Starting phenix.real_space_refine on Fri Sep 11 09:59:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pw9_20501/09_2026/6pw9_20501.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pw9_20501/09_2026/6pw9_20501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pw9_20501/09_2026/6pw9_20501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pw9_20501/09_2026/6pw9_20501.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6pw9_20501/09_2026/6pw9_20501.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pw9_20501/09_2026/6pw9_20501.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pw9_20501/09_2026/6pw9_20501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pw9_20501/09_2026/6pw9_20501.map" } resolution = 4.03 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 ------------------------------------------------------------------------------- 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 56 5.16 5 C 5597 2.51 5 N 1508 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8836 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1260 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 5470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5470 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 27, 'TRANS': 637} Chain breaks: 1 Chain: "C" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1287 Unusual residues: {'ACE': 1} Classifications: {'peptide': 160, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'ACE_C-N': 1, 'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 732 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 94} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 87 Unusual residues: {'ACO': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.74, per 1000 atoms: 0.20 Number of scatterers: 8836 At special positions: 0 Unit cell: (114.562, 100.534, 106.379, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 9 15.00 O 1666 8.00 N 1508 7.00 C 5597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 316.9 milliseconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 3 sheets defined 67.4% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 15 through 26 removed outlier: 4.107A pdb=" N LEU A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 39 removed outlier: 4.257A pdb=" N TYR A 36 " --> pdb=" O ASN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 45 removed outlier: 3.726A pdb=" N LEU A 45 " --> pdb=" O VAL A 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 42 through 45' Processing helix chain 'A' and resid 88 through 104 removed outlier: 3.924A pdb=" N MET A 92 " --> pdb=" O ILE A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 126 Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 129 through 144 removed outlier: 3.528A pdb=" N TYR B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 161 removed outlier: 4.344A pdb=" N TRP B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 176 removed outlier: 4.139A pdb=" N LYS B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 removed outlier: 4.165A pdb=" N THR B 180 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER B 181 " --> pdb=" O GLN B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 181' Processing helix chain 'B' and resid 185 through 203 removed outlier: 4.488A pdb=" N TYR B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 217 through 220 removed outlier: 4.008A pdb=" N ILE B 220 " --> pdb=" O GLU B 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 217 through 220' Processing helix chain 'B' and resid 222 through 237 removed outlier: 4.155A pdb=" N VAL B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 254 Processing helix chain 'B' and resid 257 through 269 removed outlier: 3.880A pdb=" N TYR B 261 " --> pdb=" O ASN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.824A pdb=" N ILE B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 295 Processing helix chain 'B' and resid 296 through 301 removed outlier: 4.432A pdb=" N PHE B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 301 " --> pdb=" O PRO B 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 296 through 301' Processing helix chain 'B' and resid 303 through 320 removed outlier: 3.627A pdb=" N LYS B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 336 through 357 removed outlier: 4.479A pdb=" N SER B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 removed outlier: 4.242A pdb=" N LEU B 374 " --> pdb=" O PRO B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 404 removed outlier: 3.715A pdb=" N ALA B 393 " --> pdb=" O GLN B 389 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR B 399 " --> pdb=" O GLU B 395 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B 404 " --> pdb=" O ALA B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 420 removed outlier: 4.049A pdb=" N PHE B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 437 removed outlier: 3.806A pdb=" N GLU B 433 " --> pdb=" O ARG B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 454 removed outlier: 4.201A pdb=" N ASN B 445 " --> pdb=" O ASP B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 466 Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 484 through 498 removed outlier: 3.739A pdb=" N GLN B 488 " --> pdb=" O CYS B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 521 Processing helix chain 'B' and resid 522 through 524 No H-bonds generated for 'chain 'B' and resid 522 through 524' Processing helix chain 'B' and resid 525 through 532 Processing helix chain 'B' and resid 535 through 547 removed outlier: 3.570A pdb=" N VAL B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 550 No H-bonds generated for 'chain 'B' and resid 548 through 550' Processing helix chain 'B' and resid 551 through 571 removed outlier: 3.529A pdb=" N PHE B 555 " --> pdb=" O HIS B 551 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 648 Processing helix chain 'B' and resid 653 through 668 Proline residue: B 663 - end of helix removed outlier: 3.579A pdb=" N VAL B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 683 removed outlier: 4.281A pdb=" N HIS B 675 " --> pdb=" O LYS B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 700 Processing helix chain 'B' and resid 705 through 722 Processing helix chain 'B' and resid 727 through 742 removed outlier: 3.732A pdb=" N THR B 732 " --> pdb=" O ASP B 728 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 733 " --> pdb=" O THR B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 758 removed outlier: 3.530A pdb=" N PHE B 750 " --> pdb=" O ASN B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 775 removed outlier: 3.797A pdb=" N MET B 771 " --> pdb=" O SER B 767 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 778 No H-bonds generated for 'chain 'B' and resid 776 through 778' Processing helix chain 'B' and resid 779 through 787 Processing helix chain 'B' and resid 798 through 811 Processing helix chain 'B' and resid 820 through 832 removed outlier: 3.824A pdb=" N LYS B 830 " --> pdb=" O ALA B 826 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 831 " --> pdb=" O ASN B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 839 removed outlier: 3.674A pdb=" N PHE B 838 " --> pdb=" O ALA B 835 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET B 839 " --> pdb=" O LEU B 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 835 through 839' Processing helix chain 'C' and resid 7 through 12 removed outlier: 3.588A pdb=" N LEU C 11 " --> pdb=" O ARG C 7 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET C 12 " --> pdb=" O PRO C 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 7 through 12' Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.548A pdb=" N CYS C 17 " --> pdb=" O ASN C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 35 removed outlier: 3.739A pdb=" N TYR C 31 " --> pdb=" O GLN C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 82 removed outlier: 3.605A pdb=" N ARG C 82 " --> pdb=" O ARG C 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 79 through 82' Processing helix chain 'C' and resid 86 through 102 Processing helix chain 'C' and resid 116 through 124 Processing helix chain 'C' and resid 151 through 159 Processing helix chain 'D' and resid 60 through 85 removed outlier: 3.961A pdb=" N VAL D 66 " --> pdb=" O THR D 62 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU D 82 " --> pdb=" O LYS D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 103 removed outlier: 3.845A pdb=" N LEU D 95 " --> pdb=" O LYS D 91 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU D 103 " --> pdb=" O MET D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 115 removed outlier: 3.528A pdb=" N ALA D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 129 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 10 removed outlier: 6.222A pdb=" N PHE A 51 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA A 55 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA A 58 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU A 77 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N CYS A 60 " --> pdb=" O MET A 75 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER A 66 " --> pdb=" O GLN A 69 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASN A 108 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 74 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N HIS A 112 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N THR A 76 " --> pdb=" O HIS A 112 " (cutoff:3.500A) removed outlier: 13.145A pdb=" N GLN A 114 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 14.820A pdb=" N GLY A 78 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU A 133 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLN A 151 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE A 131 " --> pdb=" O GLN A 151 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 2 through 5 removed outlier: 8.378A pdb=" N VAL C 53 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL C 77 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR C 55 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU C 75 " --> pdb=" O TYR C 55 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU C 57 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS C 69 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 106 through 112 removed outlier: 3.685A pdb=" N GLU C 132 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS C 148 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ILE C 130 " --> pdb=" O LYS C 148 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1428 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: 1.09 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1481 1.30 - 1.43: 2253 1.43 - 1.56: 5168 1.56 - 1.69: 15 1.69 - 1.82: 91 Bond restraints: 9008 Sorted by residual: bond pdb=" C1B ACO C 902 " pdb=" O4B ACO C 902 " ideal model delta sigma weight residual 1.416 1.660 -0.244 1.40e-02 5.10e+03 3.05e+02 bond pdb=" C1B ACO C 902 " pdb=" C2B ACO C 902 " ideal model delta sigma weight residual 1.531 1.345 0.186 1.20e-02 6.94e+03 2.39e+02 bond pdb=" C5P ACO C 902 " pdb=" N4P ACO C 902 " ideal model delta sigma weight residual 1.331 1.498 -0.167 1.20e-02 6.94e+03 1.93e+02 bond pdb=" C6A ACO C 902 " pdb=" N6A ACO C 902 " ideal model delta sigma weight residual 1.337 1.463 -0.126 1.00e-02 1.00e+04 1.58e+02 bond pdb=" O3A ACO C 902 " pdb=" P2A ACO C 902 " ideal model delta sigma weight residual 1.592 1.723 -0.131 1.10e-02 8.26e+03 1.43e+02 ... (remaining 9003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 11812 3.03 - 6.06: 263 6.06 - 9.09: 63 9.09 - 12.13: 19 12.13 - 15.16: 3 Bond angle restraints: 12160 Sorted by residual: angle pdb=" P1A ACO C 902 " pdb=" O3A ACO C 902 " pdb=" P2A ACO C 902 " ideal model delta sigma weight residual 136.83 121.67 15.16 1.00e+00 1.00e+00 2.30e+02 angle pdb=" N1A ACO C 902 " pdb=" C6A ACO C 902 " pdb=" N6A ACO C 902 " ideal model delta sigma weight residual 118.11 104.50 13.61 1.23e+00 6.64e-01 1.23e+02 angle pdb=" C5A ACO C 902 " pdb=" C6A ACO C 902 " pdb=" N6A ACO C 902 " ideal model delta sigma weight residual 123.59 134.97 -11.38 1.08e+00 8.64e-01 1.12e+02 angle pdb=" N1A ACO C 902 " pdb=" C2A ACO C 902 " pdb=" N3A ACO C 902 " ideal model delta sigma weight residual 128.69 119.33 9.36 1.00e+00 1.00e+00 8.76e+01 angle pdb=" C5A ACO C 902 " pdb=" C4A ACO C 902 " pdb=" N3A ACO C 902 " ideal model delta sigma weight residual 126.80 118.30 8.50 1.00e+00 1.00e+00 7.22e+01 ... (remaining 12155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.16: 4892 15.16 - 30.33: 455 30.33 - 45.49: 141 45.49 - 60.65: 16 60.65 - 75.82: 6 Dihedral angle restraints: 5510 sinusoidal: 2307 harmonic: 3203 Sorted by residual: dihedral pdb=" CA LYS B 500 " pdb=" C LYS B 500 " pdb=" N PHE B 501 " pdb=" CA PHE B 501 " ideal model delta harmonic sigma weight residual -180.00 -150.02 -29.98 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA VAL B 185 " pdb=" C VAL B 185 " pdb=" N ASP B 186 " pdb=" CA ASP B 186 " ideal model delta harmonic sigma weight residual -180.00 -152.95 -27.05 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA PHE C 102 " pdb=" C PHE C 102 " pdb=" N ASN C 103 " pdb=" CA ASN C 103 " ideal model delta harmonic sigma weight residual 180.00 154.32 25.68 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 5507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.011: 1324 1.011 - 2.022: 0 2.022 - 3.034: 0 3.034 - 4.045: 0 4.045 - 5.056: 3 Chirality restraints: 1327 Sorted by residual: chirality pdb=" C4 IHP C 901 " pdb=" C3 IHP C 901 " pdb=" C5 IHP C 901 " pdb=" O14 IHP C 901 " both_signs ideal model delta sigma weight residual False 2.48 -2.58 5.06 2.00e-01 2.50e+01 6.39e+02 chirality pdb=" C2 IHP C 901 " pdb=" C1 IHP C 901 " pdb=" C3 IHP C 901 " pdb=" O12 IHP C 901 " both_signs ideal model delta sigma weight residual False -2.52 2.50 -5.02 2.00e-01 2.50e+01 6.30e+02 chirality pdb=" C1 IHP C 901 " pdb=" C2 IHP C 901 " pdb=" C6 IHP C 901 " pdb=" O11 IHP C 901 " both_signs ideal model delta sigma weight residual False 2.32 -2.48 4.80 2.00e-01 2.50e+01 5.75e+02 ... (remaining 1324 not shown) Planarity restraints: 1549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 143 " -0.100 5.00e-02 4.00e+02 1.49e-01 3.56e+01 pdb=" N PRO A 144 " 0.258 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 707 " -0.020 2.00e-02 2.50e+03 1.73e-02 7.45e+00 pdb=" CG TRP B 707 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 707 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 707 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 707 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 707 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 707 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 707 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 707 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 707 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 565 " 0.015 2.00e-02 2.50e+03 1.74e-02 6.08e+00 pdb=" CG TYR B 565 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR B 565 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR B 565 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 565 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 565 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 565 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 565 " 0.001 2.00e-02 2.50e+03 ... (remaining 1546 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 15 2.40 - 3.03: 4155 3.03 - 3.65: 13924 3.65 - 4.28: 18970 4.28 - 4.90: 30417 Nonbonded interactions: 67481 Sorted by model distance: nonbonded pdb=" O PRO A 13 " pdb=" CD1 ILE A 16 " model vdw 1.781 3.460 nonbonded pdb=" OE2 GLU B 191 " pdb=" O ILE B 533 " model vdw 1.914 3.040 nonbonded pdb=" O GLU A 143 " pdb=" OE1 GLU A 143 " model vdw 1.918 3.040 nonbonded pdb=" CE2 TYR B 528 " pdb=" CE LYS B 532 " model vdw 2.180 3.740 nonbonded pdb=" O ILE B 784 " pdb=" OG1 THR B 788 " model vdw 2.260 3.040 ... (remaining 67476 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.950 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 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 : 0.007 0.244 9008 Z= 0.507 Angle : 1.225 15.157 12160 Z= 0.667 Chirality : 0.244 5.056 1327 Planarity : 0.008 0.149 1549 Dihedral : 13.120 75.816 3432 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.81 % Allowed : 8.18 % Favored : 90.01 % 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: -4.47 (0.20), residues: 1065 helix: -2.86 (0.15), residues: 637 sheet: -2.24 (0.57), residues: 71 loop : -2.92 (0.27), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 714 TYR 0.042 0.003 TYR B 565 PHE 0.030 0.003 PHE B 716 TRP 0.047 0.003 TRP B 707 HIS 0.007 0.002 HIS A 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.51 ( 9008) covalent geometry : angle 1.22544 / 0.67 (12160) hydrogen bonds : bond 0.12168 / 7.63 ( 483) hydrogen bonds : angle 6.94602 / 4.85 ( 1428) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 302 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.7985 (m-40) cc_final: 0.7342 (t0) REVERT: A 99 ILE cc_start: 0.8686 (pp) cc_final: 0.8269 (pp) REVERT: B 450 LYS cc_start: 0.7847 (ttpt) cc_final: 0.7600 (ttmm) REVERT: B 459 LYS cc_start: 0.8611 (ptpp) cc_final: 0.7916 (tppt) REVERT: B 503 GLU cc_start: 0.5474 (pp20) cc_final: 0.4958 (pt0) REVERT: B 528 TYR cc_start: 0.6315 (t80) cc_final: 0.5999 (t80) REVERT: B 775 LEU cc_start: 0.8055 (mm) cc_final: 0.7676 (mm) REVERT: B 803 MET cc_start: 0.8045 (tmm) cc_final: 0.7723 (tmm) REVERT: C 25 ASN cc_start: 0.8128 (m-40) cc_final: 0.7792 (m-40) REVERT: D 60 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8155 (tm) REVERT: D 92 LYS cc_start: 0.8644 (mppt) cc_final: 0.7998 (tptt) outliers start: 17 outliers final: 5 residues processed: 316 average time/residue: 0.1093 time to fit residues: 45.8584 Evaluate side-chains 192 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 186 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 ASN A 65 HIS A 114 GLN A 148 HIS ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN B 197 ASN B 212 HIS B 478 ASN B 569 HIS C 71 HIS C 120 HIS D 36 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.145291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.118322 restraints weight = 20025.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.121202 restraints weight = 12312.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.123146 restraints weight = 8838.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.124250 restraints weight = 7075.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.125146 restraints weight = 6168.074| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9008 Z= 0.155 Angle : 0.766 10.584 12160 Z= 0.386 Chirality : 0.047 0.254 1327 Planarity : 0.005 0.066 1549 Dihedral : 7.060 59.127 1204 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.74 % Allowed : 6.06 % Favored : 93.20 % 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: -2.69 (0.23), residues: 1065 helix: -1.35 (0.19), residues: 647 sheet: -1.98 (0.65), residues: 62 loop : -2.30 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 118 TYR 0.016 0.002 TYR A 73 PHE 0.019 0.002 PHE B 716 TRP 0.030 0.002 TRP B 707 HIS 0.006 0.001 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 9008) covalent geometry : angle 0.76649 / 0.39 (12160) hydrogen bonds : bond 0.04182 / 2.70 ( 483) hydrogen bonds : angle 5.14889 / 3.58 ( 1428) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 251 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 SER cc_start: 0.8464 (t) cc_final: 0.8101 (p) REVERT: A 53 ASP cc_start: 0.6972 (m-30) cc_final: 0.6704 (t70) REVERT: A 94 ASN cc_start: 0.8000 (m-40) cc_final: 0.7292 (t0) REVERT: A 98 ASN cc_start: 0.8565 (p0) cc_final: 0.8354 (p0) REVERT: A 138 TYR cc_start: 0.7873 (t80) cc_final: 0.7276 (t80) REVERT: A 141 ARG cc_start: 0.8008 (mpp80) cc_final: 0.7700 (mpp80) REVERT: A 146 ASP cc_start: 0.7281 (m-30) cc_final: 0.6445 (t70) REVERT: A 148 HIS cc_start: 0.7508 (m90) cc_final: 0.7252 (m-70) REVERT: B 273 MET cc_start: 0.7583 (mtt) cc_final: 0.7365 (mtt) REVERT: B 278 LYS cc_start: 0.8228 (mttt) cc_final: 0.7708 (mmtm) REVERT: B 358 LEU cc_start: 0.7042 (tp) cc_final: 0.6832 (pt) REVERT: B 366 LYS cc_start: 0.7422 (pptt) cc_final: 0.6871 (tmtt) REVERT: B 447 LYS cc_start: 0.8124 (mttt) cc_final: 0.7915 (mttt) REVERT: B 490 GLU cc_start: 0.8438 (tp30) cc_final: 0.8228 (tp30) REVERT: B 551 HIS cc_start: 0.8139 (t-90) cc_final: 0.7417 (t70) REVERT: B 672 ILE cc_start: 0.7152 (pt) cc_final: 0.6928 (pt) REVERT: B 726 LEU cc_start: 0.7541 (pp) cc_final: 0.6530 (tp) REVERT: B 734 LEU cc_start: 0.9009 (tt) cc_final: 0.8584 (pp) REVERT: B 803 MET cc_start: 0.8231 (tmm) cc_final: 0.7715 (tmm) REVERT: C 12 MET cc_start: 0.8178 (tmm) cc_final: 0.7912 (tmm) REVERT: C 96 ARG cc_start: 0.8251 (ptm160) cc_final: 0.8014 (ttp80) REVERT: C 98 MET cc_start: 0.8258 (mtp) cc_final: 0.8040 (mtp) REVERT: C 101 ASN cc_start: 0.8749 (p0) cc_final: 0.8527 (p0) REVERT: D 91 LYS cc_start: 0.8647 (tttp) cc_final: 0.8298 (mtmt) REVERT: D 92 LYS cc_start: 0.8483 (mppt) cc_final: 0.7756 (tptt) outliers start: 7 outliers final: 1 residues processed: 257 average time/residue: 0.1026 time to fit residues: 35.7812 Evaluate side-chains 190 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 101 optimal weight: 7.9990 chunk 25 optimal weight: 0.1980 chunk 1 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 GLN C 5 ASN C 71 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.136547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.110144 restraints weight = 20518.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.112498 restraints weight = 12969.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.114152 restraints weight = 9593.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.115041 restraints weight = 7890.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.115737 restraints weight = 7009.180| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 9008 Z= 0.239 Angle : 0.842 11.159 12160 Z= 0.436 Chirality : 0.053 0.307 1327 Planarity : 0.005 0.052 1549 Dihedral : 7.102 59.930 1204 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.53 % Allowed : 5.84 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.23), residues: 1065 helix: -1.15 (0.19), residues: 652 sheet: -1.75 (0.73), residues: 46 loop : -2.20 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 106 TYR 0.023 0.003 TYR B 349 PHE 0.030 0.003 PHE B 515 TRP 0.018 0.004 TRP B 430 HIS 0.007 0.002 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.24 ( 9008) covalent geometry : angle 0.84228 / 0.44 (12160) hydrogen bonds : bond 0.05022 / 3.19 ( 483) hydrogen bonds : angle 5.23857 / 3.63 ( 1428) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 227 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7253 (m-30) cc_final: 0.6867 (t0) REVERT: A 94 ASN cc_start: 0.8002 (m-40) cc_final: 0.7284 (t0) REVERT: A 98 ASN cc_start: 0.8507 (p0) cc_final: 0.8283 (p0) REVERT: A 138 TYR cc_start: 0.7994 (t80) cc_final: 0.7728 (t80) REVERT: A 141 ARG cc_start: 0.8139 (mpp80) cc_final: 0.7765 (mpp80) REVERT: A 146 ASP cc_start: 0.7535 (m-30) cc_final: 0.6991 (m-30) REVERT: A 148 HIS cc_start: 0.7570 (m90) cc_final: 0.7329 (m-70) REVERT: B 191 GLU cc_start: 0.7590 (tp30) cc_final: 0.7203 (tp30) REVERT: B 291 LEU cc_start: 0.8568 (tp) cc_final: 0.8355 (tp) REVERT: B 358 LEU cc_start: 0.7428 (tp) cc_final: 0.7130 (pt) REVERT: B 366 LYS cc_start: 0.7238 (pptt) cc_final: 0.6932 (tmtt) REVERT: B 447 LYS cc_start: 0.8241 (mttt) cc_final: 0.7906 (ttmm) REVERT: B 490 GLU cc_start: 0.8577 (tp30) cc_final: 0.8328 (tp30) REVERT: B 510 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7603 (pm20) REVERT: B 551 HIS cc_start: 0.8489 (t-90) cc_final: 0.7850 (t-90) REVERT: B 734 LEU cc_start: 0.9214 (tt) cc_final: 0.8848 (tt) REVERT: B 803 MET cc_start: 0.8433 (tmm) cc_final: 0.7863 (tmm) REVERT: B 827 ASN cc_start: 0.8010 (t0) cc_final: 0.7745 (t0) REVERT: C 12 MET cc_start: 0.8717 (tmm) cc_final: 0.8241 (tmm) REVERT: C 134 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8234 (mm-30) REVERT: D 91 LYS cc_start: 0.8696 (tttp) cc_final: 0.8317 (mtmt) REVERT: D 92 LYS cc_start: 0.8546 (mppt) cc_final: 0.7851 (tptt) outliers start: 5 outliers final: 0 residues processed: 230 average time/residue: 0.0932 time to fit residues: 29.7655 Evaluate side-chains 177 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 70 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 ASN ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 197 ASN B 478 ASN B 509 HIS B 736 GLN C 71 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.138766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.111374 restraints weight = 20585.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.114025 restraints weight = 12682.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.115818 restraints weight = 9182.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.116996 restraints weight = 7441.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.117592 restraints weight = 6484.773| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9008 Z= 0.152 Angle : 0.746 9.597 12160 Z= 0.378 Chirality : 0.049 0.260 1327 Planarity : 0.004 0.060 1549 Dihedral : 6.755 59.479 1204 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.43 % Allowed : 5.74 % Favored : 93.84 % 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: -1.98 (0.24), residues: 1065 helix: -0.78 (0.19), residues: 651 sheet: -1.55 (0.80), residues: 41 loop : -2.08 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 134 TYR 0.029 0.002 TYR B 154 PHE 0.023 0.002 PHE B 716 TRP 0.018 0.002 TRP B 707 HIS 0.009 0.001 HIS B 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 9008) covalent geometry : angle 0.74582 / 0.38 (12160) hydrogen bonds : bond 0.04013 / 2.57 ( 483) hydrogen bonds : angle 4.79843 / 3.32 ( 1428) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 228 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7228 (m-30) cc_final: 0.6689 (t70) REVERT: A 90 THR cc_start: 0.7457 (m) cc_final: 0.7064 (m) REVERT: A 94 ASN cc_start: 0.7903 (m-40) cc_final: 0.7406 (m110) REVERT: A 138 TYR cc_start: 0.7894 (t80) cc_final: 0.7650 (t80) REVERT: A 141 ARG cc_start: 0.8085 (mpp80) cc_final: 0.7782 (mpp80) REVERT: A 146 ASP cc_start: 0.7454 (m-30) cc_final: 0.7048 (m-30) REVERT: B 191 GLU cc_start: 0.7856 (tp30) cc_final: 0.7460 (tp30) REVERT: B 224 LEU cc_start: 0.8002 (tt) cc_final: 0.7783 (tt) REVERT: B 291 LEU cc_start: 0.8633 (tp) cc_final: 0.8401 (tp) REVERT: B 358 LEU cc_start: 0.7595 (tp) cc_final: 0.7355 (pt) REVERT: B 366 LYS cc_start: 0.7271 (pptt) cc_final: 0.6999 (tmtt) REVERT: B 447 LYS cc_start: 0.8170 (mttt) cc_final: 0.7906 (ttmm) REVERT: B 490 GLU cc_start: 0.8569 (tp30) cc_final: 0.8295 (tp30) REVERT: B 523 PHE cc_start: 0.8489 (t80) cc_final: 0.8115 (t80) REVERT: B 551 HIS cc_start: 0.8468 (t-90) cc_final: 0.7883 (t-90) REVERT: B 728 ASP cc_start: 0.7856 (p0) cc_final: 0.7610 (p0) REVERT: B 734 LEU cc_start: 0.9249 (tt) cc_final: 0.8863 (tt) REVERT: B 803 MET cc_start: 0.8308 (tmm) cc_final: 0.7694 (tmm) REVERT: B 827 ASN cc_start: 0.8103 (t0) cc_final: 0.7829 (t0) REVERT: C 7 ARG cc_start: 0.8237 (mmt-90) cc_final: 0.7981 (mmt180) REVERT: C 12 MET cc_start: 0.8623 (tmm) cc_final: 0.8092 (tmm) REVERT: C 91 MET cc_start: 0.8213 (tpp) cc_final: 0.7971 (tpp) REVERT: C 134 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8206 (mm-30) REVERT: D 91 LYS cc_start: 0.8706 (tttp) cc_final: 0.8310 (mtmt) REVERT: D 92 LYS cc_start: 0.8585 (mppt) cc_final: 0.7867 (tptt) outliers start: 4 outliers final: 0 residues processed: 230 average time/residue: 0.0979 time to fit residues: 30.8561 Evaluate side-chains 174 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 77 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 ASN A 114 GLN ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN B 327 ASN B 478 ASN B 736 GLN D 116 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.142125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.114736 restraints weight = 20265.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.117542 restraints weight = 12513.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.119449 restraints weight = 9005.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.120565 restraints weight = 7237.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.121432 restraints weight = 6324.920| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9008 Z= 0.136 Angle : 0.736 9.096 12160 Z= 0.369 Chirality : 0.048 0.242 1327 Planarity : 0.004 0.047 1549 Dihedral : 6.510 59.640 1204 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.78 (0.24), residues: 1065 helix: -0.60 (0.19), residues: 650 sheet: -1.87 (0.66), residues: 55 loop : -1.94 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 134 TYR 0.028 0.001 TYR B 154 PHE 0.019 0.001 PHE B 716 TRP 0.016 0.002 TRP C 38 HIS 0.007 0.001 HIS B 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 9008) covalent geometry : angle 0.73638 / 0.37 (12160) hydrogen bonds : bond 0.03692 / 2.38 ( 483) hydrogen bonds : angle 4.67226 / 3.27 ( 1428) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7076 (m-30) cc_final: 0.6853 (t70) REVERT: A 94 ASN cc_start: 0.7969 (m-40) cc_final: 0.7243 (t0) REVERT: A 141 ARG cc_start: 0.8068 (mpp80) cc_final: 0.7786 (mpp80) REVERT: A 146 ASP cc_start: 0.7324 (m-30) cc_final: 0.6937 (m-30) REVERT: B 166 MET cc_start: 0.3850 (ppp) cc_final: 0.3470 (ppp) REVERT: B 191 GLU cc_start: 0.7969 (tp30) cc_final: 0.7751 (tp30) REVERT: B 224 LEU cc_start: 0.7954 (tt) cc_final: 0.7670 (tt) REVERT: B 291 LEU cc_start: 0.8606 (tp) cc_final: 0.8310 (tp) REVERT: B 366 LYS cc_start: 0.7300 (pptt) cc_final: 0.6772 (tmtt) REVERT: B 490 GLU cc_start: 0.8512 (tp30) cc_final: 0.8272 (tp30) REVERT: B 510 GLU cc_start: 0.8225 (pm20) cc_final: 0.7555 (pm20) REVERT: B 523 PHE cc_start: 0.8527 (t80) cc_final: 0.8244 (t80) REVERT: B 551 HIS cc_start: 0.8379 (t-90) cc_final: 0.8007 (t-90) REVERT: B 734 LEU cc_start: 0.9232 (tt) cc_final: 0.8866 (tt) REVERT: B 803 MET cc_start: 0.8210 (tmm) cc_final: 0.7589 (tmm) REVERT: B 827 ASN cc_start: 0.8040 (t0) cc_final: 0.7774 (t0) REVERT: C 7 ARG cc_start: 0.8187 (mmt-90) cc_final: 0.7951 (mmt180) REVERT: C 134 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8212 (tp30) REVERT: C 137 TYR cc_start: 0.7604 (t80) cc_final: 0.7255 (t80) REVERT: D 91 LYS cc_start: 0.8663 (tttp) cc_final: 0.8271 (mtmt) REVERT: D 92 LYS cc_start: 0.8580 (mppt) cc_final: 0.7849 (tptt) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.0793 time to fit residues: 26.9986 Evaluate side-chains 188 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 5 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 0.0000 chunk 4 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 196 GLN B 478 ASN C 71 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.139041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.112074 restraints weight = 20203.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.114664 restraints weight = 12528.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.116417 restraints weight = 9098.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.117417 restraints weight = 7347.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.117836 restraints weight = 6440.033| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9008 Z= 0.155 Angle : 0.765 11.405 12160 Z= 0.384 Chirality : 0.049 0.241 1327 Planarity : 0.004 0.042 1549 Dihedral : 6.522 63.123 1204 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.21 % Allowed : 3.19 % Favored : 96.60 % 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: -1.58 (0.25), residues: 1065 helix: -0.47 (0.20), residues: 650 sheet: -1.54 (0.68), residues: 55 loop : -1.86 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 62 TYR 0.030 0.002 TYR C 122 PHE 0.029 0.002 PHE B 515 TRP 0.023 0.002 TRP B 486 HIS 0.008 0.001 HIS B 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 9008) covalent geometry : angle 0.76473 / 0.38 (12160) hydrogen bonds : bond 0.04050 / 2.59 ( 483) hydrogen bonds : angle 4.66108 / 3.24 ( 1428) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 244 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8443 (tp30) cc_final: 0.8160 (mm-30) REVERT: A 53 ASP cc_start: 0.7218 (m-30) cc_final: 0.7007 (t70) REVERT: A 90 THR cc_start: 0.7548 (m) cc_final: 0.7257 (m) REVERT: A 94 ASN cc_start: 0.8133 (m-40) cc_final: 0.7605 (m110) REVERT: A 141 ARG cc_start: 0.8079 (mpp80) cc_final: 0.7796 (mpp80) REVERT: A 146 ASP cc_start: 0.7444 (m-30) cc_final: 0.7064 (m-30) REVERT: B 166 MET cc_start: 0.4161 (ppp) cc_final: 0.3671 (ppp) REVERT: B 173 GLU cc_start: 0.7893 (pp20) cc_final: 0.7686 (pp20) REVERT: B 291 LEU cc_start: 0.8561 (tp) cc_final: 0.8321 (tp) REVERT: B 366 LYS cc_start: 0.7396 (pptt) cc_final: 0.6790 (tmtt) REVERT: B 447 LYS cc_start: 0.8163 (mttt) cc_final: 0.7816 (ttmm) REVERT: B 450 LYS cc_start: 0.8094 (ttpt) cc_final: 0.7745 (ttmm) REVERT: B 490 GLU cc_start: 0.8543 (tp30) cc_final: 0.8287 (tp30) REVERT: B 523 PHE cc_start: 0.8386 (t80) cc_final: 0.8066 (t80) REVERT: B 551 HIS cc_start: 0.8488 (t-90) cc_final: 0.8131 (t-90) REVERT: B 734 LEU cc_start: 0.9366 (tt) cc_final: 0.9018 (tt) REVERT: B 803 MET cc_start: 0.8266 (tmm) cc_final: 0.7651 (tmm) REVERT: B 827 ASN cc_start: 0.8052 (t0) cc_final: 0.7809 (t0) REVERT: C 7 ARG cc_start: 0.8186 (mmt-90) cc_final: 0.7947 (mmt180) REVERT: C 46 GLU cc_start: 0.8053 (pt0) cc_final: 0.7799 (pt0) REVERT: C 134 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8164 (mm-30) REVERT: D 91 LYS cc_start: 0.8641 (tttp) cc_final: 0.8312 (mtmt) REVERT: D 92 LYS cc_start: 0.8618 (mppt) cc_final: 0.8013 (tptt) REVERT: D 102 MET cc_start: 0.8750 (ppp) cc_final: 0.8446 (ppp) REVERT: D 115 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7299 (mt-10) outliers start: 2 outliers final: 1 residues processed: 246 average time/residue: 0.0849 time to fit residues: 29.0332 Evaluate side-chains 188 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 51 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 HIS ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 478 ASN D 116 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.140207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.113166 restraints weight = 20043.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.115904 restraints weight = 12108.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.117784 restraints weight = 8616.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.119041 restraints weight = 6866.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.119859 restraints weight = 5918.080| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9008 Z= 0.139 Angle : 0.743 11.362 12160 Z= 0.371 Chirality : 0.048 0.235 1327 Planarity : 0.004 0.040 1549 Dihedral : 6.389 61.646 1204 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: -1.40 (0.25), residues: 1065 helix: -0.33 (0.20), residues: 654 sheet: -1.85 (0.58), residues: 65 loop : -1.71 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 62 TYR 0.025 0.002 TYR B 495 PHE 0.023 0.002 PHE B 716 TRP 0.022 0.002 TRP B 486 HIS 0.005 0.001 HIS B 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 9008) covalent geometry : angle 0.74319 / 0.37 (12160) hydrogen bonds : bond 0.03675 / 2.37 ( 483) hydrogen bonds : angle 4.62384 / 3.25 ( 1428) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8480 (tp30) cc_final: 0.8105 (mm-30) REVERT: A 94 ASN cc_start: 0.8080 (m-40) cc_final: 0.7276 (t0) REVERT: A 98 ASN cc_start: 0.8874 (p0) cc_final: 0.8531 (p0) REVERT: A 141 ARG cc_start: 0.8110 (mpp80) cc_final: 0.7828 (mpp80) REVERT: A 146 ASP cc_start: 0.7521 (m-30) cc_final: 0.7081 (m-30) REVERT: B 166 MET cc_start: 0.4169 (ppp) cc_final: 0.3718 (ppp) REVERT: B 291 LEU cc_start: 0.8618 (tp) cc_final: 0.8246 (tp) REVERT: B 366 LYS cc_start: 0.7514 (pptt) cc_final: 0.6845 (tmtt) REVERT: B 447 LYS cc_start: 0.8127 (mttt) cc_final: 0.7862 (ttmm) REVERT: B 450 LYS cc_start: 0.7904 (ttpt) cc_final: 0.7603 (ttmm) REVERT: B 490 GLU cc_start: 0.8537 (tp30) cc_final: 0.8298 (tp30) REVERT: B 523 PHE cc_start: 0.8369 (t80) cc_final: 0.8098 (t80) REVERT: B 551 HIS cc_start: 0.8526 (t-90) cc_final: 0.8139 (t-90) REVERT: B 728 ASP cc_start: 0.7777 (p0) cc_final: 0.6989 (t0) REVERT: B 734 LEU cc_start: 0.9318 (tt) cc_final: 0.8943 (tt) REVERT: B 738 MET cc_start: 0.8672 (mpp) cc_final: 0.8396 (mpp) REVERT: B 803 MET cc_start: 0.8224 (tmm) cc_final: 0.7597 (tmm) REVERT: C 46 GLU cc_start: 0.8069 (pt0) cc_final: 0.7845 (pt0) REVERT: C 134 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8167 (tp30) REVERT: C 137 TYR cc_start: 0.7875 (t80) cc_final: 0.7467 (t80) REVERT: D 92 LYS cc_start: 0.8897 (mppt) cc_final: 0.7981 (tptt) REVERT: D 102 MET cc_start: 0.8707 (ppp) cc_final: 0.8360 (ppp) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.0878 time to fit residues: 29.6476 Evaluate side-chains 183 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 23 optimal weight: 4.9990 chunk 102 optimal weight: 0.0970 chunk 46 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 29 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN C 71 HIS C 110 HIS D 116 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.142328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.115652 restraints weight = 20170.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.118421 restraints weight = 12332.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.120268 restraints weight = 8768.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.121491 restraints weight = 7019.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.122155 restraints weight = 6083.236| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9008 Z= 0.130 Angle : 0.745 11.345 12160 Z= 0.368 Chirality : 0.047 0.222 1327 Planarity : 0.004 0.042 1549 Dihedral : 6.223 59.902 1204 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: -1.22 (0.25), residues: 1065 helix: -0.17 (0.20), residues: 651 sheet: -1.89 (0.57), residues: 65 loop : -1.62 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 106 TYR 0.022 0.002 TYR B 154 PHE 0.024 0.002 PHE B 515 TRP 0.018 0.002 TRP C 38 HIS 0.006 0.001 HIS B 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 9008) covalent geometry : angle 0.74530 / 0.37 (12160) hydrogen bonds : bond 0.03506 / 2.24 ( 483) hydrogen bonds : angle 4.58024 / 3.19 ( 1428) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8466 (tp30) cc_final: 0.8115 (mm-30) REVERT: A 94 ASN cc_start: 0.8113 (m-40) cc_final: 0.7252 (t0) REVERT: A 98 ASN cc_start: 0.8865 (p0) cc_final: 0.8520 (p0) REVERT: A 146 ASP cc_start: 0.7490 (m-30) cc_final: 0.6977 (m-30) REVERT: B 191 GLU cc_start: 0.7533 (tp30) cc_final: 0.6926 (tm-30) REVERT: B 291 LEU cc_start: 0.8540 (tp) cc_final: 0.8187 (tp) REVERT: B 366 LYS cc_start: 0.7486 (pptt) cc_final: 0.6802 (tmtt) REVERT: B 447 LYS cc_start: 0.8082 (mttt) cc_final: 0.7751 (ttmm) REVERT: B 450 LYS cc_start: 0.7889 (ttpt) cc_final: 0.7406 (ttmm) REVERT: B 503 GLU cc_start: 0.5526 (pp20) cc_final: 0.5216 (pt0) REVERT: B 523 PHE cc_start: 0.8351 (t80) cc_final: 0.8094 (t80) REVERT: B 551 HIS cc_start: 0.8449 (t-90) cc_final: 0.8062 (t-90) REVERT: B 728 ASP cc_start: 0.7664 (p0) cc_final: 0.6862 (t0) REVERT: B 734 LEU cc_start: 0.9323 (tt) cc_final: 0.8919 (tt) REVERT: B 738 MET cc_start: 0.8668 (mpp) cc_final: 0.8441 (mpp) REVERT: B 803 MET cc_start: 0.8161 (tmm) cc_final: 0.7541 (tmm) REVERT: C 46 GLU cc_start: 0.8000 (pt0) cc_final: 0.7738 (pt0) REVERT: C 134 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8173 (tp30) REVERT: C 137 TYR cc_start: 0.7793 (t80) cc_final: 0.7340 (t80) REVERT: D 91 LYS cc_start: 0.8587 (tttp) cc_final: 0.8209 (mtmt) REVERT: D 92 LYS cc_start: 0.8758 (mppt) cc_final: 0.8075 (tptt) REVERT: D 102 MET cc_start: 0.8669 (ppp) cc_final: 0.8343 (ppp) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.0869 time to fit residues: 28.9449 Evaluate side-chains 186 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 30.0000 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.0370 chunk 43 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 317 ASN B 478 ASN C 71 HIS D 116 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.140517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.113891 restraints weight = 20194.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.116596 restraints weight = 12196.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.118390 restraints weight = 8705.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.119576 restraints weight = 6970.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.120248 restraints weight = 6071.175| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9008 Z= 0.146 Angle : 0.759 10.993 12160 Z= 0.378 Chirality : 0.048 0.224 1327 Planarity : 0.004 0.042 1549 Dihedral : 6.342 62.309 1204 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.15 (0.25), residues: 1065 helix: -0.09 (0.20), residues: 653 sheet: -1.86 (0.57), residues: 65 loop : -1.66 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 141 TYR 0.031 0.002 TYR B 495 PHE 0.040 0.002 PHE B 468 TRP 0.020 0.002 TRP B 486 HIS 0.005 0.001 HIS B 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 9008) covalent geometry : angle 0.75874 / 0.38 (12160) hydrogen bonds : bond 0.03821 / 2.42 ( 483) hydrogen bonds : angle 4.54862 / 3.17 ( 1428) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8499 (tp30) cc_final: 0.8029 (mm-30) REVERT: A 94 ASN cc_start: 0.8092 (m-40) cc_final: 0.7251 (t0) REVERT: A 98 ASN cc_start: 0.8855 (p0) cc_final: 0.8495 (p0) REVERT: A 146 ASP cc_start: 0.7526 (m-30) cc_final: 0.6988 (m-30) REVERT: B 191 GLU cc_start: 0.7602 (tp30) cc_final: 0.7010 (tm-30) REVERT: B 291 LEU cc_start: 0.8644 (tp) cc_final: 0.8222 (tp) REVERT: B 366 LYS cc_start: 0.7417 (pptt) cc_final: 0.6790 (tmtt) REVERT: B 447 LYS cc_start: 0.8139 (mttt) cc_final: 0.7740 (ttmm) REVERT: B 450 LYS cc_start: 0.8034 (ttpt) cc_final: 0.7574 (ttmm) REVERT: B 503 GLU cc_start: 0.5795 (pp20) cc_final: 0.5114 (pt0) REVERT: B 523 PHE cc_start: 0.8340 (t80) cc_final: 0.7985 (t80) REVERT: B 551 HIS cc_start: 0.8497 (t-90) cc_final: 0.8049 (t70) REVERT: B 728 ASP cc_start: 0.7685 (p0) cc_final: 0.6900 (t0) REVERT: B 734 LEU cc_start: 0.9283 (tt) cc_final: 0.8853 (tt) REVERT: B 738 MET cc_start: 0.8748 (mpp) cc_final: 0.8496 (mpp) REVERT: B 803 MET cc_start: 0.8206 (tmm) cc_final: 0.7589 (tmm) REVERT: C 46 GLU cc_start: 0.8046 (pt0) cc_final: 0.7782 (pt0) REVERT: C 59 LYS cc_start: 0.8685 (tttp) cc_final: 0.8291 (tttp) REVERT: C 134 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8179 (tp30) REVERT: C 137 TYR cc_start: 0.7910 (t80) cc_final: 0.7511 (t80) REVERT: D 91 LYS cc_start: 0.8589 (tttp) cc_final: 0.8265 (mtmt) REVERT: D 92 LYS cc_start: 0.8794 (mppt) cc_final: 0.8220 (tptt) REVERT: D 102 MET cc_start: 0.8614 (ppp) cc_final: 0.8341 (ppp) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.0865 time to fit residues: 27.8182 Evaluate side-chains 181 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 73 optimal weight: 1.9990 chunk 71 optimal weight: 0.0370 chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN B 478 ASN D 116 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.140629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.114067 restraints weight = 20018.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.116713 restraints weight = 12353.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.118515 restraints weight = 8912.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.119561 restraints weight = 7187.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.120398 restraints weight = 6292.736| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9008 Z= 0.140 Angle : 0.767 12.089 12160 Z= 0.379 Chirality : 0.048 0.234 1327 Planarity : 0.004 0.042 1549 Dihedral : 6.290 62.066 1204 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: -1.11 (0.25), residues: 1065 helix: -0.06 (0.20), residues: 656 sheet: -1.95 (0.56), residues: 65 loop : -1.62 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 141 TYR 0.030 0.002 TYR B 495 PHE 0.021 0.002 PHE B 716 TRP 0.022 0.002 TRP B 486 HIS 0.005 0.001 HIS B 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 9008) covalent geometry : angle 0.76654 / 0.38 (12160) hydrogen bonds : bond 0.03766 / 2.41 ( 483) hydrogen bonds : angle 4.63373 / 3.22 ( 1428) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8426 (tp30) cc_final: 0.7996 (mm-30) REVERT: A 94 ASN cc_start: 0.8258 (m-40) cc_final: 0.7293 (t0) REVERT: A 98 ASN cc_start: 0.8767 (p0) cc_final: 0.8435 (p0) REVERT: A 141 ARG cc_start: 0.7604 (mtt90) cc_final: 0.7359 (mpp80) REVERT: A 146 ASP cc_start: 0.7510 (m-30) cc_final: 0.7018 (m-30) REVERT: B 137 ARG cc_start: 0.6707 (tmm160) cc_final: 0.6016 (ptm-80) REVERT: B 191 GLU cc_start: 0.7681 (tp30) cc_final: 0.7119 (tm-30) REVERT: B 291 LEU cc_start: 0.8650 (tp) cc_final: 0.8226 (tp) REVERT: B 366 LYS cc_start: 0.7433 (pptt) cc_final: 0.6821 (tmtt) REVERT: B 450 LYS cc_start: 0.7873 (ttpt) cc_final: 0.7486 (ttmm) REVERT: B 503 GLU cc_start: 0.5622 (pp20) cc_final: 0.5167 (pt0) REVERT: B 523 PHE cc_start: 0.8260 (t80) cc_final: 0.7900 (t80) REVERT: B 551 HIS cc_start: 0.8513 (t-90) cc_final: 0.8045 (t70) REVERT: B 710 GLU cc_start: 0.8052 (mp0) cc_final: 0.7752 (mp0) REVERT: B 714 ARG cc_start: 0.8229 (mtm-85) cc_final: 0.7786 (ttp-110) REVERT: B 728 ASP cc_start: 0.7873 (p0) cc_final: 0.7031 (t0) REVERT: B 734 LEU cc_start: 0.9311 (tt) cc_final: 0.8787 (tt) REVERT: B 738 MET cc_start: 0.8740 (mpp) cc_final: 0.8507 (mpp) REVERT: B 803 MET cc_start: 0.8220 (tmm) cc_final: 0.7596 (tmm) REVERT: C 46 GLU cc_start: 0.8026 (pt0) cc_final: 0.7771 (pt0) REVERT: C 59 LYS cc_start: 0.8639 (tttp) cc_final: 0.8096 (tttp) REVERT: C 134 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8142 (tp30) REVERT: C 137 TYR cc_start: 0.7813 (t80) cc_final: 0.7398 (t80) REVERT: D 91 LYS cc_start: 0.8697 (tttp) cc_final: 0.8280 (mtmt) REVERT: D 92 LYS cc_start: 0.8944 (mppt) cc_final: 0.8066 (tptt) REVERT: D 102 MET cc_start: 0.8617 (ppp) cc_final: 0.8403 (ppp) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.0846 time to fit residues: 28.2130 Evaluate side-chains 191 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 73 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN C 71 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.138045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.111233 restraints weight = 20255.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.113735 restraints weight = 12767.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.115405 restraints weight = 9372.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.116446 restraints weight = 7662.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.116988 restraints weight = 6748.008| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9008 Z= 0.164 Angle : 0.785 11.127 12160 Z= 0.397 Chirality : 0.050 0.228 1327 Planarity : 0.005 0.047 1549 Dihedral : 6.462 64.681 1204 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: -1.09 (0.25), residues: 1065 helix: -0.04 (0.20), residues: 653 sheet: -1.95 (0.57), residues: 65 loop : -1.62 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 141 TYR 0.042 0.002 TYR B 495 PHE 0.035 0.002 PHE B 515 TRP 0.034 0.003 TRP B 375 HIS 0.005 0.001 HIS B 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 9008) covalent geometry : angle 0.78457 / 0.40 (12160) hydrogen bonds : bond 0.04188 / 2.65 ( 483) hydrogen bonds : angle 4.70187 / 3.26 ( 1428) =============================================================================== Job complete usr+sys time: 1499.37 seconds wall clock time: 26 minutes 42.66 seconds (1602.66 seconds total)