Starting phenix.real_space_refine on Wed Feb 4 12:22:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kci_62252/02_2026/9kci_62252.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kci_62252/02_2026/9kci_62252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kci_62252/02_2026/9kci_62252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kci_62252/02_2026/9kci_62252.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kci_62252/02_2026/9kci_62252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kci_62252/02_2026/9kci_62252.map" } resolution = 2.9 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= 0.005 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: 9 Type Number sf(0) Gaussians K 3 8.98 5 Al 1 5.89 5 P 5 5.49 5 Mg 1 5.21 5 S 59 5.16 5 C 6759 2.51 5 N 1671 2.21 5 O 1983 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 10486 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7627 Classifications: {'peptide': 984} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 940} Chain: "B" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2130 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 247} Chain: "C" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 270 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "A" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 297 Unusual residues: {' K': 3, ' MG': 1, 'ALF': 1, 'CLR': 1, 'PCW': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'CLR': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 11 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 2.41, per 1000 atoms: 0.23 Number of scatterers: 10486 At special positions: 0 Unit cell: (119.52, 90.47, 170.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) K 3 19.00 S 59 16.00 P 5 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1983 8.00 N 1671 7.00 C 6759 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 250 " 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: 0.82 Conformation dependent library (CDL) restraints added in 445.3 milliseconds 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2388 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 9 sheets defined 51.1% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 98 through 123 removed outlier: 3.625A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 150 Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 261 through 264 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 282 through 313 Processing helix chain 'A' and resid 316 through 332 Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.617A pdb=" N ARG A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 370 removed outlier: 3.911A pdb=" N THR A 366 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLY A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 428 Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 466 through 474 Processing helix chain 'A' and resid 510 through 515 removed outlier: 3.771A pdb=" N LEU A 515 " --> pdb=" O PRO A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 547 Processing helix chain 'A' and resid 598 through 609 Processing helix chain 'A' and resid 620 through 631 Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 651 through 655 removed outlier: 3.778A pdb=" N VAL A 655 " --> pdb=" O VAL A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 660 Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.880A pdb=" N ASP A 672 " --> pdb=" O SER A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 Processing helix chain 'A' and resid 694 through 708 removed outlier: 3.675A pdb=" N GLN A 708 " --> pdb=" O GLY A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 739 through 745 Processing helix chain 'A' and resid 755 through 782 removed outlier: 4.190A pdb=" N VAL A 759 " --> pdb=" O PHE A 755 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER A 782 " --> pdb=" O TYR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 797 Proline residue: A 789 - end of helix Processing helix chain 'A' and resid 803 through 812 Processing helix chain 'A' and resid 815 through 821 Processing helix chain 'A' and resid 822 through 825 Processing helix chain 'A' and resid 846 through 856 Processing helix chain 'A' and resid 856 through 876 Processing helix chain 'A' and resid 879 through 884 removed outlier: 3.938A pdb=" N LEU A 884 " --> pdb=" O PRO A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 907 through 938 removed outlier: 3.998A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 948 Processing helix chain 'A' and resid 951 through 971 Processing helix chain 'A' and resid 973 through 978 Processing helix chain 'A' and resid 984 through 990 removed outlier: 3.923A pdb=" N CYS A 990 " --> pdb=" O TRP A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1011 Processing helix chain 'A' and resid 1015 through 1022 Processing helix chain 'B' and resid 14 through 20 removed outlier: 4.314A pdb=" N LEU B 18 " --> pdb=" O ALA B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 64 removed outlier: 3.633A pdb=" N THR B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 120 through 125 removed outlier: 3.909A pdb=" N LYS B 123 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN B 124 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 211 through 215 removed outlier: 3.737A pdb=" N TYR B 214 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 162 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 181 removed outlier: 3.542A pdb=" N MET A 178 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 11.803A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N CYS A 249 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LYS A 212 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLU A 251 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY A 210 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR A 253 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ALA A 208 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG A 255 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASP A 202 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS A 211 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 176 through 181 removed outlier: 3.542A pdb=" N MET A 178 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 11.803A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N CYS A 249 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LYS A 212 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLU A 251 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY A 210 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR A 253 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ALA A 208 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG A 255 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASP A 202 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 358 removed outlier: 6.362A pdb=" N GLY A 731 " --> pdb=" O MET A 748 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LEU A 750 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA A 733 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL A 712 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL A 732 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL A 714 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N MET A 734 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N GLY A 716 " --> pdb=" O MET A 734 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE A 373 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL A 616 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N SER A 375 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL A 613 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 396 through 399 removed outlier: 5.109A pdb=" N VAL A 388 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE A 592 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS A 390 " --> pdb=" O SER A 590 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N LEU A 583 " --> pdb=" O PHE A 559 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N PHE A 559 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N PHE A 585 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N HIS A 557 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY A 587 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 504 " --> pdb=" O HIS A 493 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS A 493 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 490 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 478 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LYS A 494 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LYS A 476 " --> pdb=" O LYS A 494 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 396 through 399 removed outlier: 5.109A pdb=" N VAL A 388 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE A 592 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS A 390 " --> pdb=" O SER A 590 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N CYS A 518 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N PHE A 585 " --> pdb=" O CYS A 518 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N SER A 520 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLY A 587 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N LEU A 522 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 12.604A pdb=" N ILE A 589 " --> pdb=" O LEU A 522 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 432 through 433 removed outlier: 3.835A pdb=" N VAL A 432 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 898 through 899 Processing sheet with id=AA8, first strand: chain 'B' and resid 81 through 84 Processing sheet with id=AA9, first strand: chain 'B' and resid 92 through 94 534 hydrogen bonds defined for protein. 1536 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: 1.97 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2909 1.33 - 1.45: 1609 1.45 - 1.57: 6010 1.57 - 1.69: 10 1.69 - 1.81: 93 Bond restraints: 10631 Sorted by residual: bond pdb=" C11 PCW A1110 " pdb=" O3 PCW A1110 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" C11 PCW A1106 " pdb=" O3 PCW A1106 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C11 PCW A1109 " pdb=" O3 PCW A1109 " ideal model delta sigma weight residual 1.326 1.452 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" C11 PCW A1111 " pdb=" O3 PCW A1111 " ideal model delta sigma weight residual 1.326 1.451 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C11 PCW A1107 " pdb=" O3 PCW A1107 " ideal model delta sigma weight residual 1.326 1.451 -0.125 2.00e-02 2.50e+03 3.89e+01 ... (remaining 10626 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.15: 14381 14.15 - 28.31: 4 28.31 - 42.46: 0 42.46 - 56.61: 0 56.61 - 70.76: 2 Bond angle restraints: 14387 Sorted by residual: angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F2 ALF A1101 " ideal model delta sigma weight residual 108.68 179.44 -70.76 3.00e+00 1.11e-01 5.56e+02 angle pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.63 179.02 -69.39 3.00e+00 1.11e-01 5.35e+02 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 110.21 90.12 20.09 3.00e+00 1.11e-01 4.49e+01 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F3 ALF A1101 " ideal model delta sigma weight residual 109.59 89.65 19.94 3.00e+00 1.11e-01 4.42e+01 angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F3 ALF A1101 " ideal model delta sigma weight residual 109.69 89.95 19.74 3.00e+00 1.11e-01 4.33e+01 ... (remaining 14382 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.25: 6439 33.25 - 66.49: 137 66.49 - 99.74: 15 99.74 - 132.99: 8 132.99 - 166.23: 4 Dihedral angle restraints: 6603 sinusoidal: 2893 harmonic: 3710 Sorted by residual: dihedral pdb=" N PCW A1110 " pdb=" C4 PCW A1110 " pdb=" C5 PCW A1110 " pdb=" O4P PCW A1110 " ideal model delta sinusoidal sigma weight residual -66.66 99.57 -166.23 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" N PCW A1109 " pdb=" C4 PCW A1109 " pdb=" C5 PCW A1109 " pdb=" O4P PCW A1109 " ideal model delta sinusoidal sigma weight residual -66.66 78.11 -144.77 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" N PCW A1111 " pdb=" C4 PCW A1111 " pdb=" C5 PCW A1111 " pdb=" O4P PCW A1111 " ideal model delta sinusoidal sigma weight residual 293.34 151.97 141.37 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 6600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1312 0.052 - 0.105: 249 0.105 - 0.157: 50 0.157 - 0.210: 7 0.210 - 0.262: 4 Chirality restraints: 1622 Sorted by residual: chirality pdb=" C2 PCW A1111 " pdb=" C1 PCW A1111 " pdb=" C3 PCW A1111 " pdb=" O2 PCW A1111 " both_signs ideal model delta sigma weight residual False -2.32 -2.59 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C13 CLR C 201 " pdb=" C12 CLR C 201 " pdb=" C14 CLR C 201 " pdb=" C17 CLR C 201 " both_signs ideal model delta sigma weight residual False -2.93 -2.68 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C13 CLR B 302 " pdb=" C12 CLR B 302 " pdb=" C14 CLR B 302 " pdb=" C17 CLR B 302 " both_signs ideal model delta sigma weight residual False -2.93 -2.70 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1619 not shown) Planarity restraints: 1811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 235 " -0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO A 236 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 800 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO A 801 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 801 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 801 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 291 " 0.009 2.00e-02 2.50e+03 1.01e-02 1.77e+00 pdb=" CG PHE A 291 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 291 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 291 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 291 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 291 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 291 " -0.001 2.00e-02 2.50e+03 ... (remaining 1808 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.58: 91 2.58 - 3.22: 9769 3.22 - 3.86: 20742 3.86 - 4.50: 29118 4.50 - 5.14: 46080 Nonbonded interactions: 105800 Sorted by model distance: nonbonded pdb=" F1 ALF A1101 " pdb="MG MG A1102 " model vdw 1.935 2.120 nonbonded pdb=" O THR A 378 " pdb="MG MG A1102 " model vdw 2.120 2.170 nonbonded pdb=" OD1 ASP A 717 " pdb="MG MG A1102 " model vdw 2.173 2.170 nonbonded pdb=" OE1 GLN A 856 " pdb=" OH TYR A1001 " model vdw 2.200 3.040 nonbonded pdb=" OD2 ASP A 376 " pdb=" F1 ALF A1101 " model vdw 2.201 2.990 ... (remaining 105795 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.650 Find NCS groups from input model: 0.050 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:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 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 : 0.006 0.127 10634 Z= 0.291 Angle : 1.198 70.763 14393 Z= 0.453 Chirality : 0.046 0.262 1622 Planarity : 0.004 0.054 1811 Dihedral : 15.285 166.234 4206 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.42 (0.24), residues: 1280 helix: 1.69 (0.22), residues: 572 sheet: 0.61 (0.42), residues: 143 loop : 0.37 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 445 TYR 0.013 0.001 TYR A 869 PHE 0.023 0.002 PHE A 291 TRP 0.010 0.001 TRP A 418 HIS 0.007 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00602 (10631) covalent geometry : angle 1.19868 (14387) SS BOND : bond 0.00075 ( 3) SS BOND : angle 0.42427 ( 6) hydrogen bonds : bond 0.15932 ( 512) hydrogen bonds : angle 6.04539 ( 1536) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.358 Fit side-chains REVERT: A 158 MET cc_start: 0.8429 (tpp) cc_final: 0.8205 (tpt) REVERT: A 232 THR cc_start: 0.8505 (m) cc_final: 0.8274 (m) REVERT: A 423 ARG cc_start: 0.7921 (ttp-170) cc_final: 0.7623 (ttm170) REVERT: A 470 MET cc_start: 0.7322 (ttp) cc_final: 0.7118 (ttp) REVERT: A 488 TYR cc_start: 0.7662 (p90) cc_final: 0.7453 (p90) REVERT: B 122 GLN cc_start: 0.8404 (pt0) cc_final: 0.8163 (pt0) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.6575 time to fit residues: 95.3877 Evaluate side-chains 110 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 396 GLN A 489 GLN ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.155147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.112196 restraints weight = 11295.772| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.60 r_work: 0.2926 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10634 Z= 0.123 Angle : 0.765 30.055 14393 Z= 0.328 Chirality : 0.042 0.193 1622 Planarity : 0.004 0.045 1811 Dihedral : 13.859 155.160 1822 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.46 % Allowed : 6.38 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.44 (0.24), residues: 1280 helix: 1.83 (0.22), residues: 581 sheet: 0.61 (0.40), residues: 140 loop : 0.21 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 848 TYR 0.011 0.001 TYR B 204 PHE 0.024 0.001 PHE A 291 TRP 0.008 0.001 TRP A 418 HIS 0.007 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00281 (10631) covalent geometry : angle 0.76554 (14387) SS BOND : bond 0.00212 ( 3) SS BOND : angle 0.63441 ( 6) hydrogen bonds : bond 0.04479 ( 512) hydrogen bonds : angle 4.67347 ( 1536) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.326 Fit side-chains REVERT: A 74 ARG cc_start: 0.7268 (ttp-170) cc_final: 0.6988 (ttp80) REVERT: A 232 THR cc_start: 0.8486 (m) cc_final: 0.8274 (m) REVERT: A 238 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: A 423 ARG cc_start: 0.7434 (ttp-170) cc_final: 0.7080 (ttm170) REVERT: A 438 GLU cc_start: 0.6831 (mp0) cc_final: 0.6216 (mp0) REVERT: A 816 MET cc_start: 0.8555 (mmm) cc_final: 0.8348 (mmt) REVERT: B 122 GLN cc_start: 0.8297 (pt0) cc_final: 0.7848 (pt0) outliers start: 16 outliers final: 6 residues processed: 138 average time/residue: 0.5708 time to fit residues: 84.4334 Evaluate side-chains 127 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 127 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 79 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 51 optimal weight: 6.9990 chunk 34 optimal weight: 0.4980 chunk 100 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 98 optimal weight: 0.0470 chunk 109 optimal weight: 0.0670 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 489 GLN ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.155683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.114353 restraints weight = 11313.684| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.56 r_work: 0.2982 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10634 Z= 0.103 Angle : 0.739 30.022 14393 Z= 0.311 Chirality : 0.041 0.190 1622 Planarity : 0.003 0.045 1811 Dihedral : 13.212 157.315 1822 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.91 % Allowed : 8.74 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.54 (0.24), residues: 1280 helix: 1.92 (0.22), residues: 582 sheet: 0.62 (0.40), residues: 130 loop : 0.27 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 423 TYR 0.020 0.001 TYR A 488 PHE 0.019 0.001 PHE A 793 TRP 0.010 0.001 TRP A 418 HIS 0.008 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00230 (10631) covalent geometry : angle 0.73888 (14387) SS BOND : bond 0.00138 ( 3) SS BOND : angle 0.46091 ( 6) hydrogen bonds : bond 0.03863 ( 512) hydrogen bonds : angle 4.38256 ( 1536) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.396 Fit side-chains REVERT: A 41 MET cc_start: 0.5747 (mmt) cc_final: 0.5395 (mpp) REVERT: A 74 ARG cc_start: 0.7270 (ttp-170) cc_final: 0.6981 (ttp80) REVERT: A 232 THR cc_start: 0.8489 (m) cc_final: 0.8274 (m) REVERT: A 404 GLU cc_start: 0.8305 (pm20) cc_final: 0.7945 (pm20) REVERT: A 423 ARG cc_start: 0.7469 (ttp-170) cc_final: 0.7191 (ttm170) REVERT: A 438 GLU cc_start: 0.6819 (mp0) cc_final: 0.6289 (mp0) REVERT: A 476 LYS cc_start: 0.6105 (OUTLIER) cc_final: 0.4948 (mmpt) REVERT: A 490 LEU cc_start: 0.7320 (pt) cc_final: 0.7120 (pp) REVERT: A 507 MET cc_start: 0.7302 (ttm) cc_final: 0.7078 (ttm) REVERT: A 816 MET cc_start: 0.8562 (mmm) cc_final: 0.8325 (mmt) REVERT: B 122 GLN cc_start: 0.8240 (pt0) cc_final: 0.7840 (pt0) outliers start: 10 outliers final: 4 residues processed: 141 average time/residue: 0.5644 time to fit residues: 85.8685 Evaluate side-chains 129 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 127 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 1 optimal weight: 0.4980 chunk 120 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 129 ASN A 390 HIS A 489 GLN ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.153936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.111190 restraints weight = 11383.860| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.48 r_work: 0.2986 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10634 Z= 0.109 Angle : 0.737 29.919 14393 Z= 0.311 Chirality : 0.041 0.189 1622 Planarity : 0.003 0.046 1811 Dihedral : 12.894 158.573 1822 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.46 % Allowed : 10.20 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.54 (0.24), residues: 1280 helix: 1.88 (0.22), residues: 589 sheet: 0.54 (0.38), residues: 139 loop : 0.31 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 270 TYR 0.015 0.001 TYR A 869 PHE 0.020 0.001 PHE A 793 TRP 0.011 0.001 TRP A 418 HIS 0.004 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00250 (10631) covalent geometry : angle 0.73718 (14387) SS BOND : bond 0.00140 ( 3) SS BOND : angle 0.46746 ( 6) hydrogen bonds : bond 0.03846 ( 512) hydrogen bonds : angle 4.30303 ( 1536) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.446 Fit side-chains REVERT: A 41 MET cc_start: 0.5900 (mmt) cc_final: 0.5490 (mpp) REVERT: A 74 ARG cc_start: 0.7224 (ttp-170) cc_final: 0.6934 (ttp80) REVERT: A 232 THR cc_start: 0.8458 (m) cc_final: 0.8235 (m) REVERT: A 238 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: A 404 GLU cc_start: 0.8243 (pm20) cc_final: 0.7858 (pm20) REVERT: A 423 ARG cc_start: 0.7407 (ttp-170) cc_final: 0.6993 (ttm170) REVERT: A 438 GLU cc_start: 0.6783 (mp0) cc_final: 0.6240 (mp0) REVERT: A 476 LYS cc_start: 0.6072 (OUTLIER) cc_final: 0.4944 (mmpt) REVERT: A 507 MET cc_start: 0.7407 (ttm) cc_final: 0.7087 (ttm) REVERT: A 816 MET cc_start: 0.8540 (mmm) cc_final: 0.8300 (mmt) REVERT: A 900 ASP cc_start: 0.8899 (p0) cc_final: 0.8377 (p0) REVERT: B 122 GLN cc_start: 0.8270 (pt0) cc_final: 0.7833 (pt0) outliers start: 16 outliers final: 8 residues processed: 145 average time/residue: 0.6231 time to fit residues: 97.4858 Evaluate side-chains 133 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 61 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 390 HIS A 486 ASN A 489 GLN ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN B 257 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.146539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.101653 restraints weight = 11397.958| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.71 r_work: 0.2778 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 10634 Z= 0.286 Angle : 0.872 30.161 14393 Z= 0.391 Chirality : 0.050 0.261 1622 Planarity : 0.005 0.053 1811 Dihedral : 14.398 156.995 1822 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.09 % Allowed : 11.75 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.86 (0.23), residues: 1280 helix: 1.31 (0.21), residues: 582 sheet: 0.08 (0.38), residues: 146 loop : 0.04 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 255 TYR 0.016 0.002 TYR A 488 PHE 0.027 0.002 PHE A 793 TRP 0.008 0.002 TRP A 890 HIS 0.009 0.002 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00699 (10631) covalent geometry : angle 0.87167 (14387) SS BOND : bond 0.00283 ( 3) SS BOND : angle 0.85095 ( 6) hydrogen bonds : bond 0.05790 ( 512) hydrogen bonds : angle 4.77173 ( 1536) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.438 Fit side-chains REVERT: A 74 ARG cc_start: 0.7226 (ttp-170) cc_final: 0.6921 (ttp80) REVERT: A 232 THR cc_start: 0.8519 (m) cc_final: 0.8313 (m) REVERT: A 238 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: A 423 ARG cc_start: 0.7545 (ttp-170) cc_final: 0.7003 (ttm170) REVERT: A 476 LYS cc_start: 0.6208 (OUTLIER) cc_final: 0.5795 (mmpt) REVERT: A 517 ARG cc_start: 0.5608 (mtt-85) cc_final: 0.5192 (mtp85) REVERT: A 816 MET cc_start: 0.8580 (mmm) cc_final: 0.8367 (mmt) REVERT: A 1012 ARG cc_start: 0.6266 (ttt180) cc_final: 0.5427 (mtp85) REVERT: B 261 GLN cc_start: 0.7694 (mt0) cc_final: 0.6835 (mp10) outliers start: 23 outliers final: 14 residues processed: 139 average time/residue: 0.5951 time to fit residues: 88.9569 Evaluate side-chains 132 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 396 GLN Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 263 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 163 ASN A 390 HIS A 489 GLN ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.150573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.105624 restraints weight = 11374.518| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.73 r_work: 0.2897 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10634 Z= 0.120 Angle : 0.755 30.294 14393 Z= 0.322 Chirality : 0.042 0.204 1622 Planarity : 0.003 0.051 1811 Dihedral : 13.417 153.434 1822 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.09 % Allowed : 12.75 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.22 (0.24), residues: 1280 helix: 1.70 (0.22), residues: 580 sheet: 0.16 (0.38), residues: 144 loop : 0.14 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 848 TYR 0.017 0.001 TYR A 869 PHE 0.024 0.002 PHE A 231 TRP 0.017 0.001 TRP A 418 HIS 0.006 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00276 (10631) covalent geometry : angle 0.75495 (14387) SS BOND : bond 0.00140 ( 3) SS BOND : angle 0.49032 ( 6) hydrogen bonds : bond 0.04134 ( 512) hydrogen bonds : angle 4.42235 ( 1536) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.389 Fit side-chains REVERT: A 74 ARG cc_start: 0.7257 (ttp-170) cc_final: 0.6966 (ttp80) REVERT: A 232 THR cc_start: 0.8514 (m) cc_final: 0.8302 (m) REVERT: A 291 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8105 (p90) REVERT: A 404 GLU cc_start: 0.8236 (pm20) cc_final: 0.7882 (pm20) REVERT: A 423 ARG cc_start: 0.7543 (ttp-170) cc_final: 0.7109 (ttm170) REVERT: A 816 MET cc_start: 0.8548 (mmm) cc_final: 0.8288 (mmt) REVERT: A 1012 ARG cc_start: 0.6043 (ttt180) cc_final: 0.5255 (mtp85) outliers start: 23 outliers final: 11 residues processed: 138 average time/residue: 0.6029 time to fit residues: 89.4870 Evaluate side-chains 133 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 72 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 115 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 390 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.148605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.104558 restraints weight = 11273.082| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.65 r_work: 0.2858 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10634 Z= 0.173 Angle : 0.784 30.195 14393 Z= 0.341 Chirality : 0.044 0.216 1622 Planarity : 0.004 0.051 1811 Dihedral : 13.457 151.990 1822 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.55 % Allowed : 14.30 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.14 (0.24), residues: 1280 helix: 1.61 (0.22), residues: 582 sheet: 0.26 (0.38), residues: 154 loop : 0.07 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 517 TYR 0.019 0.002 TYR A 488 PHE 0.025 0.002 PHE A 793 TRP 0.017 0.001 TRP A 418 HIS 0.006 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00422 (10631) covalent geometry : angle 0.78394 (14387) SS BOND : bond 0.00142 ( 3) SS BOND : angle 0.51572 ( 6) hydrogen bonds : bond 0.04681 ( 512) hydrogen bonds : angle 4.51357 ( 1536) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.404 Fit side-chains REVERT: A 74 ARG cc_start: 0.7217 (ttp-170) cc_final: 0.6963 (ttp80) REVERT: A 232 THR cc_start: 0.8510 (m) cc_final: 0.8294 (m) REVERT: A 291 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.8081 (p90) REVERT: A 404 GLU cc_start: 0.8227 (pm20) cc_final: 0.7910 (pm20) REVERT: A 423 ARG cc_start: 0.7488 (ttp-170) cc_final: 0.7057 (ttm170) REVERT: A 517 ARG cc_start: 0.5510 (mpt-90) cc_final: 0.5286 (mtp85) REVERT: A 816 MET cc_start: 0.8547 (mmm) cc_final: 0.8321 (mmt) REVERT: A 1012 ARG cc_start: 0.6083 (ttt180) cc_final: 0.5365 (mtp85) REVERT: B 261 GLN cc_start: 0.7662 (mt0) cc_final: 0.6873 (mp10) outliers start: 17 outliers final: 13 residues processed: 136 average time/residue: 0.5944 time to fit residues: 87.1091 Evaluate side-chains 132 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 263 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 69 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 74 optimal weight: 0.2980 chunk 105 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 98 optimal weight: 0.0570 chunk 8 optimal weight: 7.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 163 ASN A 390 HIS A 429 ASN B 145 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.152291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.108681 restraints weight = 11247.875| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.65 r_work: 0.2948 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10634 Z= 0.100 Angle : 0.739 30.262 14393 Z= 0.311 Chirality : 0.041 0.200 1622 Planarity : 0.003 0.051 1811 Dihedral : 12.625 149.890 1822 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.64 % Allowed : 14.57 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.35 (0.24), residues: 1280 helix: 1.81 (0.22), residues: 588 sheet: 0.11 (0.39), residues: 144 loop : 0.22 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 517 TYR 0.023 0.001 TYR A 488 PHE 0.021 0.001 PHE A 231 TRP 0.025 0.001 TRP A 418 HIS 0.005 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00223 (10631) covalent geometry : angle 0.73931 (14387) SS BOND : bond 0.00132 ( 3) SS BOND : angle 0.44911 ( 6) hydrogen bonds : bond 0.03623 ( 512) hydrogen bonds : angle 4.29725 ( 1536) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.249 Fit side-chains REVERT: A 41 MET cc_start: 0.5789 (mmt) cc_final: 0.5367 (mpp) REVERT: A 74 ARG cc_start: 0.7252 (ttp-170) cc_final: 0.6998 (ttp80) REVERT: A 232 THR cc_start: 0.8501 (m) cc_final: 0.8288 (m) REVERT: A 291 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8183 (p90) REVERT: A 404 GLU cc_start: 0.8264 (pm20) cc_final: 0.7922 (pm20) REVERT: A 423 ARG cc_start: 0.7428 (ttp-170) cc_final: 0.7068 (ttm170) REVERT: A 687 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: A 816 MET cc_start: 0.8558 (mmm) cc_final: 0.8343 (mmt) REVERT: A 1012 ARG cc_start: 0.5881 (ttt180) cc_final: 0.5236 (mtp85) REVERT: B 261 GLN cc_start: 0.7710 (mt0) cc_final: 0.6908 (mp10) outliers start: 18 outliers final: 10 residues processed: 141 average time/residue: 0.5743 time to fit residues: 87.2966 Evaluate side-chains 132 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 57 optimal weight: 0.0670 chunk 34 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 390 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.152021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.108671 restraints weight = 11242.688| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.68 r_work: 0.2956 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10634 Z= 0.103 Angle : 0.737 30.024 14393 Z= 0.311 Chirality : 0.041 0.197 1622 Planarity : 0.004 0.049 1811 Dihedral : 12.322 151.717 1822 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.37 % Allowed : 15.03 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.46 (0.24), residues: 1280 helix: 1.84 (0.22), residues: 589 sheet: 0.38 (0.39), residues: 153 loop : 0.28 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 848 TYR 0.017 0.001 TYR A 869 PHE 0.021 0.001 PHE A 793 TRP 0.027 0.001 TRP A 418 HIS 0.005 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00235 (10631) covalent geometry : angle 0.73740 (14387) SS BOND : bond 0.00077 ( 3) SS BOND : angle 0.28164 ( 6) hydrogen bonds : bond 0.03694 ( 512) hydrogen bonds : angle 4.24604 ( 1536) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.502 Fit side-chains REVERT: A 41 MET cc_start: 0.5789 (mmt) cc_final: 0.5388 (mpp) REVERT: A 74 ARG cc_start: 0.7338 (ttp-170) cc_final: 0.7089 (ttp80) REVERT: A 232 THR cc_start: 0.8496 (m) cc_final: 0.8284 (m) REVERT: A 291 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.8205 (p90) REVERT: A 404 GLU cc_start: 0.8274 (pm20) cc_final: 0.7967 (pm20) REVERT: A 423 ARG cc_start: 0.7511 (ttp-170) cc_final: 0.7114 (ttm170) REVERT: A 517 ARG cc_start: 0.5799 (mtp85) cc_final: 0.5544 (mmm-85) REVERT: A 683 LYS cc_start: 0.8635 (ttmm) cc_final: 0.7989 (tttp) REVERT: A 687 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: A 816 MET cc_start: 0.8548 (mmm) cc_final: 0.8338 (mmt) REVERT: A 900 ASP cc_start: 0.8955 (p0) cc_final: 0.8478 (p0) REVERT: A 1019 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8157 (mtpm) REVERT: B 234 GLN cc_start: 0.8628 (tt0) cc_final: 0.8299 (tt0) REVERT: B 261 GLN cc_start: 0.7661 (mt0) cc_final: 0.6953 (mp10) outliers start: 15 outliers final: 11 residues processed: 134 average time/residue: 0.6295 time to fit residues: 90.7903 Evaluate side-chains 132 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 54 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 60 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 80 optimal weight: 0.0570 chunk 106 optimal weight: 0.4980 chunk 4 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 390 HIS B 257 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.152517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.109050 restraints weight = 11187.827| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.62 r_work: 0.3031 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10634 Z= 0.106 Angle : 0.739 29.983 14393 Z= 0.312 Chirality : 0.041 0.196 1622 Planarity : 0.003 0.049 1811 Dihedral : 11.974 151.901 1822 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.46 % Allowed : 15.12 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.44 (0.24), residues: 1280 helix: 1.86 (0.22), residues: 588 sheet: 0.31 (0.37), residues: 164 loop : 0.25 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 517 TYR 0.021 0.001 TYR A 488 PHE 0.021 0.001 PHE A 793 TRP 0.031 0.001 TRP A 418 HIS 0.005 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00242 (10631) covalent geometry : angle 0.73959 (14387) SS BOND : bond 0.00062 ( 3) SS BOND : angle 0.30142 ( 6) hydrogen bonds : bond 0.03721 ( 512) hydrogen bonds : angle 4.26316 ( 1536) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.429 Fit side-chains REVERT: A 41 MET cc_start: 0.5817 (mmt) cc_final: 0.5390 (mpp) REVERT: A 74 ARG cc_start: 0.7470 (ttp-170) cc_final: 0.7224 (ttp80) REVERT: A 232 THR cc_start: 0.8522 (m) cc_final: 0.8315 (m) REVERT: A 291 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.8253 (p90) REVERT: A 404 GLU cc_start: 0.8333 (pm20) cc_final: 0.8035 (pm20) REVERT: A 423 ARG cc_start: 0.7677 (ttp-170) cc_final: 0.7279 (ttm170) REVERT: A 517 ARG cc_start: 0.5862 (mtp85) cc_final: 0.5605 (mtp85) REVERT: A 683 LYS cc_start: 0.8731 (ttmm) cc_final: 0.8092 (tttp) REVERT: A 900 ASP cc_start: 0.8919 (p0) cc_final: 0.8422 (p0) REVERT: A 1019 LYS cc_start: 0.8567 (mtpt) cc_final: 0.8264 (mtpm) REVERT: C 140 HIS cc_start: 0.7594 (t70) cc_final: 0.7366 (t70) outliers start: 16 outliers final: 12 residues processed: 133 average time/residue: 0.5786 time to fit residues: 83.0536 Evaluate side-chains 131 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 263 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 92 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 101 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 390 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.152666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.109707 restraints weight = 11325.760| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.63 r_work: 0.2977 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10634 Z= 0.109 Angle : 0.741 29.987 14393 Z= 0.313 Chirality : 0.041 0.196 1622 Planarity : 0.004 0.048 1811 Dihedral : 11.712 151.934 1822 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.37 % Allowed : 15.12 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.44 (0.24), residues: 1280 helix: 1.85 (0.22), residues: 588 sheet: 0.34 (0.37), residues: 164 loop : 0.25 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 517 TYR 0.017 0.001 TYR A 869 PHE 0.021 0.001 PHE A 793 TRP 0.031 0.001 TRP A 418 HIS 0.005 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00251 (10631) covalent geometry : angle 0.74065 (14387) SS BOND : bond 0.00070 ( 3) SS BOND : angle 0.30797 ( 6) hydrogen bonds : bond 0.03785 ( 512) hydrogen bonds : angle 4.24214 ( 1536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4138.88 seconds wall clock time: 71 minutes 13.13 seconds (4273.13 seconds total)