Starting phenix.real_space_refine on Wed Feb 4 09:46:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n85_49114/02_2026/9n85_49114.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n85_49114/02_2026/9n85_49114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n85_49114/02_2026/9n85_49114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n85_49114/02_2026/9n85_49114.map" model { file = "/net/cci-nas-00/data/ceres_data/9n85_49114/02_2026/9n85_49114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n85_49114/02_2026/9n85_49114.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.949 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 60 5.16 5 C 6132 2.51 5 N 1649 2.21 5 O 1866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9711 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 876, 6810 Classifications: {'peptide': 876} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 37, 'TRANS': 836} Chain: "B" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1189 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 7, 'TRANS': 136} Chain: "C" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1679 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 12, 'TRANS': 197} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.36, per 1000 atoms: 0.24 Number of scatterers: 9711 At special positions: 0 Unit cell: (120.62, 92.5, 105.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 3 15.00 Mg 1 11.99 O 1866 8.00 N 1649 7.00 C 6132 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: 0.86 Conformation dependent library (CDL) restraints added in 485.0 milliseconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2350 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 2 sheets defined 62.6% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 10 through 12 No H-bonds generated for 'chain 'A' and resid 10 through 12' Processing helix chain 'A' and resid 14 through 32 removed outlier: 3.520A pdb=" N ASN A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 46 removed outlier: 3.651A pdb=" N ASN A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 64 Processing helix chain 'A' and resid 69 through 82 Processing helix chain 'A' and resid 84 through 97 Processing helix chain 'A' and resid 108 through 121 removed outlier: 3.572A pdb=" N CYS A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 169 through 182 removed outlier: 3.666A pdb=" N ILE A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 201 Processing helix chain 'A' and resid 203 through 210 removed outlier: 4.644A pdb=" N ALA A 207 " --> pdb=" O PHE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 226 removed outlier: 3.865A pdb=" N PHE A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 248 Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 252 through 257 removed outlier: 4.535A pdb=" N GLY A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 removed outlier: 3.610A pdb=" N ILE A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 304 removed outlier: 3.738A pdb=" N TRP A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 330 removed outlier: 3.501A pdb=" N GLY A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLN A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 343 through 360 removed outlier: 3.631A pdb=" N GLY A 349 " --> pdb=" O CYS A 345 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 375 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 379 through 393 removed outlier: 3.522A pdb=" N ARG A 383 " --> pdb=" O ASP A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 417 Proline residue: A 404 - end of helix Proline residue: A 411 - end of helix Processing helix chain 'A' and resid 421 through 439 Processing helix chain 'A' and resid 448 through 460 Processing helix chain 'A' and resid 463 through 484 removed outlier: 3.648A pdb=" N ASN A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 515 Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 523 through 538 removed outlier: 3.897A pdb=" N VAL A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 556 removed outlier: 3.544A pdb=" N GLU A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 564 Processing helix chain 'A' and resid 586 through 596 removed outlier: 4.207A pdb=" N GLN A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 619 removed outlier: 4.085A pdb=" N SER A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 619 " --> pdb=" O PHE A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 removed outlier: 3.697A pdb=" N ALA A 628 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 631 " --> pdb=" O ASP A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 659 removed outlier: 4.340A pdb=" N PHE A 653 " --> pdb=" O ALA A 649 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLY A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE A 656 " --> pdb=" O PRO A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 682 removed outlier: 4.204A pdb=" N ARG A 679 " --> pdb=" O GLY A 675 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA A 680 " --> pdb=" O ASP A 676 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU A 681 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN A 682 " --> pdb=" O CYS A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 703 removed outlier: 4.356A pdb=" N ASP A 690 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU A 691 " --> pdb=" O PRO A 687 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN A 702 " --> pdb=" O GLU A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 722 removed outlier: 4.072A pdb=" N GLN A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 744 removed outlier: 3.705A pdb=" N LEU A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 777 removed outlier: 3.561A pdb=" N LEU A 758 " --> pdb=" O MET A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 801 removed outlier: 3.638A pdb=" N LEU A 798 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 799 " --> pdb=" O GLU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 808 removed outlier: 4.206A pdb=" N ASP A 807 " --> pdb=" O HIS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 830 removed outlier: 3.826A pdb=" N CYS A 817 " --> pdb=" O GLY A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 839 removed outlier: 3.833A pdb=" N VAL A 837 " --> pdb=" O VAL A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 851 removed outlier: 3.619A pdb=" N GLU A 845 " --> pdb=" O PRO A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 876 removed outlier: 3.627A pdb=" N ALA A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 160 Processing helix chain 'C' and resid 25 through 32 Processing helix chain 'C' and resid 94 through 100 removed outlier: 3.906A pdb=" N TYR C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 110 Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.617A pdb=" N ILE C 126 " --> pdb=" O LYS C 123 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS C 127 " --> pdb=" O VAL C 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 127' Processing helix chain 'C' and resid 132 through 136 removed outlier: 3.765A pdb=" N ILE C 136 " --> pdb=" O ALA C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 143 Processing helix chain 'C' and resid 158 through 170 removed outlier: 3.577A pdb=" N ILE C 169 " --> pdb=" O ALA C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 207 Processing sheet with id=AA1, first strand: chain 'B' and resid 94 through 95 removed outlier: 3.593A pdb=" N GLU B 58 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU B 47 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR B 64 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA B 45 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASP B 66 " --> pdb=" O ASN B 43 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ASN B 43 " --> pdb=" O ASP B 66 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS B 68 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE B 41 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU B 70 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLU B 39 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HIS B 72 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU B 37 " --> pdb=" O HIS B 72 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU B 129 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS B 126 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA B 118 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ALA B 111 " --> pdb=" O ASN B 105 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN B 105 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 54 removed outlier: 7.049A pdb=" N PHE C 11 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N TRP C 64 " --> pdb=" O PHE C 11 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU C 13 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR C 66 " --> pdb=" O LEU C 13 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU C 15 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N CYS C 85 " --> pdb=" O GLN C 10 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LYS C 12 " --> pdb=" O CYS C 85 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILE C 87 " --> pdb=" O LYS C 12 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL C 14 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N MET C 89 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL C 16 " --> pdb=" O MET C 89 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ASP C 91 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA C 86 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N CYS C 120 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE C 88 " --> pdb=" O CYS C 120 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ASN C 122 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N PHE C 90 " --> pdb=" O ASN C 122 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN C 145 " --> pdb=" O ILE C 117 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1542 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: 1.53 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3250 1.34 - 1.46: 1430 1.46 - 1.57: 5116 1.57 - 1.69: 5 1.69 - 1.81: 90 Bond restraints: 9891 Sorted by residual: bond pdb=" C VAL B 22 " pdb=" N PRO B 23 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.47e+00 bond pdb=" N VAL A 705 " pdb=" CA VAL A 705 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.90e-02 2.77e+03 1.35e+00 bond pdb=" C ASN A 704 " pdb=" N VAL A 705 " ideal model delta sigma weight residual 1.329 1.345 -0.016 1.40e-02 5.10e+03 1.28e+00 bond pdb=" CA VAL B 22 " pdb=" C VAL B 22 " ideal model delta sigma weight residual 1.520 1.530 -0.010 8.80e-03 1.29e+04 1.27e+00 bond pdb=" C2' GTP C 301 " pdb=" C3' GTP C 301 " ideal model delta sigma weight residual 1.524 1.506 0.018 2.00e-02 2.50e+03 8.19e-01 ... (remaining 9886 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 13180 1.76 - 3.52: 174 3.52 - 5.28: 51 5.28 - 7.03: 10 7.03 - 8.79: 3 Bond angle restraints: 13418 Sorted by residual: angle pdb=" C VAL B 21 " pdb=" N VAL B 22 " pdb=" CA VAL B 22 " ideal model delta sigma weight residual 120.24 125.52 -5.28 6.30e-01 2.52e+00 7.04e+01 angle pdb=" C ASN A 704 " pdb=" N VAL A 705 " pdb=" CA VAL A 705 " ideal model delta sigma weight residual 121.70 130.49 -8.79 1.80e+00 3.09e-01 2.39e+01 angle pdb=" C VAL B 22 " pdb=" CA VAL B 22 " pdb=" CB VAL B 22 " ideal model delta sigma weight residual 114.35 110.21 4.14 1.06e+00 8.90e-01 1.53e+01 angle pdb=" C TYR C 80 " pdb=" CA TYR C 80 " pdb=" CB TYR C 80 " ideal model delta sigma weight residual 111.50 107.03 4.47 1.29e+00 6.01e-01 1.20e+01 angle pdb=" N THR C 25 " pdb=" CA THR C 25 " pdb=" C THR C 25 " ideal model delta sigma weight residual 113.12 109.51 3.61 1.25e+00 6.40e-01 8.36e+00 ... (remaining 13413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.27: 5916 29.27 - 58.53: 141 58.53 - 87.80: 5 87.80 - 117.07: 4 117.07 - 146.34: 1 Dihedral angle restraints: 6067 sinusoidal: 2458 harmonic: 3609 Sorted by residual: dihedral pdb=" C8 GTP C 301 " pdb=" C1' GTP C 301 " pdb=" N9 GTP C 301 " pdb=" O4' GTP C 301 " ideal model delta sinusoidal sigma weight residual 104.59 -41.74 146.34 1 2.00e+01 2.50e-03 4.40e+01 dihedral pdb=" O3B GTP C 301 " pdb=" O3A GTP C 301 " pdb=" PB GTP C 301 " pdb=" PA GTP C 301 " ideal model delta sinusoidal sigma weight residual -68.92 45.90 -114.82 1 2.00e+01 2.50e-03 3.41e+01 dihedral pdb=" C4' GTP C 301 " pdb=" C5' GTP C 301 " pdb=" O5' GTP C 301 " pdb=" PA GTP C 301 " ideal model delta sinusoidal sigma weight residual 260.87 154.03 106.84 1 2.00e+01 2.50e-03 3.10e+01 ... (remaining 6064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 813 0.027 - 0.054: 448 0.054 - 0.082: 162 0.082 - 0.109: 87 0.109 - 0.136: 17 Chirality restraints: 1527 Sorted by residual: chirality pdb=" CA PRO B 23 " pdb=" N PRO B 23 " pdb=" C PRO B 23 " pdb=" CB PRO B 23 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ARG A 105 " pdb=" N ARG A 105 " pdb=" C ARG A 105 " pdb=" CB ARG A 105 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA PRO A 258 " pdb=" N PRO A 258 " pdb=" C PRO A 258 " pdb=" CB PRO A 258 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 1524 not shown) Planarity restraints: 1746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 396 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO A 397 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 397 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 397 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 57 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.53e+00 pdb=" N PRO C 58 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 58 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 58 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 22 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO B 23 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 23 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 23 " 0.022 5.00e-02 4.00e+02 ... (remaining 1743 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 55 2.52 - 3.12: 7639 3.12 - 3.71: 14939 3.71 - 4.31: 20589 4.31 - 4.90: 34912 Nonbonded interactions: 78134 Sorted by model distance: nonbonded pdb=" O1B GTP C 301 " pdb="MG MG C 302 " model vdw 1.928 2.170 nonbonded pdb=" O1G GTP C 301 " pdb="MG MG C 302 " model vdw 1.930 2.170 nonbonded pdb=" OH TYR C 146 " pdb=" OD1 ASP C 148 " model vdw 2.166 3.040 nonbonded pdb=" O MET A 630 " pdb=" OG SER A 633 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THR C 24 " pdb=" OD2 ASP C 65 " model vdw 2.225 3.040 ... (remaining 78129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 5.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.520 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:7.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 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 : 0.004 0.039 9891 Z= 0.171 Angle : 0.594 8.793 13418 Z= 0.309 Chirality : 0.041 0.136 1527 Planarity : 0.004 0.053 1746 Dihedral : 12.714 146.336 3717 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.35 % Favored : 92.24 % Rotamer: Outliers : 2.84 % Allowed : 8.14 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.25), residues: 1224 helix: 1.54 (0.20), residues: 702 sheet: -0.32 (0.54), residues: 100 loop : -2.12 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 215 TYR 0.008 0.001 TYR C 80 PHE 0.016 0.001 PHE C 26 TRP 0.016 0.001 TRP A 342 HIS 0.003 0.001 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 9891) covalent geometry : angle 0.59380 (13418) hydrogen bonds : bond 0.13076 ( 522) hydrogen bonds : angle 5.20045 ( 1542) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 243 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.8351 (mt) cc_final: 0.8135 (mm) REVERT: A 104 TYR cc_start: 0.7024 (p90) cc_final: 0.6680 (p90) REVERT: A 650 PHE cc_start: 0.6107 (t80) cc_final: 0.5848 (t80) REVERT: A 663 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.6098 (pm20) REVERT: A 667 CYS cc_start: 0.3309 (OUTLIER) cc_final: 0.1171 (m) REVERT: A 682 GLN cc_start: 0.1949 (OUTLIER) cc_final: 0.1212 (mp-120) REVERT: A 722 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7908 (mm) REVERT: A 787 VAL cc_start: 0.9068 (OUTLIER) cc_final: 0.8833 (t) REVERT: A 788 MET cc_start: 0.3999 (mpp) cc_final: 0.3296 (mmm) REVERT: B 152 LYS cc_start: 0.8376 (ttmm) cc_final: 0.7711 (mttp) REVERT: B 153 GLU cc_start: 0.7686 (tt0) cc_final: 0.7466 (tt0) REVERT: C 62 ASN cc_start: 0.5684 (m110) cc_final: 0.5368 (m110) REVERT: C 123 LYS cc_start: 0.5566 (mttt) cc_final: 0.5280 (mttt) outliers start: 30 outliers final: 9 residues processed: 266 average time/residue: 0.6057 time to fit residues: 172.0157 Evaluate side-chains 151 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 663 GLU Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 59 TRP Chi-restraints excluded: chain C residue 80 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.0980 chunk 113 optimal weight: 0.0470 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 682 GLN A 737 ASN A 784 HIS B 117 HIS C 53 HIS C 145 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.162368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.104918 restraints weight = 14332.264| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.70 r_work: 0.3305 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 9891 Z= 0.172 Angle : 0.719 10.671 13418 Z= 0.365 Chirality : 0.044 0.176 1527 Planarity : 0.005 0.056 1746 Dihedral : 8.996 137.476 1352 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.94 % Favored : 92.57 % Rotamer: Outliers : 4.45 % Allowed : 17.03 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.25), residues: 1224 helix: 1.56 (0.20), residues: 703 sheet: -0.03 (0.55), residues: 87 loop : -2.14 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 95 TYR 0.013 0.001 TYR C 79 PHE 0.023 0.002 PHE C 26 TRP 0.011 0.001 TRP A 342 HIS 0.007 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 9891) covalent geometry : angle 0.71917 (13418) hydrogen bonds : bond 0.03806 ( 522) hydrogen bonds : angle 4.17429 ( 1542) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 MET cc_start: 0.8187 (tpt) cc_final: 0.7955 (tpt) REVERT: A 394 LEU cc_start: 0.7262 (mt) cc_final: 0.7007 (mt) REVERT: A 458 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7438 (tm-30) REVERT: A 508 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7941 (pt0) REVERT: A 583 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7769 (tm) REVERT: A 589 GLN cc_start: 0.8375 (mp10) cc_final: 0.8047 (mp10) REVERT: A 650 PHE cc_start: 0.5522 (t80) cc_final: 0.5317 (t80) REVERT: A 663 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.6115 (pm20) REVERT: A 667 CYS cc_start: 0.3380 (OUTLIER) cc_final: 0.1088 (m) REVERT: A 722 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7803 (mm) REVERT: B 95 TYR cc_start: 0.8029 (m-10) cc_final: 0.7450 (m-10) REVERT: C 38 LYS cc_start: 0.7539 (mtpp) cc_final: 0.7297 (mmtt) REVERT: C 62 ASN cc_start: 0.7290 (m110) cc_final: 0.6951 (m110) REVERT: C 94 SER cc_start: 0.7685 (OUTLIER) cc_final: 0.7345 (p) REVERT: C 128 ASP cc_start: 0.7993 (t0) cc_final: 0.7524 (t0) REVERT: C 202 GLU cc_start: 0.8734 (tp30) cc_final: 0.8521 (tp30) REVERT: C 211 GLU cc_start: 0.6929 (pm20) cc_final: 0.6687 (pm20) outliers start: 47 outliers final: 17 residues processed: 181 average time/residue: 0.5346 time to fit residues: 104.4087 Evaluate side-chains 136 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 663 GLU Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 829 PHE Chi-restraints excluded: chain B residue 59 TRP Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 112 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 54 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.0570 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 GLN A 740 GLN A 774 GLN B 94 HIS C 156 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.162687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.104546 restraints weight = 14448.781| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.71 r_work: 0.3298 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.6146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9891 Z= 0.188 Angle : 0.753 12.506 13418 Z= 0.382 Chirality : 0.045 0.199 1527 Planarity : 0.005 0.077 1746 Dihedral : 8.974 138.595 1342 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.52 % Favored : 92.16 % Rotamer: Outliers : 5.30 % Allowed : 17.69 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.25), residues: 1224 helix: 1.21 (0.19), residues: 718 sheet: 0.02 (0.56), residues: 86 loop : -2.45 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 151 TYR 0.016 0.002 TYR A 76 PHE 0.025 0.002 PHE C 26 TRP 0.018 0.001 TRP A 430 HIS 0.006 0.002 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 9891) covalent geometry : angle 0.75283 (13418) hydrogen bonds : bond 0.04253 ( 522) hydrogen bonds : angle 4.30919 ( 1542) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 122 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7827 (tp30) REVERT: A 31 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6875 (mt-10) REVERT: A 90 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8223 (mt-10) REVERT: A 98 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.7916 (t) REVERT: A 353 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.8068 (mtm) REVERT: A 458 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8115 (tm-30) REVERT: A 614 MET cc_start: 0.7543 (ppp) cc_final: 0.7326 (ptt) REVERT: A 667 CYS cc_start: 0.3444 (OUTLIER) cc_final: 0.2795 (m) REVERT: A 722 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7787 (mm) REVERT: A 754 MET cc_start: 0.7645 (tpp) cc_final: 0.7351 (ppp) REVERT: A 803 HIS cc_start: 0.6878 (OUTLIER) cc_final: 0.6667 (p90) REVERT: B 67 VAL cc_start: 0.8621 (m) cc_final: 0.8417 (t) REVERT: C 36 GLU cc_start: 0.8722 (tp30) cc_final: 0.8398 (mm-30) REVERT: C 38 LYS cc_start: 0.8186 (mtpp) cc_final: 0.7635 (mmtt) REVERT: C 196 GLN cc_start: 0.9246 (tp40) cc_final: 0.8928 (tp-100) REVERT: C 200 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7521 (m-30) outliers start: 56 outliers final: 17 residues processed: 158 average time/residue: 0.5345 time to fit residues: 90.9975 Evaluate side-chains 114 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 803 HIS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 59 TRP Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 200 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 GLN B 117 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.160820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.101413 restraints weight = 14191.242| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.73 r_work: 0.3243 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.7158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9891 Z= 0.162 Angle : 0.696 13.318 13418 Z= 0.344 Chirality : 0.043 0.152 1527 Planarity : 0.005 0.054 1746 Dihedral : 8.759 140.625 1339 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.62 % Favored : 92.81 % Rotamer: Outliers : 3.41 % Allowed : 20.72 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.25), residues: 1224 helix: 1.50 (0.20), residues: 714 sheet: 0.11 (0.59), residues: 86 loop : -2.36 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 465 TYR 0.014 0.001 TYR A 646 PHE 0.011 0.001 PHE B 48 TRP 0.022 0.002 TRP A 430 HIS 0.005 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9891) covalent geometry : angle 0.69570 (13418) hydrogen bonds : bond 0.03511 ( 522) hydrogen bonds : angle 4.14048 ( 1542) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7592 (tp30) REVERT: A 722 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7765 (mm) REVERT: A 754 MET cc_start: 0.7660 (tpp) cc_final: 0.7216 (ppp) REVERT: B 19 GLN cc_start: 0.3417 (OUTLIER) cc_final: 0.3107 (mt0) REVERT: B 43 ASN cc_start: 0.8122 (t0) cc_final: 0.7733 (t0) REVERT: B 59 TRP cc_start: 0.6636 (OUTLIER) cc_final: 0.5758 (m-10) REVERT: C 127 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7705 (tppt) REVERT: C 128 ASP cc_start: 0.8644 (t0) cc_final: 0.8307 (t0) REVERT: C 196 GLN cc_start: 0.9258 (tp-100) cc_final: 0.8898 (tp-100) REVERT: C 198 GLU cc_start: 0.9089 (tp30) cc_final: 0.8679 (mm-30) REVERT: C 200 ASP cc_start: 0.8334 (m-30) cc_final: 0.7498 (m-30) REVERT: C 206 THR cc_start: 0.8321 (m) cc_final: 0.8106 (p) outliers start: 36 outliers final: 17 residues processed: 131 average time/residue: 0.5139 time to fit residues: 73.1071 Evaluate side-chains 110 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 829 PHE Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 59 TRP Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 127 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 115 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 64 optimal weight: 0.0770 chunk 60 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 GLN C 53 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.160083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.100717 restraints weight = 14182.821| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.72 r_work: 0.3227 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.7704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9891 Z= 0.150 Angle : 0.682 13.900 13418 Z= 0.334 Chirality : 0.042 0.170 1527 Planarity : 0.004 0.055 1746 Dihedral : 8.563 140.055 1336 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.86 % Favored : 92.57 % Rotamer: Outliers : 3.03 % Allowed : 20.53 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.25), residues: 1224 helix: 1.55 (0.20), residues: 717 sheet: 0.10 (0.59), residues: 86 loop : -2.32 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 840 TYR 0.010 0.001 TYR A 448 PHE 0.014 0.001 PHE C 26 TRP 0.015 0.001 TRP A 342 HIS 0.004 0.001 HIS A 597 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9891) covalent geometry : angle 0.68230 (13418) hydrogen bonds : bond 0.03397 ( 522) hydrogen bonds : angle 4.03927 ( 1542) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7714 (tp30) REVERT: A 98 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8146 (t) REVERT: A 754 MET cc_start: 0.7794 (tpp) cc_final: 0.7296 (ppp) REVERT: B 19 GLN cc_start: 0.3400 (OUTLIER) cc_final: 0.3176 (mt0) REVERT: B 43 ASN cc_start: 0.8244 (t0) cc_final: 0.7961 (t0) REVERT: C 38 LYS cc_start: 0.8095 (mtpp) cc_final: 0.7502 (mmtt) REVERT: C 127 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7775 (tppt) REVERT: C 128 ASP cc_start: 0.8718 (t0) cc_final: 0.8398 (t0) REVERT: C 196 GLN cc_start: 0.9235 (tp-100) cc_final: 0.8768 (tp-100) REVERT: C 200 ASP cc_start: 0.8358 (m-30) cc_final: 0.7442 (m-30) outliers start: 32 outliers final: 16 residues processed: 122 average time/residue: 0.4844 time to fit residues: 64.6987 Evaluate side-chains 104 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 829 PHE Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 59 TRP Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 127 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 95 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 82 optimal weight: 30.0000 chunk 83 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.157117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.096535 restraints weight = 14200.259| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.76 r_work: 0.3197 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.8187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9891 Z= 0.155 Angle : 0.681 11.882 13418 Z= 0.334 Chirality : 0.043 0.296 1527 Planarity : 0.004 0.054 1746 Dihedral : 8.533 138.687 1336 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.19 % Favored : 92.24 % Rotamer: Outliers : 2.93 % Allowed : 20.81 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.25), residues: 1224 helix: 1.54 (0.20), residues: 718 sheet: 0.34 (0.59), residues: 81 loop : -2.37 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 157 TYR 0.009 0.001 TYR A 448 PHE 0.013 0.001 PHE B 48 TRP 0.015 0.001 TRP A 342 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 9891) covalent geometry : angle 0.68063 (13418) hydrogen bonds : bond 0.03436 ( 522) hydrogen bonds : angle 4.02396 ( 1542) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7702 (tp30) REVERT: A 98 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8209 (t) REVERT: A 388 MET cc_start: 0.8481 (tpt) cc_final: 0.7930 (tpt) REVERT: A 613 ARG cc_start: 0.6980 (tmm160) cc_final: 0.6654 (ttp-110) REVERT: A 754 MET cc_start: 0.7800 (tpp) cc_final: 0.7304 (ppp) REVERT: B 37 GLU cc_start: 0.7819 (pp20) cc_final: 0.6880 (mt-10) REVERT: B 43 ASN cc_start: 0.8288 (t0) cc_final: 0.8049 (t0) REVERT: B 59 TRP cc_start: 0.6754 (OUTLIER) cc_final: 0.5927 (m-10) REVERT: C 127 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7893 (tppt) REVERT: C 128 ASP cc_start: 0.8774 (t0) cc_final: 0.8504 (t0) REVERT: C 196 GLN cc_start: 0.9223 (tp-100) cc_final: 0.8735 (tp-100) REVERT: C 200 ASP cc_start: 0.8387 (m-30) cc_final: 0.7450 (m-30) outliers start: 31 outliers final: 18 residues processed: 115 average time/residue: 0.5604 time to fit residues: 69.5927 Evaluate side-chains 103 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 829 PHE Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 59 TRP Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 127 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 95 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 0.1980 chunk 120 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 GLN B 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.160232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.100969 restraints weight = 14166.340| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.71 r_work: 0.3248 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.8418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9891 Z= 0.130 Angle : 0.663 11.828 13418 Z= 0.326 Chirality : 0.042 0.259 1527 Planarity : 0.004 0.055 1746 Dihedral : 8.313 134.178 1336 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.54 % Favored : 92.89 % Rotamer: Outliers : 2.55 % Allowed : 21.57 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.25), residues: 1224 helix: 1.64 (0.20), residues: 715 sheet: 0.15 (0.57), residues: 87 loop : -2.35 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 465 TYR 0.006 0.001 TYR A 104 PHE 0.013 0.001 PHE C 26 TRP 0.015 0.001 TRP A 342 HIS 0.003 0.001 HIS A 784 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9891) covalent geometry : angle 0.66305 (13418) hydrogen bonds : bond 0.03217 ( 522) hydrogen bonds : angle 3.98348 ( 1542) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7948 (tt0) REVERT: A 98 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8221 (t) REVERT: A 603 ILE cc_start: 0.7940 (pt) cc_final: 0.7526 (mt) REVERT: A 613 ARG cc_start: 0.6950 (tmm160) cc_final: 0.6588 (ttp-110) REVERT: A 614 MET cc_start: 0.7608 (ppp) cc_final: 0.7263 (ptt) REVERT: A 754 MET cc_start: 0.7746 (tpp) cc_final: 0.7245 (ppp) REVERT: A 803 HIS cc_start: 0.7162 (OUTLIER) cc_final: 0.6840 (p90) REVERT: B 19 GLN cc_start: 0.3523 (OUTLIER) cc_final: 0.3008 (mm-40) REVERT: B 43 ASN cc_start: 0.8263 (t0) cc_final: 0.8004 (t0) REVERT: C 196 GLN cc_start: 0.9175 (tp-100) cc_final: 0.8641 (tp-100) REVERT: C 200 ASP cc_start: 0.8266 (m-30) cc_final: 0.7373 (m-30) outliers start: 27 outliers final: 14 residues processed: 117 average time/residue: 0.5116 time to fit residues: 64.9336 Evaluate side-chains 100 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 803 HIS Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 59 TRP Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 127 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 10 optimal weight: 0.0670 chunk 100 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 58 optimal weight: 0.0030 chunk 116 optimal weight: 1.9990 overall best weight: 0.3328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN C 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.159753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.099741 restraints weight = 14174.731| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.73 r_work: 0.3259 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.8575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9891 Z= 0.125 Angle : 0.696 14.056 13418 Z= 0.339 Chirality : 0.041 0.258 1527 Planarity : 0.004 0.055 1746 Dihedral : 8.105 129.036 1336 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.78 % Favored : 92.65 % Rotamer: Outliers : 2.18 % Allowed : 22.42 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1224 helix: 1.72 (0.20), residues: 717 sheet: 0.31 (0.60), residues: 81 loop : -2.36 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 465 TYR 0.007 0.001 TYR A 104 PHE 0.013 0.001 PHE C 26 TRP 0.014 0.001 TRP A 342 HIS 0.003 0.001 HIS A 784 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9891) covalent geometry : angle 0.69552 (13418) hydrogen bonds : bond 0.03024 ( 522) hydrogen bonds : angle 3.97272 ( 1542) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7950 (tt0) REVERT: A 98 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8240 (t) REVERT: A 179 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8157 (tp40) REVERT: A 613 ARG cc_start: 0.6969 (tmm160) cc_final: 0.6634 (ttp-110) REVERT: A 614 MET cc_start: 0.7585 (ppp) cc_final: 0.7273 (ptt) REVERT: A 667 CYS cc_start: 0.4134 (OUTLIER) cc_final: 0.3540 (m) REVERT: A 754 MET cc_start: 0.7739 (tpp) cc_final: 0.7233 (ppp) REVERT: A 803 HIS cc_start: 0.7029 (OUTLIER) cc_final: 0.6618 (p90) REVERT: B 37 GLU cc_start: 0.7797 (pp20) cc_final: 0.6882 (mt-10) REVERT: B 43 ASN cc_start: 0.8236 (t0) cc_final: 0.8016 (t0) REVERT: C 34 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8458 (pm20) REVERT: C 196 GLN cc_start: 0.9151 (tp-100) cc_final: 0.8594 (tp-100) REVERT: C 200 ASP cc_start: 0.8252 (m-30) cc_final: 0.7380 (m-30) outliers start: 23 outliers final: 13 residues processed: 108 average time/residue: 0.5198 time to fit residues: 60.9232 Evaluate side-chains 97 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 803 HIS Chi-restraints excluded: chain B residue 59 TRP Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 127 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 11 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 26 optimal weight: 0.0770 chunk 13 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 36 optimal weight: 0.0770 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.158878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.098958 restraints weight = 14058.860| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.69 r_work: 0.3245 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.8703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9891 Z= 0.133 Angle : 0.705 13.385 13418 Z= 0.345 Chirality : 0.041 0.247 1527 Planarity : 0.004 0.054 1746 Dihedral : 8.065 128.374 1336 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.11 % Favored : 92.40 % Rotamer: Outliers : 2.18 % Allowed : 22.14 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.25), residues: 1224 helix: 1.76 (0.20), residues: 713 sheet: 0.26 (0.58), residues: 86 loop : -2.30 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 465 TYR 0.007 0.001 TYR A 448 PHE 0.012 0.001 PHE C 26 TRP 0.013 0.001 TRP A 342 HIS 0.003 0.001 HIS A 784 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9891) covalent geometry : angle 0.70509 (13418) hydrogen bonds : bond 0.03173 ( 522) hydrogen bonds : angle 4.01317 ( 1542) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7967 (tt0) REVERT: A 98 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8248 (t) REVERT: A 179 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8154 (tp40) REVERT: A 603 ILE cc_start: 0.7943 (pt) cc_final: 0.7498 (mt) REVERT: A 613 ARG cc_start: 0.7028 (tmm160) cc_final: 0.6648 (ttp-110) REVERT: A 614 MET cc_start: 0.7638 (ppp) cc_final: 0.7370 (ptt) REVERT: A 667 CYS cc_start: 0.3852 (OUTLIER) cc_final: 0.3227 (m) REVERT: A 754 MET cc_start: 0.7800 (tpp) cc_final: 0.7267 (ppp) REVERT: A 803 HIS cc_start: 0.7124 (OUTLIER) cc_final: 0.6728 (p90) REVERT: B 37 GLU cc_start: 0.7798 (pp20) cc_final: 0.6965 (mt-10) REVERT: B 43 ASN cc_start: 0.8312 (t0) cc_final: 0.8014 (t0) REVERT: C 196 GLN cc_start: 0.9134 (tp-100) cc_final: 0.8627 (tp-100) REVERT: C 200 ASP cc_start: 0.8296 (m-30) cc_final: 0.7506 (m-30) outliers start: 23 outliers final: 12 residues processed: 105 average time/residue: 0.4994 time to fit residues: 57.2490 Evaluate side-chains 98 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 803 HIS Chi-restraints excluded: chain B residue 59 TRP Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 127 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 8 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 30 optimal weight: 0.0980 chunk 102 optimal weight: 0.6980 chunk 74 optimal weight: 30.0000 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 0.0050 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.158618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098591 restraints weight = 13990.498| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.67 r_work: 0.3237 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.8899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9891 Z= 0.136 Angle : 0.719 17.482 13418 Z= 0.351 Chirality : 0.042 0.246 1527 Planarity : 0.004 0.055 1746 Dihedral : 7.987 126.184 1336 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.19 % Favored : 92.32 % Rotamer: Outliers : 1.89 % Allowed : 22.89 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.25), residues: 1224 helix: 1.76 (0.20), residues: 713 sheet: 0.19 (0.56), residues: 92 loop : -2.31 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 465 TYR 0.006 0.001 TYR A 104 PHE 0.012 0.001 PHE C 26 TRP 0.013 0.001 TRP A 342 HIS 0.003 0.001 HIS A 784 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9891) covalent geometry : angle 0.71910 (13418) hydrogen bonds : bond 0.03115 ( 522) hydrogen bonds : angle 4.02921 ( 1542) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8256 (t) REVERT: A 179 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8124 (tp40) REVERT: A 603 ILE cc_start: 0.8005 (pt) cc_final: 0.7574 (mt) REVERT: A 613 ARG cc_start: 0.7045 (tmm160) cc_final: 0.6613 (ttp-110) REVERT: A 614 MET cc_start: 0.7656 (ppp) cc_final: 0.7411 (ptt) REVERT: A 667 CYS cc_start: 0.3983 (OUTLIER) cc_final: 0.3369 (m) REVERT: A 754 MET cc_start: 0.7859 (tpp) cc_final: 0.7323 (ppp) REVERT: A 803 HIS cc_start: 0.7065 (OUTLIER) cc_final: 0.6615 (p90) REVERT: B 37 GLU cc_start: 0.7785 (pp20) cc_final: 0.7077 (mt-10) REVERT: B 43 ASN cc_start: 0.8339 (t0) cc_final: 0.8034 (t0) REVERT: C 196 GLN cc_start: 0.9095 (tp-100) cc_final: 0.8571 (tp-100) REVERT: C 200 ASP cc_start: 0.8337 (m-30) cc_final: 0.7524 (m-30) outliers start: 20 outliers final: 13 residues processed: 102 average time/residue: 0.5118 time to fit residues: 56.6112 Evaluate side-chains 95 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 803 HIS Chi-restraints excluded: chain B residue 59 TRP Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 127 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 59 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 89 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.157822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.097518 restraints weight = 14107.408| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.69 r_work: 0.3215 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.9050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9891 Z= 0.146 Angle : 0.737 15.625 13418 Z= 0.360 Chirality : 0.042 0.243 1527 Planarity : 0.004 0.054 1746 Dihedral : 8.030 127.417 1336 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.86 % Favored : 92.65 % Rotamer: Outliers : 1.70 % Allowed : 23.27 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.25), residues: 1224 helix: 1.73 (0.20), residues: 719 sheet: 0.13 (0.56), residues: 92 loop : -2.25 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 465 TYR 0.012 0.001 TYR A 448 PHE 0.012 0.001 PHE C 26 TRP 0.011 0.001 TRP A 342 HIS 0.004 0.001 HIS A 784 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9891) covalent geometry : angle 0.73660 (13418) hydrogen bonds : bond 0.03304 ( 522) hydrogen bonds : angle 4.07040 ( 1542) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4822.31 seconds wall clock time: 82 minutes 46.74 seconds (4966.74 seconds total)