Starting phenix.real_space_refine on Fri Mar 6 02:42:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nhc_12323/03_2026/7nhc_12323.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nhc_12323/03_2026/7nhc_12323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nhc_12323/03_2026/7nhc_12323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nhc_12323/03_2026/7nhc_12323.map" model { file = "/net/cci-nas-00/data/ceres_data/7nhc_12323/03_2026/7nhc_12323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nhc_12323/03_2026/7nhc_12323.cif" } resolution = 2.87 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= 0.002 sd= 0.042 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 P 23 5.49 5 S 100 5.16 5 C 8764 2.51 5 N 2440 2.21 5 O 2705 1.98 5 H 13727 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27759 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 11524 Classifications: {'peptide': 716} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 31, 'TRANS': 684} Chain: "B" Number of atoms: 11436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 11436 Classifications: {'peptide': 717} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 30, 'TRANS': 686} Chain breaks: 2 Chain: "C" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 4053 Classifications: {'peptide': 247} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 234} Chain: "E" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 255 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "D" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 491 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 11} Time building chain proxies: 4.32, per 1000 atoms: 0.16 Number of scatterers: 27759 At special positions: 0 Unit cell: (100.65, 102.3, 146.025, 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) S 100 16.00 P 23 15.00 O 2705 8.00 N 2440 7.00 C 8764 6.00 H 13727 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 775.9 milliseconds 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3174 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 15 sheets defined 53.3% alpha, 13.0% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 5.49 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 removed outlier: 3.517A pdb=" N VAL A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 25 removed outlier: 3.826A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 50 removed outlier: 3.564A pdb=" N PHE A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.729A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 186 Processing helix chain 'A' and resid 187 through 200 removed outlier: 3.722A pdb=" N GLN A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ARG A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLY A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR A 200 " --> pdb=" O ARG A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.617A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 404 through 415 removed outlier: 4.549A pdb=" N GLN A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 452 removed outlier: 4.727A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.936A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 582 through 603 removed outlier: 3.763A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.672A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 removed outlier: 3.602A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 3.747A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 124 Processing helix chain 'B' and resid 138 through 154 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 175 removed outlier: 3.570A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.730A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 290 Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.599A pdb=" N ASN B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.731A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 377 through 381 removed outlier: 4.002A pdb=" N TYR B 380 " --> pdb=" O ASP B 377 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE B 381 " --> pdb=" O LEU B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 381' Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 455 through 472 Processing helix chain 'B' and resid 504 through 512 removed outlier: 3.652A pdb=" N MET B 507 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.557A pdb=" N GLY B 588 " --> pdb=" O SER B 585 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 589 " --> pdb=" O LYS B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 585 through 589' Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 672 through 677 removed outlier: 4.030A pdb=" N LEU B 675 " --> pdb=" O ARG B 672 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN B 676 " --> pdb=" O SER B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 700 Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.085A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 713 through 732 Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.550A pdb=" N GLU C 6 " --> pdb=" O GLU C 2 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 92 through 103 removed outlier: 4.009A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.768A pdb=" N VAL C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 172 removed outlier: 3.741A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 179 through 192 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.608A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.660A pdb=" N PHE A 117 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.815A pdb=" N TYR B 483 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 291 removed outlier: 6.540A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 317 through 324 removed outlier: 10.261A pdb=" N TRP A 317 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 9.501A pdb=" N MET A 548 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N GLU A 319 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLY A 546 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 542 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 380 removed outlier: 4.205A pdb=" N GLN B 367 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 627 through 631 removed outlier: 3.604A pdb=" N GLY A 622 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 184 Processing sheet with id=AB2, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.811A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB4, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.477A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N THR C 81 " --> pdb=" O MET C 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 135 removed outlier: 6.040A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET C 243 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 141 through 146 701 hydrogen bonds defined for protein. 1959 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 7.32 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13700 1.03 - 1.23: 31 1.23 - 1.42: 6011 1.42 - 1.62: 8176 1.62 - 1.81: 173 Bond restraints: 28091 Sorted by residual: bond pdb=" CG ARG A 185 " pdb=" CD ARG A 185 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.82e+00 bond pdb=" CA PHE B 412 " pdb=" CB PHE B 412 " ideal model delta sigma weight residual 1.527 1.550 -0.023 1.39e-02 5.18e+03 2.82e+00 bond pdb=" C GLU A 181 " pdb=" O GLU A 181 " ideal model delta sigma weight residual 1.237 1.253 -0.017 1.16e-02 7.43e+03 2.09e+00 bond pdb=" C PRO A 265 " pdb=" N ARG A 266 " ideal model delta sigma weight residual 1.333 1.312 0.021 1.59e-02 3.96e+03 1.68e+00 bond pdb=" CA GLU A 181 " pdb=" C GLU A 181 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.26e-02 6.30e+03 1.22e+00 ... (remaining 28086 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 50351 1.82 - 3.65: 360 3.65 - 5.47: 26 5.47 - 7.30: 2 7.30 - 9.12: 1 Bond angle restraints: 50740 Sorted by residual: angle pdb=" CA GLU A 181 " pdb=" CB GLU A 181 " pdb=" CG GLU A 181 " ideal model delta sigma weight residual 114.10 123.22 -9.12 2.00e+00 2.50e-01 2.08e+01 angle pdb=" N GLU A 181 " pdb=" CA GLU A 181 " pdb=" CB GLU A 181 " ideal model delta sigma weight residual 110.07 104.71 5.36 1.45e+00 4.76e-01 1.37e+01 angle pdb=" C GLU A 181 " pdb=" CA GLU A 181 " pdb=" CB GLU A 181 " ideal model delta sigma weight residual 110.90 116.14 -5.24 1.58e+00 4.01e-01 1.10e+01 angle pdb=" C HIS A 326 " pdb=" N GLU A 327 " pdb=" CA GLU A 327 " ideal model delta sigma weight residual 121.54 127.31 -5.77 1.91e+00 2.74e-01 9.13e+00 angle pdb=" CA GLY B 513 " pdb=" C GLY B 513 " pdb=" N VAL B 514 " ideal model delta sigma weight residual 114.65 117.31 -2.66 9.20e-01 1.18e+00 8.35e+00 ... (remaining 50735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 12027 17.87 - 35.73: 864 35.73 - 53.60: 216 53.60 - 71.47: 72 71.47 - 89.33: 24 Dihedral angle restraints: 13203 sinusoidal: 7482 harmonic: 5721 Sorted by residual: dihedral pdb=" CA LYS B 736 " pdb=" C LYS B 736 " pdb=" N LYS B 737 " pdb=" CA LYS B 737 " ideal model delta harmonic sigma weight residual -180.00 -156.37 -23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLY A 58 " pdb=" C GLY A 58 " pdb=" N GLU A 59 " pdb=" CA GLU A 59 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA CYS C 196 " pdb=" C CYS C 196 " pdb=" N LYS C 197 " pdb=" CA LYS C 197 " ideal model delta harmonic sigma weight residual 180.00 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 13200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1377 0.030 - 0.059: 545 0.059 - 0.089: 130 0.089 - 0.118: 70 0.118 - 0.148: 19 Chirality restraints: 2141 Sorted by residual: chirality pdb=" C1' A D 4 " pdb=" O4' A D 4 " pdb=" C2' A D 4 " pdb=" N9 A D 4 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ILE B 667 " pdb=" N ILE B 667 " pdb=" C ILE B 667 " pdb=" CB ILE B 667 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA ILE B 302 " pdb=" N ILE B 302 " pdb=" C ILE B 302 " pdb=" CB ILE B 302 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 2138 not shown) Planarity restraints: 4048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 496 " -0.327 9.50e-02 1.11e+02 1.09e-01 1.40e+01 pdb=" NE ARG A 496 " 0.026 2.00e-02 2.50e+03 pdb=" CZ ARG A 496 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 496 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 496 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG A 496 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 496 " 0.010 2.00e-02 2.50e+03 pdb="HH21 ARG A 496 " -0.004 2.00e-02 2.50e+03 pdb="HH22 ARG A 496 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 4 " -0.029 2.00e-02 2.50e+03 1.18e-02 4.52e+00 pdb=" N9 A D 4 " 0.029 2.00e-02 2.50e+03 pdb=" C8 A D 4 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A D 4 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A D 4 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A D 4 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A D 4 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A D 4 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A D 4 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A D 4 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A D 4 " 0.003 2.00e-02 2.50e+03 pdb=" H8 A D 4 " 0.001 2.00e-02 2.50e+03 pdb=" H2 A D 4 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 181 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C GLU A 181 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU A 181 " 0.012 2.00e-02 2.50e+03 pdb=" N MET A 182 " 0.011 2.00e-02 2.50e+03 ... (remaining 4045 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1241 2.18 - 2.79: 56358 2.79 - 3.39: 79443 3.39 - 4.00: 105464 4.00 - 4.60: 164712 Nonbonded interactions: 407218 Sorted by model distance: nonbonded pdb=" O TRP A 699 " pdb="HD21 ASN A 703 " model vdw 1.579 2.450 nonbonded pdb=" O GLY A 152 " pdb=" HZ2 LYS A 172 " model vdw 1.580 2.450 nonbonded pdb=" OP2 G D 5 " pdb=" H22 G D 5 " model vdw 1.588 2.450 nonbonded pdb=" O LYS C 190 " pdb="HE21 GLN C 194 " model vdw 1.588 2.450 nonbonded pdb=" OD2 ASP B 593 " pdb=" HH TYR B 620 " model vdw 1.591 2.450 ... (remaining 407213 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 30.720 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 : 0.002 0.059 14364 Z= 0.116 Angle : 0.512 9.121 19477 Z= 0.287 Chirality : 0.037 0.148 2141 Planarity : 0.005 0.146 2426 Dihedral : 14.218 89.335 5642 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1670 helix: 1.03 (0.19), residues: 790 sheet: -0.50 (0.42), residues: 144 loop : -0.72 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 185 TYR 0.013 0.001 TYR A 130 PHE 0.015 0.001 PHE A 176 TRP 0.009 0.001 TRP A 188 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00236 (14364) covalent geometry : angle 0.51204 (19477) hydrogen bonds : bond 0.12722 ( 706) hydrogen bonds : angle 5.82114 ( 1979) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 305 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ASN cc_start: 0.7596 (t0) cc_final: 0.7320 (t0) REVERT: A 423 ILE cc_start: 0.7375 (tp) cc_final: 0.7149 (tp) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 1.4435 time to fit residues: 476.7584 Evaluate side-chains 222 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN B 137 GLN B 671 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.164273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.135435 restraints weight = 43363.888| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.45 r_work: 0.3276 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14364 Z= 0.127 Angle : 0.516 6.885 19477 Z= 0.278 Chirality : 0.038 0.167 2141 Planarity : 0.004 0.094 2426 Dihedral : 9.977 74.011 2186 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.07 % Allowed : 11.10 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 1670 helix: 1.17 (0.18), residues: 796 sheet: -0.54 (0.41), residues: 148 loop : -0.72 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 185 TYR 0.011 0.001 TYR A 130 PHE 0.016 0.001 PHE A 176 TRP 0.007 0.001 TRP A 188 HIS 0.003 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00275 (14364) covalent geometry : angle 0.51637 (19477) hydrogen bonds : bond 0.04755 ( 706) hydrogen bonds : angle 4.90195 ( 1979) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 235 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6805 (tpp) REVERT: A 610 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6553 (mt-10) REVERT: A 674 ASP cc_start: 0.8278 (m-30) cc_final: 0.8022 (m-30) REVERT: B 172 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7461 (mm-30) REVERT: C 1 MET cc_start: 0.6602 (tpt) cc_final: 0.5940 (tpt) REVERT: C 2 GLU cc_start: 0.7059 (pm20) cc_final: 0.6813 (pm20) outliers start: 16 outliers final: 6 residues processed: 240 average time/residue: 1.3068 time to fit residues: 342.8135 Evaluate side-chains 228 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 219 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 119 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 248 GLN A 408 GLN B 65 GLN B 115 GLN B 314 ASN B 460 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.154362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.122899 restraints weight = 43963.814| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.53 r_work: 0.3180 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 14364 Z= 0.235 Angle : 0.589 6.525 19477 Z= 0.316 Chirality : 0.042 0.189 2141 Planarity : 0.005 0.050 2426 Dihedral : 10.259 74.231 2186 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.87 % Allowed : 11.97 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.20), residues: 1670 helix: 0.88 (0.18), residues: 802 sheet: -0.35 (0.41), residues: 148 loop : -0.93 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 185 TYR 0.013 0.002 TYR A 540 PHE 0.018 0.002 PHE A 176 TRP 0.009 0.002 TRP A 368 HIS 0.006 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00558 (14364) covalent geometry : angle 0.58920 (19477) hydrogen bonds : bond 0.05327 ( 706) hydrogen bonds : angle 4.77892 ( 1979) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 254 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ILE cc_start: 0.8903 (mm) cc_final: 0.8650 (mp) REVERT: A 372 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6211 (mp0) REVERT: A 382 ASP cc_start: 0.7530 (t0) cc_final: 0.7102 (m-30) REVERT: A 610 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6774 (mt-10) REVERT: B 172 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7609 (mm-30) REVERT: B 698 LYS cc_start: 0.7974 (tttt) cc_final: 0.7757 (mtmt) REVERT: C 1 MET cc_start: 0.6678 (tpt) cc_final: 0.6250 (tpt) REVERT: C 3 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.6395 (ptp-170) REVERT: C 175 ARG cc_start: 0.8370 (mmm-85) cc_final: 0.8045 (tpt-90) outliers start: 28 outliers final: 8 residues processed: 237 average time/residue: 1.3116 time to fit residues: 340.8147 Evaluate side-chains 226 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 214 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 71 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 137 optimal weight: 0.4980 chunk 36 optimal weight: 0.0670 overall best weight: 1.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 239 ASN B 314 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.157585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.128712 restraints weight = 43501.664| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.44 r_work: 0.3241 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14364 Z= 0.140 Angle : 0.527 6.100 19477 Z= 0.280 Chirality : 0.039 0.183 2141 Planarity : 0.004 0.039 2426 Dihedral : 10.075 73.768 2186 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.74 % Allowed : 13.24 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.20), residues: 1670 helix: 1.09 (0.18), residues: 806 sheet: -0.39 (0.40), residues: 153 loop : -0.82 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 185 TYR 0.012 0.001 TYR A 131 PHE 0.017 0.001 PHE A 176 TRP 0.008 0.001 TRP A 368 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00317 (14364) covalent geometry : angle 0.52687 (19477) hydrogen bonds : bond 0.04481 ( 706) hydrogen bonds : angle 4.62062 ( 1979) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 245 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7142 (tmm) cc_final: 0.6711 (tmt) REVERT: A 12 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6896 (tpp) REVERT: A 382 ASP cc_start: 0.7419 (t0) cc_final: 0.7054 (m-30) REVERT: A 610 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6756 (mt-10) REVERT: B 1 MET cc_start: 0.7900 (ttp) cc_final: 0.7631 (ttm) REVERT: B 172 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7613 (mm-30) REVERT: B 398 ASP cc_start: 0.7482 (t0) cc_final: 0.7253 (t0) REVERT: B 480 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8198 (mtpm) REVERT: B 628 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8232 (mp) REVERT: B 698 LYS cc_start: 0.7960 (tttt) cc_final: 0.7752 (mtmt) REVERT: C 1 MET cc_start: 0.6675 (tpt) cc_final: 0.6284 (tpt) REVERT: C 3 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.6414 (ptp-170) REVERT: C 175 ARG cc_start: 0.8352 (mmm-85) cc_final: 0.8053 (tpt-90) outliers start: 26 outliers final: 9 residues processed: 230 average time/residue: 1.3251 time to fit residues: 334.1436 Evaluate side-chains 227 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 212 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 53 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 65 GLN B 314 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.154779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.123736 restraints weight = 43727.059| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.52 r_work: 0.3160 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14364 Z= 0.207 Angle : 0.561 6.056 19477 Z= 0.300 Chirality : 0.041 0.197 2141 Planarity : 0.004 0.041 2426 Dihedral : 10.209 74.968 2186 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.21 % Allowed : 13.91 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.20), residues: 1670 helix: 0.98 (0.18), residues: 807 sheet: -0.47 (0.40), residues: 153 loop : -0.88 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 168 TYR 0.015 0.002 TYR A 131 PHE 0.018 0.001 PHE A 176 TRP 0.008 0.001 TRP A 368 HIS 0.005 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00486 (14364) covalent geometry : angle 0.56134 (19477) hydrogen bonds : bond 0.04880 ( 706) hydrogen bonds : angle 4.62831 ( 1979) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ARG cc_start: 0.8665 (mtm180) cc_final: 0.8231 (mtm180) REVERT: A 372 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6339 (mp0) REVERT: A 382 ASP cc_start: 0.7526 (t0) cc_final: 0.7061 (m-30) REVERT: A 610 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6747 (mt-10) REVERT: B 1 MET cc_start: 0.7915 (ttp) cc_final: 0.7657 (ttm) REVERT: B 172 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7593 (mm-30) REVERT: B 398 ASP cc_start: 0.7640 (t0) cc_final: 0.7385 (t0) REVERT: B 628 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8171 (mp) REVERT: B 674 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.6952 (mm) REVERT: B 698 LYS cc_start: 0.7893 (tttt) cc_final: 0.7657 (mtmt) REVERT: C 1 MET cc_start: 0.6636 (tpt) cc_final: 0.6258 (tpt) REVERT: C 3 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.6234 (ptp-170) REVERT: C 175 ARG cc_start: 0.8402 (mmm-85) cc_final: 0.8128 (tpt-90) REVERT: C 188 GLU cc_start: 0.7827 (tp30) cc_final: 0.7297 (tp30) REVERT: C 216 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7560 (ttp-170) outliers start: 33 outliers final: 10 residues processed: 239 average time/residue: 1.3304 time to fit residues: 347.1707 Evaluate side-chains 235 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 216 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 67 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 chunk 107 optimal weight: 0.0980 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 161 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.154900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.125165 restraints weight = 43532.488| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.55 r_work: 0.3227 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14364 Z= 0.151 Angle : 0.523 6.652 19477 Z= 0.279 Chirality : 0.039 0.188 2141 Planarity : 0.004 0.039 2426 Dihedral : 10.111 73.784 2186 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.61 % Allowed : 14.72 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.20), residues: 1670 helix: 1.14 (0.18), residues: 801 sheet: -0.48 (0.40), residues: 153 loop : -0.85 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 168 TYR 0.014 0.001 TYR A 131 PHE 0.017 0.001 PHE A 176 TRP 0.008 0.001 TRP A 368 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00350 (14364) covalent geometry : angle 0.52338 (19477) hydrogen bonds : bond 0.04429 ( 706) hydrogen bonds : angle 4.54139 ( 1979) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 239 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6936 (tpp) REVERT: A 372 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6344 (mp0) REVERT: A 382 ASP cc_start: 0.7466 (t0) cc_final: 0.7102 (m-30) REVERT: A 610 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6798 (mt-10) REVERT: B 1 MET cc_start: 0.7913 (ttp) cc_final: 0.7597 (ttm) REVERT: B 172 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7693 (mm-30) REVERT: B 398 ASP cc_start: 0.7673 (t0) cc_final: 0.7414 (t0) REVERT: B 480 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8220 (mtpm) REVERT: B 628 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8286 (mp) REVERT: B 674 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7012 (mm) REVERT: B 698 LYS cc_start: 0.8008 (tttt) cc_final: 0.7797 (mtmt) REVERT: C 1 MET cc_start: 0.6779 (tpt) cc_final: 0.6331 (tpt) REVERT: C 3 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.6353 (ptp-170) REVERT: C 143 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7128 (ttm110) REVERT: C 175 ARG cc_start: 0.8402 (mmm-85) cc_final: 0.8166 (tpt-90) outliers start: 24 outliers final: 7 residues processed: 226 average time/residue: 1.3099 time to fit residues: 323.3486 Evaluate side-chains 228 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 143 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 17 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 314 ASN B 533 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.155832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.124862 restraints weight = 43649.584| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.53 r_work: 0.3192 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14364 Z= 0.130 Angle : 0.510 6.581 19477 Z= 0.270 Chirality : 0.038 0.182 2141 Planarity : 0.004 0.039 2426 Dihedral : 10.035 73.728 2186 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.54 % Allowed : 15.45 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.20), residues: 1670 helix: 1.28 (0.18), residues: 801 sheet: -0.41 (0.41), residues: 153 loop : -0.79 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 75 TYR 0.014 0.001 TYR A 131 PHE 0.016 0.001 PHE A 176 TRP 0.007 0.001 TRP A 368 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00298 (14364) covalent geometry : angle 0.50987 (19477) hydrogen bonds : bond 0.04178 ( 706) hydrogen bonds : angle 4.44944 ( 1979) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 237 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7730 (mm-30) REVERT: A 372 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6254 (mp0) REVERT: A 382 ASP cc_start: 0.7468 (t0) cc_final: 0.7017 (m-30) REVERT: A 607 MET cc_start: 0.8189 (mmm) cc_final: 0.7351 (tpp) REVERT: A 610 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6816 (mt-10) REVERT: B 1 MET cc_start: 0.7792 (ttp) cc_final: 0.7588 (ttm) REVERT: B 172 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7575 (mm-30) REVERT: B 398 ASP cc_start: 0.7625 (t0) cc_final: 0.7355 (t0) REVERT: B 628 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8149 (mp) REVERT: B 674 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.6988 (mm) REVERT: B 698 LYS cc_start: 0.7853 (tttt) cc_final: 0.7627 (mtmt) REVERT: C 3 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.6163 (ptp-170) REVERT: C 143 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.7022 (ttm110) REVERT: C 175 ARG cc_start: 0.8399 (mmm-85) cc_final: 0.8124 (tpt-90) REVERT: C 188 GLU cc_start: 0.7784 (tp30) cc_final: 0.7246 (tp30) outliers start: 23 outliers final: 7 residues processed: 225 average time/residue: 1.3466 time to fit residues: 330.6852 Evaluate side-chains 224 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 143 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 73 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 138 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.157026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.126061 restraints weight = 43655.421| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.53 r_work: 0.3232 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14364 Z= 0.114 Angle : 0.495 6.824 19477 Z= 0.261 Chirality : 0.037 0.177 2141 Planarity : 0.004 0.078 2426 Dihedral : 9.945 73.670 2186 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.34 % Allowed : 16.05 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.20), residues: 1670 helix: 1.46 (0.18), residues: 801 sheet: -0.23 (0.42), residues: 141 loop : -0.80 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 75 TYR 0.015 0.001 TYR A 131 PHE 0.015 0.001 PHE A 176 TRP 0.007 0.001 TRP A 368 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00257 (14364) covalent geometry : angle 0.49521 (19477) hydrogen bonds : bond 0.03923 ( 706) hydrogen bonds : angle 4.35571 ( 1979) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 238 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7706 (mm-30) REVERT: A 382 ASP cc_start: 0.7424 (t0) cc_final: 0.6980 (m-30) REVERT: A 610 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6712 (mt-10) REVERT: B 1 MET cc_start: 0.7750 (ttp) cc_final: 0.7545 (ttm) REVERT: B 172 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7614 (mm-30) REVERT: B 398 ASP cc_start: 0.7628 (t0) cc_final: 0.7377 (t0) REVERT: B 698 LYS cc_start: 0.7877 (tttt) cc_final: 0.7535 (mtmt) REVERT: C 1 MET cc_start: 0.6596 (tpt) cc_final: 0.6119 (tpt) REVERT: C 175 ARG cc_start: 0.8389 (mmm-85) cc_final: 0.8122 (tpt-90) REVERT: C 188 GLU cc_start: 0.7764 (tp30) cc_final: 0.7183 (tp30) outliers start: 20 outliers final: 8 residues processed: 226 average time/residue: 1.2699 time to fit residues: 314.6504 Evaluate side-chains 221 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 210 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 133 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.154344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.124356 restraints weight = 43454.185| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.58 r_work: 0.3204 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14364 Z= 0.185 Angle : 0.542 7.250 19477 Z= 0.287 Chirality : 0.040 0.193 2141 Planarity : 0.004 0.059 2426 Dihedral : 10.081 74.516 2186 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.54 % Allowed : 16.12 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.20), residues: 1670 helix: 1.28 (0.18), residues: 801 sheet: -0.48 (0.40), residues: 153 loop : -0.79 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 75 TYR 0.024 0.002 TYR A 131 PHE 0.014 0.001 PHE A 520 TRP 0.008 0.001 TRP A 368 HIS 0.005 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00438 (14364) covalent geometry : angle 0.54157 (19477) hydrogen bonds : bond 0.04462 ( 706) hydrogen bonds : angle 4.45223 ( 1979) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6947 (tpp) REVERT: A 52 HIS cc_start: 0.7205 (OUTLIER) cc_final: 0.6506 (t70) REVERT: A 155 MET cc_start: 0.7783 (ttt) cc_final: 0.7564 (ptm) REVERT: A 168 ARG cc_start: 0.8680 (mtm180) cc_final: 0.8457 (mtp180) REVERT: A 252 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7738 (mm-30) REVERT: A 382 ASP cc_start: 0.7471 (t0) cc_final: 0.7013 (m-30) REVERT: A 419 ASP cc_start: 0.8305 (p0) cc_final: 0.8105 (p0) REVERT: A 607 MET cc_start: 0.8289 (mmm) cc_final: 0.7486 (tpp) REVERT: A 610 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6854 (mt-10) REVERT: B 1 MET cc_start: 0.7841 (ttp) cc_final: 0.7588 (ttm) REVERT: B 172 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7685 (mm-30) REVERT: B 398 ASP cc_start: 0.7657 (t0) cc_final: 0.7378 (t0) REVERT: B 674 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7063 (mm) REVERT: B 698 LYS cc_start: 0.7932 (tttt) cc_final: 0.7706 (mtmt) REVERT: C 1 MET cc_start: 0.6673 (tpt) cc_final: 0.6190 (tpt) REVERT: C 3 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.6241 (ptp-170) REVERT: C 188 GLU cc_start: 0.7773 (tp30) cc_final: 0.7206 (tp30) outliers start: 23 outliers final: 8 residues processed: 220 average time/residue: 1.3470 time to fit residues: 322.6625 Evaluate side-chains 224 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.157769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.127975 restraints weight = 43435.288| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.55 r_work: 0.3226 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14364 Z= 0.119 Angle : 0.506 7.630 19477 Z= 0.266 Chirality : 0.038 0.178 2141 Planarity : 0.004 0.055 2426 Dihedral : 9.967 73.653 2186 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.00 % Allowed : 16.79 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.20), residues: 1670 helix: 1.46 (0.18), residues: 801 sheet: -0.24 (0.42), residues: 141 loop : -0.81 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 75 TYR 0.011 0.001 TYR A 131 PHE 0.012 0.001 PHE A 176 TRP 0.007 0.001 TRP A 368 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00271 (14364) covalent geometry : angle 0.50624 (19477) hydrogen bonds : bond 0.03979 ( 706) hydrogen bonds : angle 4.38234 ( 1979) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 211 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ARG cc_start: 0.8716 (mtm180) cc_final: 0.8478 (mtm180) REVERT: A 252 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7708 (mm-30) REVERT: A 382 ASP cc_start: 0.7418 (t0) cc_final: 0.6962 (m-30) REVERT: A 607 MET cc_start: 0.8309 (mmm) cc_final: 0.7817 (tpp) REVERT: A 610 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6678 (mp0) REVERT: B 1 MET cc_start: 0.7776 (ttp) cc_final: 0.7547 (ttm) REVERT: B 172 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7618 (mm-30) REVERT: B 398 ASP cc_start: 0.7666 (t0) cc_final: 0.7395 (t0) REVERT: B 698 LYS cc_start: 0.7871 (tttt) cc_final: 0.7656 (mtmt) REVERT: C 3 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.6199 (ptp-170) REVERT: C 175 ARG cc_start: 0.8357 (mmm-85) cc_final: 0.8094 (tpt-90) REVERT: C 188 GLU cc_start: 0.7770 (tp30) cc_final: 0.7221 (tp30) outliers start: 15 outliers final: 9 residues processed: 218 average time/residue: 1.3559 time to fit residues: 323.1124 Evaluate side-chains 223 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 53 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.158182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.128640 restraints weight = 43157.535| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.51 r_work: 0.3256 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14364 Z= 0.142 Angle : 0.514 7.379 19477 Z= 0.270 Chirality : 0.038 0.184 2141 Planarity : 0.004 0.051 2426 Dihedral : 9.985 73.755 2186 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.40 % Allowed : 16.25 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.20), residues: 1670 helix: 1.43 (0.18), residues: 801 sheet: -0.37 (0.41), residues: 146 loop : -0.76 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 75 TYR 0.014 0.001 TYR A 131 PHE 0.012 0.001 PHE A 520 TRP 0.007 0.001 TRP A 368 HIS 0.003 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00333 (14364) covalent geometry : angle 0.51413 (19477) hydrogen bonds : bond 0.04126 ( 706) hydrogen bonds : angle 4.35913 ( 1979) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9542.61 seconds wall clock time: 161 minutes 51.78 seconds (9711.78 seconds total)