Starting phenix.real_space_refine on Sun Sep 13 06:34:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9roh_54119/09_2026/9roh_54119_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9roh_54119/09_2026/9roh_54119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9roh_54119/09_2026/9roh_54119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9roh_54119/09_2026/9roh_54119.map" model { file = "/net/cci-nas-00/data/ceres_data/9roh_54119/09_2026/9roh_54119_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9roh_54119/09_2026/9roh_54119_trim.cif" } resolution = 2.92 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= 0.021 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: 7 Type Number sf(0) Gaussians P 1 5.49 5 S 61 5.16 5 Na 2 4.78 5 C 6605 2.51 5 N 1700 2.21 5 O 1932 1.98 5 H 10176 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 20477 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 15234 Classifications: {'peptide': 984} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 942} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 4572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4572 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 261} Chain: "C" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 543 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {' NA': 2, 'CLR': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Unusual residues: {'CLR': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.91, per 1000 atoms: 0.14 Number of scatterers: 20477 At special positions: 0 Unit cell: (81.9852, 85.7118, 185.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 61 16.00 P 1 15.00 Na 2 11.00 O 1932 8.00 N 1700 7.00 C 6605 6.00 H 10176 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied NAG-ASN " NAG B 402 " - " ASN B 158 " " NAG B 403 " - " ASN B 193 " " NAG B 404 " - " ASN B 265 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 557.4 milliseconds 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 11 sheets defined 49.5% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 81 through 87 removed outlier: 3.668A pdb=" N PHE A 87 " --> pdb=" O CYS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 112 Processing helix chain 'A' and resid 117 through 149 removed outlier: 3.525A pdb=" N ILE A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.615A pdb=" N LEU A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 304 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 325 through 344 Processing helix chain 'A' and resid 350 through 359 removed outlier: 3.970A pdb=" N VAL A 354 " --> pdb=" O ASN A 350 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.614A pdb=" N VAL A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 454 Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 500 through 507 removed outlier: 3.783A pdb=" N ARG A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 538 removed outlier: 3.651A pdb=" N LYS A 525 " --> pdb=" O ASP A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 610 through 622 Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 646 through 650 removed outlier: 3.523A pdb=" N ALA A 650 " --> pdb=" O PRO A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 662 Processing helix chain 'A' and resid 664 through 675 Processing helix chain 'A' and resid 684 through 698 removed outlier: 3.699A pdb=" N GLN A 698 " --> pdb=" O GLY A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 710 No H-bonds generated for 'chain 'A' and resid 708 through 710' Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'A' and resid 745 through 771 removed outlier: 3.982A pdb=" N VAL A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 786 Proline residue: A 779 - end of helix Processing helix chain 'A' and resid 793 through 805 Processing helix chain 'A' and resid 806 through 813 removed outlier: 3.578A pdb=" N ILE A 810 " --> pdb=" O MET A 806 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A 813 " --> pdb=" O ALA A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 845 Processing helix chain 'A' and resid 846 through 867 removed outlier: 3.593A pdb=" N ILE A 850 " --> pdb=" O GLN A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 874 removed outlier: 4.309A pdb=" N VAL A 874 " --> pdb=" O GLY A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 882 Processing helix chain 'A' and resid 897 through 928 removed outlier: 3.816A pdb=" N ALA A 922 " --> pdb=" O VAL A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 941 through 961 Processing helix chain 'A' and resid 963 through 968 Processing helix chain 'A' and resid 974 through 980 Processing helix chain 'A' and resid 981 through 1002 Processing helix chain 'A' and resid 1005 through 1011 Processing helix chain 'B' and resid 28 through 61 Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 111 through 118 removed outlier: 6.208A pdb=" N ASP B 114 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N SER B 115 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.597A pdb=" N TRP B 155 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'B' and resid 246 through 251 removed outlier: 4.409A pdb=" N LEU B 250 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 57 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 163 Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 184 removed outlier: 6.840A pdb=" N THR A 243 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA A 198 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG A 245 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASP A 192 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 187 through 188 Processing sheet with id=AA4, first strand: chain 'A' and resid 602 through 603 removed outlier: 5.773A pdb=" N THR A 362 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N THR A 705 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL A 702 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N VAL A 722 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL A 704 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N MET A 724 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N GLY A 706 " --> pdb=" O MET A 724 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 388 removed outlier: 7.304A pdb=" N SER A 580 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N MET A 381 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU A 578 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE A 383 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 11.397A pdb=" N VAL A 576 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N PHE A 575 " --> pdb=" O HIS A 547 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N HIS A 547 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY A 577 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLU A 484 " --> pdb=" O LYS A 466 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LYS A 466 " --> pdb=" O GLU A 484 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 386 through 388 removed outlier: 7.304A pdb=" N SER A 580 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N MET A 381 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU A 578 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE A 383 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 11.397A pdb=" N VAL A 576 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N PHE A 575 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE A 511 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N GLY A 577 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 11.366A pdb=" N LEU A 513 " --> pdb=" O GLY A 577 " (cutoff:3.500A) removed outlier: 16.698A pdb=" N MET A 579 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 605 through 606 removed outlier: 6.608A pdb=" N MET A 605 " --> pdb=" O PHE A 680 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 655 " --> pdb=" O ALA A 681 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 888 through 889 Processing sheet with id=AA9, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AB1, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.981A pdb=" N ARG B 273 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS B 216 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU B 275 " --> pdb=" O THR B 214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 123 through 124 521 hydrogen bonds defined for protein. 1482 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: 5.00 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10150 1.03 - 1.23: 68 1.23 - 1.43: 4230 1.43 - 1.62: 6154 1.62 - 1.82: 91 Bond restraints: 20693 Sorted by residual: bond pdb=" OD1 PHD A 366 " pdb=" P PHD A 366 " ideal model delta sigma weight residual 1.816 1.780 0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" CA PHD A 366 " pdb=" C PHD A 366 " ideal model delta sigma weight residual 1.525 1.558 -0.033 2.10e-02 2.27e+03 2.53e+00 bond pdb=" N PHD A 366 " pdb=" CA PHD A 366 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.50e+00 bond pdb=" C PHD A 366 " pdb=" O PHD A 366 " ideal model delta sigma weight residual 1.231 1.261 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" N LYS A 367 " pdb=" CA LYS A 367 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.90e-02 2.77e+03 2.13e+00 ... (remaining 20688 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.23: 37444 7.23 - 14.46: 6 14.46 - 21.69: 0 21.69 - 28.93: 0 28.93 - 36.16: 3 Bond angle restraints: 37453 Sorted by residual: angle pdb=" C SER B 195 " pdb=" CA SER B 195 " pdb=" HA SER B 195 " ideal model delta sigma weight residual 109.00 72.84 36.16 3.00e+00 1.11e-01 1.45e+02 angle pdb=" N SER B 195 " pdb=" CA SER B 195 " pdb=" HA SER B 195 " ideal model delta sigma weight residual 110.00 76.69 33.31 3.00e+00 1.11e-01 1.23e+02 angle pdb=" CB SER B 195 " pdb=" CA SER B 195 " pdb=" HA SER B 195 " ideal model delta sigma weight residual 109.00 77.42 31.58 3.00e+00 1.11e-01 1.11e+02 angle pdb=" C LEU B 25 " pdb=" CA LEU B 25 " pdb=" CB LEU B 25 " ideal model delta sigma weight residual 115.79 110.80 4.99 1.19e+00 7.06e-01 1.76e+01 angle pdb=" CB LYS A 651 " pdb=" CG LYS A 651 " pdb=" CD LYS A 651 " ideal model delta sigma weight residual 111.30 119.96 -8.66 2.30e+00 1.89e-01 1.42e+01 ... (remaining 37448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 8794 17.59 - 35.18: 778 35.18 - 52.77: 258 52.77 - 70.36: 73 70.36 - 87.95: 18 Dihedral angle restraints: 9921 sinusoidal: 5564 harmonic: 4357 Sorted by residual: dihedral pdb=" CA LYS B 223 " pdb=" C LYS B 223 " pdb=" N VAL B 224 " pdb=" CA VAL B 224 " ideal model delta harmonic sigma weight residual 180.00 158.61 21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" C SER B 195 " pdb=" N SER B 195 " pdb=" CA SER B 195 " pdb=" CB SER B 195 " ideal model delta harmonic sigma weight residual -122.60 -132.95 10.35 0 2.50e+00 1.60e-01 1.71e+01 dihedral pdb=" N SER B 195 " pdb=" C SER B 195 " pdb=" CA SER B 195 " pdb=" CB SER B 195 " ideal model delta harmonic sigma weight residual 122.80 132.59 -9.79 0 2.50e+00 1.60e-01 1.53e+01 ... (remaining 9918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1534 0.086 - 0.173: 95 0.173 - 0.259: 0 0.259 - 0.345: 0 0.345 - 0.432: 1 Chirality restraints: 1630 Sorted by residual: chirality pdb=" CA SER B 195 " pdb=" N SER B 195 " pdb=" C SER B 195 " pdb=" CB SER B 195 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" C1 NAG B 403 " pdb=" ND2 ASN B 193 " pdb=" C2 NAG B 403 " pdb=" O5 NAG B 403 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA ILE B 176 " pdb=" N ILE B 176 " pdb=" C ILE B 176 " pdb=" CB ILE B 176 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 1627 not shown) Planarity restraints: 3058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHD A 366 " -0.025 2.00e-02 2.50e+03 5.00e-02 2.50e+01 pdb=" C PHD A 366 " 0.087 2.00e-02 2.50e+03 pdb=" O PHD A 366 " -0.032 2.00e-02 2.50e+03 pdb=" N LYS A 367 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 365 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C SER A 365 " 0.032 2.00e-02 2.50e+03 pdb=" O SER A 365 " -0.012 2.00e-02 2.50e+03 pdb=" N PHD A 366 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHD A 366 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" N LYS A 367 " 0.030 2.00e-02 2.50e+03 pdb=" CA LYS A 367 " -0.007 2.00e-02 2.50e+03 pdb=" H LYS A 367 " -0.013 2.00e-02 2.50e+03 ... (remaining 3055 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 365 2.08 - 2.71: 34201 2.71 - 3.34: 61527 3.34 - 3.97: 76877 3.97 - 4.60: 120737 Nonbonded interactions: 293707 Sorted by model distance: nonbonded pdb=" OE1 GLU B 154 " pdb=" H GLU B 154 " model vdw 1.448 2.450 nonbonded pdb=" OE1 GLN A 686 " pdb=" H GLN A 686 " model vdw 1.472 2.450 nonbonded pdb=" H SER A 212 " pdb=" OD1 ASP A 609 " model vdw 1.519 2.450 nonbonded pdb=" H SER A 218 " pdb=" O ARG A 230 " model vdw 1.617 2.450 nonbonded pdb=" OG SER A 841 " pdb=" HH TYR B 39 " model vdw 1.626 2.450 ... (remaining 293702 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 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: 0.080 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.690 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.823 10524 Z= 0.812 Angle : 0.599 10.841 14288 Z= 0.296 Chirality : 0.041 0.432 1630 Planarity : 0.003 0.050 1821 Dihedral : 15.249 87.951 4105 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.73 % Favored : 95.20 % Rotamer: Outliers : 1.17 % Allowed : 15.44 % Favored : 83.39 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.24), residues: 1291 helix: 1.68 (0.22), residues: 578 sheet: -0.53 (0.47), residues: 126 loop : -1.03 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 648 TYR 0.014 0.001 TYR A 859 PHE 0.008 0.001 PHE A 783 TRP 0.004 0.001 TRP A 921 HIS 0.001 0.000 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (10517) covalent geometry : angle 0.59817 / 0.30 (14273) SS BOND : bond 0.00126 / 0.06 ( 3) SS BOND : angle 0.75830 / 0.42 ( 6) hydrogen bonds : bond 0.11814 / 7.91 ( 514) hydrogen bonds : angle 5.26966 / 3.80 ( 1482) Misc. bond : bond 0.82261 / 43.30 ( 1) link_NAG-ASN : bond 0.00095 / 0.05 ( 3) link_NAG-ASN : angle 1.08491 / 0.62 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 579 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7983 (tpp) outliers start: 13 outliers final: 12 residues processed: 69 average time/residue: 0.9083 time to fit residues: 70.1121 Evaluate side-chains 67 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 184 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.159684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.092536 restraints weight = 52315.864| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.15 r_work: 0.3025 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.0497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10524 Z= 0.180 Angle : 0.564 6.182 14288 Z= 0.292 Chirality : 0.042 0.431 1630 Planarity : 0.003 0.038 1821 Dihedral : 6.780 54.143 1686 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.88 % Favored : 95.04 % Rotamer: Outliers : 1.80 % Allowed : 14.63 % Favored : 83.57 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.24), residues: 1291 helix: 1.47 (0.21), residues: 591 sheet: -0.55 (0.47), residues: 126 loop : -1.08 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 150 TYR 0.017 0.001 TYR A 859 PHE 0.012 0.001 PHE A 783 TRP 0.004 0.001 TRP A 880 HIS 0.002 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (10517) covalent geometry : angle 0.56364 / 0.29 (14273) SS BOND : bond 0.00175 / 0.08 ( 3) SS BOND : angle 0.92576 / 0.51 ( 6) hydrogen bonds : bond 0.04138 / 2.83 ( 514) hydrogen bonds : angle 4.64350 / 3.29 ( 1482) Misc. bond : bond 0.00054 / 0.03 ( 1) link_NAG-ASN : bond 0.00207 / 0.10 ( 3) link_NAG-ASN : angle 1.05401 / 0.52 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 939 MET cc_start: 0.9110 (mmm) cc_final: 0.8896 (mmm) REVERT: B 121 MET cc_start: 0.9193 (ttm) cc_final: 0.8742 (tmm) REVERT: C 32 ASP cc_start: 0.8844 (p0) cc_final: 0.8492 (p0) outliers start: 20 outliers final: 11 residues processed: 73 average time/residue: 0.8902 time to fit residues: 73.3107 Evaluate side-chains 65 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 127 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 115 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.160076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.093090 restraints weight = 52305.817| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.17 r_work: 0.3035 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.0637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10524 Z= 0.143 Angle : 0.539 6.602 14288 Z= 0.276 Chirality : 0.041 0.431 1630 Planarity : 0.003 0.038 1821 Dihedral : 6.535 59.400 1678 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.89 % Rotamer: Outliers : 1.71 % Allowed : 14.90 % Favored : 83.39 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.24), residues: 1291 helix: 1.51 (0.21), residues: 592 sheet: -0.55 (0.47), residues: 126 loop : -1.05 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 503 TYR 0.013 0.001 TYR A 859 PHE 0.011 0.001 PHE A 783 TRP 0.004 0.001 TRP A 896 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (10517) covalent geometry : angle 0.53875 / 0.28 (14273) SS BOND : bond 0.00149 / 0.07 ( 3) SS BOND : angle 0.81041 / 0.44 ( 6) hydrogen bonds : bond 0.03740 / 2.57 ( 514) hydrogen bonds : angle 4.45434 / 3.16 ( 1482) Misc. bond : bond 0.00136 / 0.07 ( 1) link_NAG-ASN : bond 0.00186 / 0.09 ( 3) link_NAG-ASN : angle 1.08807 / 0.55 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 MET cc_start: 0.9186 (ttm) cc_final: 0.8860 (tmm) REVERT: B 143 ARG cc_start: 0.7297 (ptm160) cc_final: 0.7056 (ptm160) REVERT: C 32 ASP cc_start: 0.8636 (p0) cc_final: 0.8225 (p0) outliers start: 19 outliers final: 12 residues processed: 73 average time/residue: 0.9173 time to fit residues: 75.2246 Evaluate side-chains 68 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 79 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.159006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.091971 restraints weight = 52440.668| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.41 r_work: 0.3013 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10524 Z= 0.168 Angle : 0.545 6.940 14288 Z= 0.279 Chirality : 0.042 0.431 1630 Planarity : 0.003 0.037 1821 Dihedral : 6.336 52.315 1672 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.27 % Favored : 94.66 % Rotamer: Outliers : 1.89 % Allowed : 14.99 % Favored : 83.12 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.24), residues: 1291 helix: 1.60 (0.21), residues: 586 sheet: -0.40 (0.47), residues: 121 loop : -1.12 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 503 TYR 0.017 0.001 TYR A 859 PHE 0.012 0.001 PHE A 783 TRP 0.004 0.001 TRP A 896 HIS 0.001 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (10517) covalent geometry : angle 0.54472 / 0.28 (14273) SS BOND : bond 0.00158 / 0.07 ( 3) SS BOND : angle 0.85954 / 0.47 ( 6) hydrogen bonds : bond 0.03599 / 2.47 ( 514) hydrogen bonds : angle 4.40175 / 3.13 ( 1482) Misc. bond : bond 0.00033 / 0.02 ( 1) link_NAG-ASN : bond 0.00103 / 0.04 ( 3) link_NAG-ASN : angle 1.10817 / 0.56 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 MET cc_start: 0.9083 (ttm) cc_final: 0.8731 (tmm) REVERT: B 143 ARG cc_start: 0.7302 (ptm160) cc_final: 0.6905 (ptt180) REVERT: B 154 GLU cc_start: 0.8845 (mp0) cc_final: 0.8637 (mp0) REVERT: C 32 ASP cc_start: 0.8437 (p0) cc_final: 0.8070 (p0) outliers start: 21 outliers final: 15 residues processed: 78 average time/residue: 0.8762 time to fit residues: 76.9412 Evaluate side-chains 71 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 50.0000 chunk 56 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 80 optimal weight: 0.4980 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.158917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.091616 restraints weight = 52163.462| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.13 r_work: 0.3028 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10524 Z= 0.153 Angle : 0.537 6.859 14288 Z= 0.274 Chirality : 0.041 0.436 1630 Planarity : 0.003 0.036 1821 Dihedral : 6.257 52.257 1672 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.19 % Favored : 94.73 % Rotamer: Outliers : 1.80 % Allowed : 14.99 % Favored : 83.21 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1291 helix: 1.65 (0.21), residues: 586 sheet: -0.46 (0.48), residues: 123 loop : -1.08 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.016 0.001 TYR A 859 PHE 0.011 0.001 PHE A 783 TRP 0.004 0.001 TRP A 896 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (10517) covalent geometry : angle 0.53666 / 0.27 (14273) SS BOND : bond 0.00148 / 0.07 ( 3) SS BOND : angle 0.83425 / 0.46 ( 6) hydrogen bonds : bond 0.03473 / 2.38 ( 514) hydrogen bonds : angle 4.32564 / 3.08 ( 1482) Misc. bond : bond 0.00034 / 0.02 ( 1) link_NAG-ASN : bond 0.00147 / 0.07 ( 3) link_NAG-ASN : angle 1.15720 / 0.61 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 939 MET cc_start: 0.9093 (mmm) cc_final: 0.8861 (mmm) REVERT: B 121 MET cc_start: 0.9199 (ttm) cc_final: 0.8901 (tmm) REVERT: B 143 ARG cc_start: 0.7345 (ptm160) cc_final: 0.6943 (ptt180) REVERT: B 154 GLU cc_start: 0.8993 (mp0) cc_final: 0.8782 (mp0) REVERT: C 32 ASP cc_start: 0.8486 (p0) cc_final: 0.8208 (p0) outliers start: 20 outliers final: 14 residues processed: 76 average time/residue: 0.9712 time to fit residues: 82.7264 Evaluate side-chains 72 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 121 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 53 optimal weight: 40.0000 chunk 81 optimal weight: 1.9990 chunk 18 optimal weight: 30.0000 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.159000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.092239 restraints weight = 52160.273| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.09 r_work: 0.3024 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10524 Z= 0.176 Angle : 0.547 7.074 14288 Z= 0.279 Chirality : 0.042 0.433 1630 Planarity : 0.003 0.037 1821 Dihedral : 6.204 53.314 1670 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.96 % Favored : 94.97 % Rotamer: Outliers : 2.15 % Allowed : 14.72 % Favored : 83.12 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.24), residues: 1291 helix: 1.67 (0.21), residues: 586 sheet: -0.37 (0.48), residues: 121 loop : -1.10 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.017 0.001 TYR A 859 PHE 0.012 0.001 PHE A 783 TRP 0.004 0.001 TRP A 896 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (10517) covalent geometry : angle 0.54610 / 0.28 (14273) SS BOND : bond 0.00163 / 0.07 ( 3) SS BOND : angle 0.88041 / 0.48 ( 6) hydrogen bonds : bond 0.03467 / 2.38 ( 514) hydrogen bonds : angle 4.30254 / 3.06 ( 1482) Misc. bond : bond 0.00017 / 0.01 ( 1) link_NAG-ASN : bond 0.00129 / 0.05 ( 3) link_NAG-ASN : angle 1.19880 / 0.62 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 ASN cc_start: 0.8986 (t160) cc_final: 0.8364 (m110) REVERT: B 121 MET cc_start: 0.9174 (ttm) cc_final: 0.8927 (tmm) REVERT: B 143 ARG cc_start: 0.7397 (ptm160) cc_final: 0.7091 (ptt180) REVERT: B 154 GLU cc_start: 0.9011 (mp0) cc_final: 0.8784 (mp0) REVERT: C 32 ASP cc_start: 0.8478 (p0) cc_final: 0.8151 (p0) outliers start: 24 outliers final: 18 residues processed: 77 average time/residue: 0.9092 time to fit residues: 78.6346 Evaluate side-chains 76 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 55 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 38 optimal weight: 50.0000 chunk 8 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.159167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.092757 restraints weight = 51958.128| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.10 r_work: 0.3024 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10524 Z= 0.155 Angle : 0.544 8.162 14288 Z= 0.275 Chirality : 0.041 0.433 1630 Planarity : 0.003 0.036 1821 Dihedral : 6.162 53.001 1670 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.27 % Favored : 94.66 % Rotamer: Outliers : 1.71 % Allowed : 15.17 % Favored : 83.12 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.24), residues: 1291 helix: 1.68 (0.21), residues: 586 sheet: -0.40 (0.48), residues: 123 loop : -1.06 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 503 TYR 0.013 0.001 TYR A 859 PHE 0.011 0.001 PHE A 783 TRP 0.004 0.001 TRP A 896 HIS 0.001 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (10517) covalent geometry : angle 0.54327 / 0.28 (14273) SS BOND : bond 0.00153 / 0.07 ( 3) SS BOND : angle 0.83250 / 0.46 ( 6) hydrogen bonds : bond 0.03399 / 2.33 ( 514) hydrogen bonds : angle 4.26959 / 3.04 ( 1482) Misc. bond : bond 0.00023 / 0.01 ( 1) link_NAG-ASN : bond 0.00131 / 0.06 ( 3) link_NAG-ASN : angle 1.16810 / 0.62 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 ASN cc_start: 0.9004 (t160) cc_final: 0.8432 (m110) REVERT: B 121 MET cc_start: 0.9186 (ttm) cc_final: 0.8938 (tmm) REVERT: B 154 GLU cc_start: 0.9023 (mp0) cc_final: 0.8796 (mp0) REVERT: C 32 ASP cc_start: 0.8448 (p0) cc_final: 0.8121 (p0) outliers start: 19 outliers final: 16 residues processed: 73 average time/residue: 0.9213 time to fit residues: 75.3088 Evaluate side-chains 73 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 68 optimal weight: 0.0770 chunk 24 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 21 optimal weight: 30.0000 chunk 52 optimal weight: 8.9990 chunk 45 optimal weight: 30.0000 chunk 38 optimal weight: 50.0000 chunk 70 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.158620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.091595 restraints weight = 52118.701| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.13 r_work: 0.3011 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10524 Z= 0.193 Angle : 0.558 8.108 14288 Z= 0.284 Chirality : 0.042 0.433 1630 Planarity : 0.003 0.036 1821 Dihedral : 6.114 54.148 1668 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.50 % Favored : 94.42 % Rotamer: Outliers : 1.71 % Allowed : 15.35 % Favored : 82.94 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1291 helix: 1.66 (0.21), residues: 586 sheet: -0.41 (0.48), residues: 123 loop : -1.10 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 648 TYR 0.014 0.001 TYR A 859 PHE 0.013 0.001 PHE A 783 TRP 0.004 0.001 TRP A 896 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (10517) covalent geometry : angle 0.55700 / 0.28 (14273) SS BOND : bond 0.00176 / 0.08 ( 3) SS BOND : angle 0.91932 / 0.51 ( 6) hydrogen bonds : bond 0.03458 / 2.37 ( 514) hydrogen bonds : angle 4.27476 / 3.04 ( 1482) Misc. bond : bond 0.00004 / 0.00 ( 1) link_NAG-ASN : bond 0.00143 / 0.06 ( 3) link_NAG-ASN : angle 1.22271 / 0.64 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.563 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: A 374 ASN cc_start: 0.9016 (t160) cc_final: 0.8514 (m-40) REVERT: B 121 MET cc_start: 0.9199 (ttm) cc_final: 0.8956 (tmm) REVERT: B 154 GLU cc_start: 0.9038 (mp0) cc_final: 0.8807 (mp0) REVERT: C 32 ASP cc_start: 0.8437 (p0) cc_final: 0.8109 (p0) outliers start: 19 outliers final: 18 residues processed: 72 average time/residue: 0.9066 time to fit residues: 73.0463 Evaluate side-chains 75 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 51 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 38 optimal weight: 50.0000 chunk 29 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 396 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.159218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.092225 restraints weight = 52348.716| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.17 r_work: 0.3026 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10524 Z= 0.149 Angle : 0.549 9.266 14288 Z= 0.276 Chirality : 0.041 0.430 1630 Planarity : 0.003 0.038 1821 Dihedral : 5.857 53.077 1668 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.57 % Favored : 95.35 % Rotamer: Outliers : 1.71 % Allowed : 15.44 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.24), residues: 1291 helix: 1.73 (0.21), residues: 586 sheet: -0.38 (0.49), residues: 123 loop : -1.01 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 648 TYR 0.015 0.001 TYR A 859 PHE 0.010 0.001 PHE A 783 TRP 0.004 0.001 TRP A 896 HIS 0.001 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (10517) covalent geometry : angle 0.54840 / 0.28 (14273) SS BOND : bond 0.00125 / 0.06 ( 3) SS BOND : angle 0.80698 / 0.45 ( 6) hydrogen bonds : bond 0.03330 / 2.28 ( 514) hydrogen bonds : angle 4.20966 / 2.99 ( 1482) Misc. bond : bond 0.00020 / 0.01 ( 1) link_NAG-ASN : bond 0.00145 / 0.07 ( 3) link_NAG-ASN : angle 1.19999 / 0.65 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.590 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: A 374 ASN cc_start: 0.9010 (t160) cc_final: 0.8512 (m-40) REVERT: B 121 MET cc_start: 0.9212 (ttm) cc_final: 0.8969 (tmm) REVERT: B 143 ARG cc_start: 0.7287 (ptm160) cc_final: 0.7033 (ptt180) REVERT: B 154 GLU cc_start: 0.9044 (mp0) cc_final: 0.8823 (mp0) outliers start: 19 outliers final: 17 residues processed: 71 average time/residue: 0.9226 time to fit residues: 73.2501 Evaluate side-chains 72 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 123 optimal weight: 0.3980 chunk 12 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.160251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.093343 restraints weight = 51893.731| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.18 r_work: 0.3047 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 10524 Z= 0.105 Angle : 0.535 8.782 14288 Z= 0.269 Chirality : 0.041 0.432 1630 Planarity : 0.003 0.038 1821 Dihedral : 5.640 52.572 1668 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.42 % Favored : 95.51 % Rotamer: Outliers : 1.71 % Allowed : 15.35 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.24), residues: 1291 helix: 1.84 (0.22), residues: 586 sheet: -0.34 (0.49), residues: 123 loop : -0.93 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 648 TYR 0.008 0.001 TYR A 859 PHE 0.007 0.001 PHE A 383 TRP 0.005 0.001 TRP A 880 HIS 0.001 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (10517) covalent geometry : angle 0.53416 / 0.27 (14273) SS BOND : bond 0.00111 / 0.05 ( 3) SS BOND : angle 0.68930 / 0.39 ( 6) hydrogen bonds : bond 0.03183 / 2.17 ( 514) hydrogen bonds : angle 4.11103 / 2.93 ( 1482) Misc. bond : bond 0.00052 / 0.03 ( 1) link_NAG-ASN : bond 0.00165 / 0.08 ( 3) link_NAG-ASN : angle 1.22066 / 0.65 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 ASN cc_start: 0.9005 (t160) cc_final: 0.8502 (m-40) REVERT: A 376 MET cc_start: 0.7425 (tpp) cc_final: 0.7188 (tpp) REVERT: A 579 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7872 (tpp) REVERT: A 837 GLU cc_start: 0.8755 (pm20) cc_final: 0.8399 (pm20) REVERT: B 143 ARG cc_start: 0.7195 (ptm160) cc_final: 0.6898 (ptt180) REVERT: B 154 GLU cc_start: 0.9044 (mp0) cc_final: 0.8826 (mp0) outliers start: 19 outliers final: 16 residues processed: 73 average time/residue: 0.9623 time to fit residues: 78.4757 Evaluate side-chains 75 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 1 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 35 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 53 optimal weight: 0.0980 chunk 43 optimal weight: 40.0000 chunk 84 optimal weight: 2.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.159002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.092122 restraints weight = 52258.114| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.15 r_work: 0.3017 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10524 Z= 0.205 Angle : 0.575 11.746 14288 Z= 0.288 Chirality : 0.042 0.433 1630 Planarity : 0.003 0.037 1821 Dihedral : 5.738 54.568 1667 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.11 % Favored : 94.81 % Rotamer: Outliers : 1.53 % Allowed : 15.80 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.24), residues: 1291 helix: 1.79 (0.21), residues: 586 sheet: -0.40 (0.49), residues: 123 loop : -1.01 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 648 TYR 0.010 0.001 TYR A 859 PHE 0.013 0.001 PHE A 783 TRP 0.005 0.001 TRP A 896 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 (10517) covalent geometry : angle 0.57406 / 0.29 (14273) SS BOND : bond 0.00157 / 0.07 ( 3) SS BOND : angle 0.91721 / 0.51 ( 6) hydrogen bonds : bond 0.03325 / 2.28 ( 514) hydrogen bonds : angle 4.18611 / 2.98 ( 1482) Misc. bond : bond 0.00016 / 0.01 ( 1) link_NAG-ASN : bond 0.00138 / 0.06 ( 3) link_NAG-ASN : angle 1.21432 / 0.65 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7782.57 seconds wall clock time: 132 minutes 31.56 seconds (7951.56 seconds total)