: 0.6693 (m-40) REVERT: C 83 GLU cc_start: 0.7315 (tp30) cc_final: 0.6909 (mt-10) REVERT: D 64 HIS cc_start: 0.3831 (OUTLIER) cc_final: 0.3463 (m-70) outliers start: 54 outliers final: 32 residues processed: 182 average time/residue: 0.0804 time to fit residues: 21.8965 Evaluate side-chains 159 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 436 HIS Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain B residue 561 PHE Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 103 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 54 optimal weight: 0.0170 chunk 76 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN A 560 ASN B 122 HIS ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 HIS B 556 GLN C 77 GLN C 85 GLN D 52 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.193296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.144961 restraints weight = 11377.246| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 3.20 r_work: 0.3423 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.8958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 10989 Z= 0.167 Angle : 0.597 9.999 14815 Z= 0.315 Chirality : 0.043 0.180 1593 Planarity : 0.005 0.083 1881 Dihedral : 10.040 78.506 1482 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 5.15 % Allowed : 24.67 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.24), residues: 1276 helix: 1.93 (0.22), residues: 550 sheet: -0.41 (0.71), residues: 67 loop : -1.76 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 52 TYR 0.016 0.002 TYR B 108 PHE 0.024 0.002 PHE A 404 TRP 0.009 0.001 TRP A 571 HIS 0.019 0.002 HIS D 64 Details of bonding type rmsd covalent geometry : bond 0.00381 (10972) covalent geometry : angle 0.58640 (14803) SS BOND : bond 0.01258 ( 3) SS BOND : angle 3.29369 ( 6) hydrogen bonds : bond 0.06467 ( 448) hydrogen bonds : angle 3.89226 ( 1284) metal coordination : bond 0.04172 ( 14) metal coordination : angle 4.46215 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 127 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 ARG cc_start: 0.7014 (mtt180) cc_final: 0.6709 (mtp-110) REVERT: A 167 ASP cc_start: 0.6298 (t70) cc_final: 0.5851 (t0) REVERT: A 216 GLU cc_start: 0.7904 (tp30) cc_final: 0.6865 (mp0) REVERT: A 310 MET cc_start: 0.8264 (mtm) cc_final: 0.7953 (mtm) REVERT: A 371 TYR cc_start: 0.7920 (m-80) cc_final: 0.7600 (m-80) REVERT: A 425 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.5028 (p90) REVERT: A 550 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6991 (pt0) REVERT: B 18 PHE cc_start: 0.5621 (OUTLIER) cc_final: 0.4301 (m-10) REVERT: B 95 LYS cc_start: 0.8143 (mmmt) cc_final: 0.7788 (mmtt) REVERT: B 101 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7784 (pp) REVERT: B 190 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8292 (tm-30) REVERT: B 198 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7240 (mt) REVERT: B 227 GLU cc_start: 0.7428 (tp30) cc_final: 0.6957 (tt0) REVERT: B 390 PHE cc_start: 0.7283 (t80) cc_final: 0.6723 (t80) REVERT: B 436 HIS cc_start: 0.6521 (OUTLIER) cc_final: 0.5604 (t-90) REVERT: B 554 GLN cc_start: 0.6526 (OUTLIER) cc_final: 0.5483 (mt0) REVERT: B 598 ASP cc_start: 0.3851 (OUTLIER) cc_final: 0.3588 (p0) REVERT: C 65 ASN cc_start: 0.7258 (t0) cc_final: 0.6994 (m110) REVERT: C 83 GLU cc_start: 0.7539 (tp30) cc_final: 0.7289 (mt-10) REVERT: D 35 GLU cc_start: 0.7189 (tp30) cc_final: 0.6943 (tt0) REVERT: D 37 TYR cc_start: 0.7758 (t80) cc_final: 0.7384 (t80) REVERT: D 42 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6184 (tt0) outliers start: 62 outliers final: 32 residues processed: 181 average time/residue: 0.0833 time to fit residues: 22.4004 Evaluate side-chains 158 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 436 HIS Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 103 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 45 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN A 560 ASN A 583 ASN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 HIS B 587 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.188126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141138 restraints weight = 11529.522| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 3.27 r_work: 0.3337 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.9805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.118 10989 Z= 0.274 Angle : 0.730 10.863 14815 Z= 0.382 Chirality : 0.048 0.191 1593 Planarity : 0.006 0.095 1881 Dihedral : 10.657 82.134 1477 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.90 % Favored : 93.03 % Rotamer: Outliers : 4.90 % Allowed : 26.08 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.23), residues: 1276 helix: 1.33 (0.22), residues: 557 sheet: -0.38 (0.82), residues: 52 loop : -1.99 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 244 TYR 0.018 0.002 TYR D 43 PHE 0.029 0.002 PHE A 404 TRP 0.017 0.002 TRP B 338 HIS 0.012 0.002 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00679 (10972) covalent geometry : angle 0.71996 (14803) SS BOND : bond 0.01928 ( 3) SS BOND : angle 4.48608 ( 6) hydrogen bonds : bond 0.08361 ( 448) hydrogen bonds : angle 4.37136 ( 1284) metal coordination : bond 0.03894 ( 14) metal coordination : angle 4.30520 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 120 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 ARG cc_start: 0.7026 (mtt180) cc_final: 0.6700 (mtp-110) REVERT: A 167 ASP cc_start: 0.6707 (t70) cc_final: 0.6133 (t0) REVERT: A 216 GLU cc_start: 0.7888 (tp30) cc_final: 0.7148 (mp0) REVERT: A 344 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8016 (mt) REVERT: A 425 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.5459 (p90) REVERT: A 441 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7874 (mp) REVERT: A 550 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7223 (pt0) REVERT: A 698 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.5565 (ptt90) REVERT: B 95 LYS cc_start: 0.8178 (mmmt) cc_final: 0.7787 (mmtt) REVERT: B 99 ASN cc_start: 0.7014 (p0) cc_final: 0.6661 (m-40) REVERT: B 102 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7913 (ptpp) REVERT: B 170 LYS cc_start: 0.7021 (tppt) cc_final: 0.6518 (ttmt) REVERT: B 190 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8066 (pp30) REVERT: B 198 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7276 (mt) REVERT: B 275 ASP cc_start: 0.5272 (m-30) cc_final: 0.4942 (m-30) REVERT: B 317 PHE cc_start: 0.6947 (m-80) cc_final: 0.6736 (m-80) REVERT: B 390 PHE cc_start: 0.7266 (t80) cc_final: 0.6638 (t80) REVERT: B 436 HIS cc_start: 0.6806 (OUTLIER) cc_final: 0.6096 (t-90) REVERT: B 438 HIS cc_start: 0.6190 (m90) cc_final: 0.5948 (m90) REVERT: B 554 GLN cc_start: 0.6844 (OUTLIER) cc_final: 0.6558 (mt0) REVERT: B 598 ASP cc_start: 0.3718 (OUTLIER) cc_final: 0.3449 (p0) REVERT: C 65 ASN cc_start: 0.7585 (t0) cc_final: 0.7332 (m-40) REVERT: C 83 GLU cc_start: 0.7650 (tp30) cc_final: 0.7427 (mt-10) REVERT: E 216 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7749 (mt-10) REVERT: E 229 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6102 (tp30) REVERT: D 37 TYR cc_start: 0.7848 (t80) cc_final: 0.7413 (t80) REVERT: D 42 GLU cc_start: 0.6988 (tm-30) cc_final: 0.6251 (tt0) outliers start: 59 outliers final: 35 residues processed: 172 average time/residue: 0.0956 time to fit residues: 24.0515 Evaluate side-chains 160 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 112 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 436 HIS Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 229 GLU Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 103 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 33 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 71 optimal weight: 0.0870 chunk 63 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 126 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.194280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.146521 restraints weight = 11314.425| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.78 r_work: 0.3456 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.9872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10989 Z= 0.120 Angle : 0.540 9.908 14815 Z= 0.283 Chirality : 0.040 0.164 1593 Planarity : 0.004 0.085 1881 Dihedral : 10.041 84.514 1477 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.41 % Allowed : 28.32 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.24), residues: 1276 helix: 2.00 (0.22), residues: 550 sheet: 0.56 (0.93), residues: 42 loop : -1.69 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 244 TYR 0.011 0.001 TYR B 108 PHE 0.016 0.001 PHE A 404 TRP 0.011 0.001 TRP B 346 HIS 0.006 0.001 HIS B 291 Details of bonding type rmsd covalent geometry : bond 0.00249 (10972) covalent geometry : angle 0.53461 (14803) SS BOND : bond 0.00916 ( 3) SS BOND : angle 3.16823 ( 6) hydrogen bonds : bond 0.05672 ( 448) hydrogen bonds : angle 3.85421 ( 1284) metal coordination : bond 0.01811 ( 14) metal coordination : angle 2.21702 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 ARG cc_start: 0.6926 (mtt180) cc_final: 0.6658 (mtp-110) REVERT: A 167 ASP cc_start: 0.6221 (t70) cc_final: 0.5784 (t0) REVERT: A 216 GLU cc_start: 0.7854 (tp30) cc_final: 0.6929 (mp0) REVERT: A 310 MET cc_start: 0.8201 (mtm) cc_final: 0.7913 (mtm) REVERT: A 371 TYR cc_start: 0.7909 (m-80) cc_final: 0.7666 (m-80) REVERT: A 425 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.5080 (p90) REVERT: A 550 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7214 (pt0) REVERT: A 698 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.5933 (ptt90) REVERT: B 95 LYS cc_start: 0.8240 (mmmt) cc_final: 0.7849 (mmtt) REVERT: B 170 LYS cc_start: 0.6966 (tppt) cc_final: 0.6445 (ttmt) REVERT: B 188 ASP cc_start: 0.8060 (t0) cc_final: 0.7746 (t0) REVERT: B 190 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8143 (pp30) REVERT: B 227 GLU cc_start: 0.7326 (tp30) cc_final: 0.6810 (tt0) REVERT: B 258 THR cc_start: 0.7476 (t) cc_final: 0.7197 (m) REVERT: B 380 LYS cc_start: 0.7452 (mttp) cc_final: 0.6976 (mtmt) REVERT: B 390 PHE cc_start: 0.7360 (t80) cc_final: 0.6831 (t80) REVERT: B 436 HIS cc_start: 0.6692 (OUTLIER) cc_final: 0.5717 (t-90) REVERT: B 438 HIS cc_start: 0.6207 (m90) cc_final: 0.5794 (m-70) REVERT: B 444 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7187 (mp10) REVERT: B 554 GLN cc_start: 0.6612 (OUTLIER) cc_final: 0.6370 (mt0) REVERT: B 598 ASP cc_start: 0.3985 (OUTLIER) cc_final: 0.3766 (p0) REVERT: C 16 SER cc_start: 0.8296 (t) cc_final: 0.7438 (p) REVERT: C 65 ASN cc_start: 0.7240 (t0) cc_final: 0.7010 (m110) REVERT: C 83 GLU cc_start: 0.7593 (tp30) cc_final: 0.7388 (mt-10) REVERT: D 37 TYR cc_start: 0.7814 (t80) cc_final: 0.7427 (t80) REVERT: D 42 GLU cc_start: 0.6793 (tm-30) cc_final: 0.6053 (tt0) outliers start: 41 outliers final: 26 residues processed: 174 average time/residue: 0.0823 time to fit residues: 21.2031 Evaluate side-chains 160 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 436 HIS Chi-restraints excluded: chain B residue 444 GLN Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 99 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 62 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 31 optimal weight: 0.0170 chunk 1 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.1220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 ASN B 206 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.193674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.147791 restraints weight = 11414.050| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.69 r_work: 0.3428 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 1.0023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10989 Z= 0.144 Angle : 0.566 11.428 14815 Z= 0.296 Chirality : 0.041 0.158 1593 Planarity : 0.005 0.087 1881 Dihedral : 9.922 84.084 1477 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.07 % Allowed : 27.82 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.24), residues: 1276 helix: 1.93 (0.22), residues: 552 sheet: -0.04 (0.88), residues: 48 loop : -1.66 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 244 TYR 0.015 0.001 TYR E 238 PHE 0.021 0.001 PHE A 404 TRP 0.013 0.001 TRP B 346 HIS 0.008 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00333 (10972) covalent geometry : angle 0.55955 (14803) SS BOND : bond 0.00975 ( 3) SS BOND : angle 3.21050 ( 6) hydrogen bonds : bond 0.06112 ( 448) hydrogen bonds : angle 3.95181 ( 1284) metal coordination : bond 0.02456 ( 14) metal coordination : angle 3.05958 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 126 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 117 ARG cc_start: 0.7066 (mtt180) cc_final: 0.6768 (mtp-110) REVERT: A 167 ASP cc_start: 0.6359 (t70) cc_final: 0.5877 (t0) REVERT: A 216 GLU cc_start: 0.7864 (tp30) cc_final: 0.6929 (mp0) REVERT: A 371 TYR cc_start: 0.7908 (m-80) cc_final: 0.7681 (m-80) REVERT: A 425 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.5238 (p90) REVERT: A 550 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7180 (pt0) REVERT: A 698 ARG cc_start: 0.6666 (OUTLIER) cc_final: 0.5885 (ptt90) REVERT: B 95 LYS cc_start: 0.8240 (mmmt) cc_final: 0.7876 (mmtt) REVERT: B 102 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7948 (ptpp) REVERT: B 170 LYS cc_start: 0.7097 (tppt) cc_final: 0.6618 (ttmt) REVERT: B 190 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8100 (pp30) REVERT: B 198 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7327 (mt) REVERT: B 380 LYS cc_start: 0.7536 (mttp) cc_final: 0.7057 (mtmt) REVERT: B 390 PHE cc_start: 0.7302 (t80) cc_final: 0.6817 (t80) REVERT: B 438 HIS cc_start: 0.6259 (m90) cc_final: 0.5864 (m-70) REVERT: B 444 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7250 (mp10) REVERT: B 554 GLN cc_start: 0.6672 (OUTLIER) cc_final: 0.6352 (mt0) REVERT: C 16 SER cc_start: 0.8276 (t) cc_final: 0.7528 (p) REVERT: C 65 ASN cc_start: 0.7468 (t0) cc_final: 0.7059 (m110) REVERT: C 83 GLU cc_start: 0.7616 (tp30) cc_final: 0.7409 (mt-10) REVERT: C 91 ASN cc_start: 0.6829 (OUTLIER) cc_final: 0.6433 (m110) REVERT: E 229 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6221 (tp30) REVERT: D 37 TYR cc_start: 0.7783 (t80) cc_final: 0.7555 (t80) REVERT: D 42 GLU cc_start: 0.6850 (tm-30) cc_final: 0.6158 (tt0) outliers start: 49 outliers final: 34 residues processed: 168 average time/residue: 0.0928 time to fit residues: 22.9511 Evaluate side-chains 162 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 118 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 436 HIS Chi-restraints excluded: chain B residue 444 GLN Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 229 GLU Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 99 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 ASN B 206 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN D 91 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.195929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.149537 restraints weight = 11317.955| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.76 r_work: 0.3458 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 1.0105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10989 Z= 0.123 Angle : 0.536 11.614 14815 Z= 0.283 Chirality : 0.040 0.162 1593 Planarity : 0.004 0.084 1881 Dihedral : 9.647 84.765 1475 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.99 % Allowed : 27.82 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.24), residues: 1276 helix: 2.09 (0.22), residues: 553 sheet: 0.38 (0.90), residues: 47 loop : -1.60 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 244 TYR 0.012 0.001 TYR E 238 PHE 0.018 0.001 PHE A 404 TRP 0.015 0.001 TRP B 346 HIS 0.006 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00273 (10972) covalent geometry : angle 0.52753 (14803) SS BOND : bond 0.01066 ( 3) SS BOND : angle 4.02119 ( 6) hydrogen bonds : bond 0.05509 ( 448) hydrogen bonds : angle 3.84435 ( 1284) metal coordination : bond 0.01849 ( 14) metal coordination : angle 2.44940 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 123 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 117 ARG cc_start: 0.6967 (mtt180) cc_final: 0.6672 (mtp-110) REVERT: A 167 ASP cc_start: 0.6196 (t70) cc_final: 0.5752 (t0) REVERT: A 216 GLU cc_start: 0.7881 (tp30) cc_final: 0.6945 (mp0) REVERT: A 425 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.5171 (p90) REVERT: A 441 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8027 (mp) REVERT: A 550 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7171 (pt0) REVERT: A 698 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.5956 (ptt90) REVERT: B 95 LYS cc_start: 0.8222 (mmmt) cc_final: 0.7850 (mmtt) REVERT: B 102 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7854 (ptpp) REVERT: B 170 LYS cc_start: 0.7103 (tppt) cc_final: 0.6630 (ttmt) REVERT: B 188 ASP cc_start: 0.8115 (t0) cc_final: 0.7802 (t0) REVERT: B 190 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8113 (pp30) REVERT: B 198 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7245 (mt) REVERT: B 227 GLU cc_start: 0.7355 (tp30) cc_final: 0.6867 (tt0) REVERT: B 380 LYS cc_start: 0.7540 (mttp) cc_final: 0.7087 (mtmt) REVERT: B 390 PHE cc_start: 0.7287 (t80) cc_final: 0.6788 (t80) REVERT: B 438 HIS cc_start: 0.6246 (m90) cc_final: 0.5840 (m-70) REVERT: B 444 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7201 (mp10) REVERT: B 554 GLN cc_start: 0.6557 (OUTLIER) cc_final: 0.6267 (mt0) REVERT: C 16 SER cc_start: 0.8155 (t) cc_final: 0.7517 (p) REVERT: C 65 ASN cc_start: 0.7374 (t0) cc_final: 0.6976 (m110) REVERT: C 83 GLU cc_start: 0.7651 (tp30) cc_final: 0.7394 (mt-10) REVERT: C 91 ASN cc_start: 0.6600 (OUTLIER) cc_final: 0.6301 (m110) REVERT: E 229 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6221 (tp30) REVERT: D 37 TYR cc_start: 0.7724 (t80) cc_final: 0.7465 (t80) REVERT: D 42 GLU cc_start: 0.6849 (tm-30) cc_final: 0.6163 (tt0) outliers start: 48 outliers final: 33 residues processed: 166 average time/residue: 0.0834 time to fit residues: 20.5050 Evaluate side-chains 163 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 436 HIS Chi-restraints excluded: chain B residue 444 GLN Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 229 GLU Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain D residue 89 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 100 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 126 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 ASN B 206 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS D 91 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.196645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.148312 restraints weight = 11350.556| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 3.21 r_work: 0.3464 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 1.0175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10989 Z= 0.120 Angle : 0.537 11.681 14815 Z= 0.280 Chirality : 0.040 0.156 1593 Planarity : 0.004 0.083 1881 Dihedral : 9.444 85.530 1475 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.99 % Allowed : 28.16 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1276 helix: 2.16 (0.22), residues: 555 sheet: 0.49 (0.92), residues: 47 loop : -1.53 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 244 TYR 0.012 0.001 TYR E 238 PHE 0.017 0.001 PHE A 404 TRP 0.016 0.001 TRP B 346 HIS 0.006 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00264 (10972) covalent geometry : angle 0.52951 (14803) SS BOND : bond 0.00960 ( 3) SS BOND : angle 3.91305 ( 6) hydrogen bonds : bond 0.05310 ( 448) hydrogen bonds : angle 3.77763 ( 1284) metal coordination : bond 0.01748 ( 14) metal coordination : angle 2.41051 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 126 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 117 ARG cc_start: 0.6972 (mtt180) cc_final: 0.6646 (mtp-110) REVERT: A 167 ASP cc_start: 0.6178 (t70) cc_final: 0.5750 (t0) REVERT: A 216 GLU cc_start: 0.7892 (tp30) cc_final: 0.6933 (mp0) REVERT: A 425 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.5135 (p90) REVERT: A 441 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.7990 (mp) REVERT: A 550 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7040 (pt0) REVERT: A 698 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.5925 (ptt90) REVERT: B 95 LYS cc_start: 0.8202 (mmmt) cc_final: 0.7840 (mmtt) REVERT: B 102 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7883 (ptpp) REVERT: B 170 LYS cc_start: 0.7093 (tppt) cc_final: 0.6664 (ttmt) REVERT: B 188 ASP cc_start: 0.8098 (t0) cc_final: 0.7785 (t0) REVERT: B 190 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8145 (pp30) REVERT: B 198 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7377 (mt) REVERT: B 227 GLU cc_start: 0.7311 (tp30) cc_final: 0.6868 (tt0) REVERT: B 380 LYS cc_start: 0.7532 (mttp) cc_final: 0.7065 (mtmt) REVERT: B 390 PHE cc_start: 0.7293 (t80) cc_final: 0.6785 (t80) REVERT: B 438 HIS cc_start: 0.6252 (m90) cc_final: 0.5903 (m-70) REVERT: B 444 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7200 (mp10) REVERT: B 455 LYS cc_start: 0.7471 (tppt) cc_final: 0.7220 (tppt) REVERT: B 554 GLN cc_start: 0.6518 (OUTLIER) cc_final: 0.6274 (mt0) REVERT: C 16 SER cc_start: 0.8079 (t) cc_final: 0.7446 (p) REVERT: C 65 ASN cc_start: 0.7376 (t0) cc_final: 0.7032 (m110) REVERT: C 83 GLU cc_start: 0.7655 (tp30) cc_final: 0.7379 (mt-10) REVERT: E 229 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.6317 (tp30) REVERT: D 37 TYR cc_start: 0.7696 (t80) cc_final: 0.7491 (t80) REVERT: D 42 GLU cc_start: 0.6858 (tm-30) cc_final: 0.6160 (tt0) outliers start: 48 outliers final: 35 residues processed: 168 average time/residue: 0.0912 time to fit residues: 22.7115 Evaluate side-chains 167 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 122 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 436 HIS Chi-restraints excluded: chain B residue 444 GLN Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 229 GLU Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 99 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 0.0270 chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 ASN B 206 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS C 91 ASN D 91 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.193646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.148171 restraints weight = 11349.804| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.86 r_work: 0.3420 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 1.0302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 10989 Z= 0.154 Angle : 0.571 11.661 14815 Z= 0.301 Chirality : 0.042 0.159 1593 Planarity : 0.005 0.087 1881 Dihedral : 9.676 84.009 1475 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.32 % Allowed : 27.82 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.24), residues: 1276 helix: 1.89 (0.22), residues: 562 sheet: 0.05 (0.89), residues: 48 loop : -1.60 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 14 TYR 0.014 0.001 TYR E 238 PHE 0.022 0.001 PHE A 404 TRP 0.018 0.001 TRP B 346 HIS 0.008 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00363 (10972) covalent geometry : angle 0.56186 (14803) SS BOND : bond 0.01050 ( 3) SS BOND : angle 4.12427 ( 6) hydrogen bonds : bond 0.06098 ( 448) hydrogen bonds : angle 3.92857 ( 1284) metal coordination : bond 0.02529 ( 14) metal coordination : angle 3.20499 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2442.77 seconds wall clock time: 42 minutes 40.95 seconds (2560.95 seconds total)