Starting phenix.real_space_refine on Thu Jul 2 23:27:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jl1_22369/07_2026/7jl1_22369.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jl1_22369/07_2026/7jl1_22369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jl1_22369/07_2026/7jl1_22369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jl1_22369/07_2026/7jl1_22369.map" model { file = "/net/cci-nas-00/data/ceres_data/7jl1_22369/07_2026/7jl1_22369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jl1_22369/07_2026/7jl1_22369.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7jl1_22369/07_2026/7jl1_22369.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jl1_22369/07_2026/7jl1_22369.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4056 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Zn 1 6.06 5 Al 1 5.89 5 P 30 5.49 5 Mg 1 5.21 5 S 41 5.16 5 C 4451 2.51 5 N 1220 2.21 5 O 1383 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7132 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5184 Classifications: {'peptide': 656} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 25, 'TRANS': 630} Chain breaks: 6 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "X" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 300 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 7, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 12} Chain: "Y" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 295 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 8} Link IDs: {'rna3p': 13} Chain: "B" Number of atoms: 1319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1319 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 46 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4362 SG CYS A 810 69.713 98.163 31.557 1.00 61.48 S ATOM 4388 SG CYS A 813 72.965 99.873 31.865 1.00 62.37 S ATOM 4728 SG CYS A 864 71.899 99.040 28.358 1.00 71.24 S ATOM 4767 SG CYS A 869 72.980 96.306 30.728 1.00 76.60 S Time building chain proxies: 1.46, per 1000 atoms: 0.20 Number of scatterers: 7132 At special positions: 0 Unit cell: (96.9088, 121.918, 67.732, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 S 41 16.00 P 30 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1383 8.00 N 1220 7.00 C 4451 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: 0.72 Conformation dependent library (CDL) restraints added in 374.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2004 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 813 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 869 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 864 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 810 " Number of angles added : 6 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 7 sheets defined 42.1% alpha, 14.8% beta 9 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 269 through 285 removed outlier: 3.701A pdb=" N LYS A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE A 285 " --> pdb=" O HIS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 316 removed outlier: 4.653A pdb=" N ARG A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 341 removed outlier: 3.719A pdb=" N GLU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 358 removed outlier: 4.118A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.583A pdb=" N PHE A 366 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 377 Processing helix chain 'A' and resid 381 through 396 Processing helix chain 'A' and resid 419 through 434 removed outlier: 3.583A pdb=" N LEU A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 453 removed outlier: 3.616A pdb=" N GLN A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 490 removed outlier: 3.515A pdb=" N TYR A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 521 removed outlier: 3.858A pdb=" N GLU A 510 " --> pdb=" O THR A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 558 removed outlier: 4.239A pdb=" N ARG A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 574 removed outlier: 3.703A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 592 Processing helix chain 'A' and resid 593 through 602 removed outlier: 3.618A pdb=" N ARG A 602 " --> pdb=" O GLU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 607 Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 636 through 649 removed outlier: 3.669A pdb=" N VAL A 640 " --> pdb=" O THR A 636 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 686 removed outlier: 3.517A pdb=" N LYS A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 701 Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 744 through 768 removed outlier: 3.682A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 752 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 766 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 768 " --> pdb=" O SER A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 771 No H-bonds generated for 'chain 'A' and resid 769 through 771' Processing helix chain 'A' and resid 774 through 794 Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 835 through 841 Processing sheet with id=AA1, first strand: chain 'A' and resid 321 through 324 removed outlier: 6.328A pdb=" N VAL A 293 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU A 346 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N PHE A 295 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N MET A 369 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU A 408 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE A 371 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE A 261 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 462 removed outlier: 6.687A pdb=" N THR A 630 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA A 696 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU A 632 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY A 659 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 666 through 667 Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819 removed outlier: 7.529A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 894 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 903 " --> pdb=" O VAL A 894 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 874 through 879 Processing sheet with id=AA6, first strand: chain 'B' and resid 272 through 274 removed outlier: 3.990A pdb=" N ILE B 426 " --> pdb=" O ASP B 318 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU B 316 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR B 390 " --> pdb=" O GLY B 377 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TYR B 400 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N SER B 391 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU B 398 " --> pdb=" O SER B 391 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 301 through 303 removed outlier: 4.273A pdb=" N TRP B 325 " --> pdb=" O TRP B 351 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU B 357 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS B 361 " --> pdb=" O LYS B 364 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 840 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1329 1.32 - 1.45: 1908 1.45 - 1.57: 3981 1.57 - 1.69: 57 1.69 - 1.81: 60 Bond restraints: 7335 Sorted by residual: bond pdb=" F2 ALF A2002 " pdb="AL ALF A2002 " ideal model delta sigma weight residual 1.685 1.799 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" F3 ALF A2002 " pdb="AL ALF A2002 " ideal model delta sigma weight residual 1.685 1.781 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" F4 ALF A2002 " pdb="AL ALF A2002 " ideal model delta sigma weight residual 1.686 1.779 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" F1 ALF A2002 " pdb="AL ALF A2002 " ideal model delta sigma weight residual 1.684 1.768 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" N CYS A 490 " pdb=" CA CYS A 490 " ideal model delta sigma weight residual 1.455 1.491 -0.035 1.33e-02 5.65e+03 7.06e+00 ... (remaining 7330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.88: 10052 13.88 - 27.76: 4 27.76 - 41.64: 0 41.64 - 55.53: 0 55.53 - 69.41: 2 Bond angle restraints: 10058 Sorted by residual: angle pdb=" F1 ALF A2002 " pdb="AL ALF A2002 " pdb=" F2 ALF A2002 " ideal model delta sigma weight residual 108.68 178.09 -69.41 3.00e+00 1.11e-01 5.35e+02 angle pdb=" F3 ALF A2002 " pdb="AL ALF A2002 " pdb=" F4 ALF A2002 " ideal model delta sigma weight residual 109.63 177.66 -68.03 3.00e+00 1.11e-01 5.14e+02 angle pdb=" F2 ALF A2002 " pdb="AL ALF A2002 " pdb=" F3 ALF A2002 " ideal model delta sigma weight residual 109.59 88.94 20.65 3.00e+00 1.11e-01 4.74e+01 angle pdb=" F1 ALF A2002 " pdb="AL ALF A2002 " pdb=" F4 ALF A2002 " ideal model delta sigma weight residual 109.02 88.94 20.08 3.00e+00 1.11e-01 4.48e+01 angle pdb=" F2 ALF A2002 " pdb="AL ALF A2002 " pdb=" F4 ALF A2002 " ideal model delta sigma weight residual 110.21 91.34 18.87 3.00e+00 1.11e-01 3.96e+01 ... (remaining 10053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 4246 35.43 - 70.85: 81 70.85 - 106.28: 4 106.28 - 141.70: 2 141.70 - 177.12: 3 Dihedral angle restraints: 4336 sinusoidal: 1917 harmonic: 2419 Sorted by residual: dihedral pdb=" C5' ADP A2001 " pdb=" O5' ADP A2001 " pdb=" PA ADP A2001 " pdb=" O2A ADP A2001 " ideal model delta sinusoidal sigma weight residual 300.00 164.34 135.66 1 2.00e+01 2.50e-03 4.12e+01 dihedral pdb=" O2A ADP A2001 " pdb=" O3A ADP A2001 " pdb=" PA ADP A2001 " pdb=" PB ADP A2001 " ideal model delta sinusoidal sigma weight residual -60.00 56.28 -116.28 1 2.00e+01 2.50e-03 3.46e+01 dihedral pdb=" CA THR A 347 " pdb=" C THR A 347 " pdb=" N PRO A 348 " pdb=" CA PRO A 348 " ideal model delta harmonic sigma weight residual -180.00 -154.28 -25.72 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 4333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 877 0.061 - 0.121: 251 0.121 - 0.182: 32 0.182 - 0.243: 2 0.243 - 0.303: 2 Chirality restraints: 1164 Sorted by residual: chirality pdb=" C3' G Y 4 " pdb=" C4' G Y 4 " pdb=" O3' G Y 4 " pdb=" C2' G Y 4 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C3' A X 2 " pdb=" C4' A X 2 " pdb=" O3' A X 2 " pdb=" C2' A X 2 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA LEU A 493 " pdb=" N LEU A 493 " pdb=" C LEU A 493 " pdb=" CB LEU A 493 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.59e-01 ... (remaining 1161 not shown) Planarity restraints: 1158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A X 2 " 0.042 2.00e-02 2.50e+03 1.85e-02 9.43e+00 pdb=" N9 A X 2 " -0.041 2.00e-02 2.50e+03 pdb=" C8 A X 2 " -0.006 2.00e-02 2.50e+03 pdb=" N7 A X 2 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A X 2 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A X 2 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A X 2 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A X 2 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A X 2 " -0.005 2.00e-02 2.50e+03 pdb=" N3 A X 2 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A X 2 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 313 " 0.015 2.00e-02 2.50e+03 1.72e-02 4.46e+00 pdb=" CG HIS B 313 " -0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS B 313 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS B 313 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS B 313 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS B 313 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 411 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO B 412 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 412 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 412 " -0.028 5.00e-02 4.00e+02 ... (remaining 1155 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 14 2.36 - 3.00: 3988 3.00 - 3.63: 9937 3.63 - 4.27: 14913 4.27 - 4.90: 25060 Nonbonded interactions: 53912 Sorted by model distance: nonbonded pdb=" F1 ALF A2002 " pdb="MG MG A2003 " model vdw 1.727 2.120 nonbonded pdb=" O1B ADP A2001 " pdb="MG MG A2003 " model vdw 1.793 2.170 nonbonded pdb=" F4 ALF A2002 " pdb="MG MG A2003 " model vdw 1.813 2.120 nonbonded pdb=" O1B ADP A2001 " pdb=" F4 ALF A2002 " model vdw 2.014 2.990 nonbonded pdb=" O2B ADP A2001 " pdb=" F2 ALF A2002 " model vdw 2.064 2.990 ... (remaining 53907 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.770 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 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 : 0.011 0.114 7339 Z= 0.476 Angle : 1.385 69.407 10064 Z= 0.600 Chirality : 0.054 0.303 1164 Planarity : 0.005 0.050 1158 Dihedral : 15.465 177.125 2760 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.14 % Allowed : 6.44 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.29), residues: 805 helix: 1.22 (0.30), residues: 302 sheet: 0.06 (0.45), residues: 144 loop : -0.35 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 296 TYR 0.031 0.003 TYR A 303 PHE 0.019 0.003 PHE A 295 TRP 0.013 0.002 TRP B 315 HIS 0.020 0.002 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.01072 / 0.48 ( 7335) covalent geometry : angle 1.38226 / 0.60 (10058) hydrogen bonds : bond 0.15475 / 10.10 ( 319) hydrogen bonds : angle 6.65900 / 4.74 ( 886) metal coordination : bond 0.00757 / 0.37 ( 4) metal coordination : angle 3.76063 / 2.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 283 LYS cc_start: 0.8412 (tppt) cc_final: 0.8197 (ttpt) REVERT: A 387 MET cc_start: 0.8925 (mmp) cc_final: 0.8701 (mmt) REVERT: A 435 ASP cc_start: 0.8639 (t0) cc_final: 0.7757 (t0) REVERT: A 492 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7656 (p0) REVERT: A 610 LYS cc_start: 0.7917 (mtpp) cc_final: 0.7415 (mtpp) REVERT: A 690 ASP cc_start: 0.8452 (p0) cc_final: 0.8165 (p0) REVERT: A 692 ASN cc_start: 0.8152 (m-40) cc_final: 0.7544 (t0) REVERT: A 756 TYR cc_start: 0.7623 (t80) cc_final: 0.7403 (t80) REVERT: A 761 MET cc_start: 0.7522 (ttp) cc_final: 0.7241 (ttp) REVERT: A 859 ARG cc_start: 0.7700 (tpp-160) cc_final: 0.7319 (tpp80) REVERT: B 321 ASN cc_start: 0.8208 (t0) cc_final: 0.7864 (t0) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.0813 time to fit residues: 18.4889 Evaluate side-chains 131 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 376 ASN A 573 ASN A 782 HIS A 876 HIS ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.159838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.126623 restraints weight = 8183.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.126261 restraints weight = 7551.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.127533 restraints weight = 7905.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.128095 restraints weight = 5571.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.128474 restraints weight = 4799.302| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7339 Z= 0.161 Angle : 0.638 7.703 10064 Z= 0.326 Chirality : 0.044 0.235 1164 Planarity : 0.004 0.038 1158 Dihedral : 12.025 164.676 1218 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.43 % Allowed : 12.88 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.30), residues: 805 helix: 1.51 (0.29), residues: 304 sheet: 0.11 (0.46), residues: 154 loop : -0.13 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 637 TYR 0.021 0.002 TYR A 541 PHE 0.016 0.001 PHE A 913 TRP 0.013 0.001 TRP B 257 HIS 0.007 0.001 HIS A 782 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 7335) covalent geometry : angle 0.62705 / 0.33 (10058) hydrogen bonds : bond 0.05639 / 3.80 ( 319) hydrogen bonds : angle 4.90254 / 3.53 ( 886) metal coordination : bond 0.00373 / 0.18 ( 4) metal coordination : angle 4.79633 / 2.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.234 Fit side-chains REVERT: A 241 PHE cc_start: 0.7963 (m-80) cc_final: 0.7742 (m-80) REVERT: A 283 LYS cc_start: 0.8525 (tppt) cc_final: 0.8035 (tttp) REVERT: A 387 MET cc_start: 0.9038 (mmp) cc_final: 0.8780 (mmt) REVERT: A 481 ASP cc_start: 0.8074 (m-30) cc_final: 0.7788 (m-30) REVERT: A 610 LYS cc_start: 0.7766 (mtpp) cc_final: 0.7478 (mttm) REVERT: A 692 ASN cc_start: 0.8283 (m-40) cc_final: 0.7758 (t0) REVERT: A 756 TYR cc_start: 0.7517 (t80) cc_final: 0.7291 (t80) REVERT: A 761 MET cc_start: 0.7409 (ttp) cc_final: 0.7141 (ttp) REVERT: A 792 ASP cc_start: 0.8419 (m-30) cc_final: 0.8062 (m-30) REVERT: A 822 ASP cc_start: 0.8440 (m-30) cc_final: 0.7775 (t0) REVERT: B 321 ASN cc_start: 0.8062 (t0) cc_final: 0.7804 (t0) REVERT: B 362 MET cc_start: 0.7616 (mmm) cc_final: 0.7038 (mtp) outliers start: 17 outliers final: 11 residues processed: 149 average time/residue: 0.0810 time to fit residues: 16.3472 Evaluate side-chains 139 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 916 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 678 GLN A 876 HIS B 313 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.158030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.124988 restraints weight = 8088.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.123395 restraints weight = 8413.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.125543 restraints weight = 8859.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.126204 restraints weight = 5538.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.126961 restraints weight = 5277.672| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7339 Z= 0.211 Angle : 0.644 8.303 10064 Z= 0.328 Chirality : 0.045 0.254 1164 Planarity : 0.004 0.041 1158 Dihedral : 11.788 166.393 1216 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.58 % Allowed : 16.74 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.29), residues: 805 helix: 1.42 (0.29), residues: 303 sheet: -0.10 (0.45), residues: 155 loop : -0.30 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 637 TYR 0.019 0.002 TYR A 303 PHE 0.015 0.002 PHE A 913 TRP 0.009 0.001 TRP B 257 HIS 0.008 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 ( 7335) covalent geometry : angle 0.63246 / 0.33 (10058) hydrogen bonds : bond 0.05811 / 3.90 ( 319) hydrogen bonds : angle 4.76038 / 3.41 ( 886) metal coordination : bond 0.00333 / 0.16 ( 4) metal coordination : angle 5.03312 / 2.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.227 Fit side-chains REVERT: A 241 PHE cc_start: 0.7970 (m-80) cc_final: 0.7765 (m-80) REVERT: A 283 LYS cc_start: 0.8617 (tppt) cc_final: 0.8166 (ttpp) REVERT: A 387 MET cc_start: 0.9089 (mmp) cc_final: 0.8843 (mmt) REVERT: A 610 LYS cc_start: 0.7888 (mtpp) cc_final: 0.7677 (mtpt) REVERT: A 657 LYS cc_start: 0.8693 (tptm) cc_final: 0.8182 (tppt) REVERT: A 692 ASN cc_start: 0.8474 (m-40) cc_final: 0.7747 (t0) REVERT: A 756 TYR cc_start: 0.7507 (t80) cc_final: 0.7248 (t80) REVERT: A 761 MET cc_start: 0.7454 (ttp) cc_final: 0.7219 (ttp) REVERT: A 822 ASP cc_start: 0.8402 (m-30) cc_final: 0.7713 (t0) REVERT: B 321 ASN cc_start: 0.8123 (t0) cc_final: 0.7905 (t0) REVERT: B 362 MET cc_start: 0.7666 (mmm) cc_final: 0.7452 (ttm) outliers start: 25 outliers final: 21 residues processed: 140 average time/residue: 0.0734 time to fit residues: 13.9957 Evaluate side-chains 142 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 678 GLN A 876 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.160299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.126994 restraints weight = 8184.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.125594 restraints weight = 7958.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.127573 restraints weight = 7683.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.128040 restraints weight = 5513.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.128654 restraints weight = 5838.828| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7339 Z= 0.178 Angle : 0.604 7.732 10064 Z= 0.308 Chirality : 0.044 0.243 1164 Planarity : 0.003 0.042 1158 Dihedral : 11.720 165.916 1216 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.01 % Allowed : 19.74 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.30), residues: 805 helix: 1.53 (0.29), residues: 303 sheet: -0.14 (0.44), residues: 155 loop : -0.35 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 637 TYR 0.017 0.002 TYR A 303 PHE 0.013 0.002 PHE A 911 TRP 0.011 0.001 TRP B 257 HIS 0.006 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 ( 7335) covalent geometry : angle 0.59290 / 0.31 (10058) hydrogen bonds : bond 0.05331 / 3.59 ( 319) hydrogen bonds : angle 4.57618 / 3.27 ( 886) metal coordination : bond 0.00244 / 0.12 ( 4) metal coordination : angle 4.67059 / 2.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 283 LYS cc_start: 0.8629 (tppt) cc_final: 0.8166 (ttpp) REVERT: A 387 MET cc_start: 0.9093 (mmp) cc_final: 0.8836 (mmt) REVERT: A 541 TYR cc_start: 0.7607 (m-80) cc_final: 0.7331 (m-80) REVERT: A 657 LYS cc_start: 0.8680 (tptm) cc_final: 0.8172 (tppt) REVERT: A 692 ASN cc_start: 0.8633 (m-40) cc_final: 0.7818 (t0) REVERT: A 756 TYR cc_start: 0.7519 (t80) cc_final: 0.7249 (t80) REVERT: A 761 MET cc_start: 0.7421 (ttp) cc_final: 0.7179 (ttp) REVERT: A 822 ASP cc_start: 0.8340 (m-30) cc_final: 0.7669 (t0) outliers start: 28 outliers final: 24 residues processed: 149 average time/residue: 0.0748 time to fit residues: 14.9561 Evaluate side-chains 148 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 762 ASN Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 43 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 72 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 678 GLN A 782 HIS A 876 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.161609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.127005 restraints weight = 8213.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.127585 restraints weight = 7461.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.129081 restraints weight = 6655.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.129265 restraints weight = 4911.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.129493 restraints weight = 4650.851| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7339 Z= 0.115 Angle : 0.548 6.097 10064 Z= 0.279 Chirality : 0.042 0.214 1164 Planarity : 0.003 0.042 1158 Dihedral : 11.615 165.296 1216 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.15 % Allowed : 22.03 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.30), residues: 805 helix: 1.79 (0.29), residues: 304 sheet: -0.04 (0.44), residues: 159 loop : -0.26 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 320 TYR 0.013 0.001 TYR A 390 PHE 0.011 0.001 PHE A 590 TRP 0.014 0.001 TRP B 257 HIS 0.008 0.001 HIS A 782 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 7335) covalent geometry : angle 0.54047 / 0.28 (10058) hydrogen bonds : bond 0.04407 / 2.97 ( 319) hydrogen bonds : angle 4.27005 / 3.04 ( 886) metal coordination : bond 0.00152 / 0.08 ( 4) metal coordination : angle 3.74784 / 1.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 LYS cc_start: 0.8633 (tppt) cc_final: 0.7953 (tttp) REVERT: A 387 MET cc_start: 0.8979 (mmp) cc_final: 0.8695 (mmt) REVERT: A 435 ASP cc_start: 0.8582 (t0) cc_final: 0.7895 (t0) REVERT: A 657 LYS cc_start: 0.8641 (tptm) cc_final: 0.8162 (tppt) REVERT: A 690 ASP cc_start: 0.8376 (p0) cc_final: 0.8038 (p0) REVERT: A 692 ASN cc_start: 0.8629 (m-40) cc_final: 0.7818 (t0) REVERT: A 756 TYR cc_start: 0.7490 (t80) cc_final: 0.7193 (t80) REVERT: A 761 MET cc_start: 0.7336 (ttp) cc_final: 0.7130 (ttp) REVERT: A 822 ASP cc_start: 0.8344 (m-30) cc_final: 0.7553 (t0) outliers start: 22 outliers final: 20 residues processed: 158 average time/residue: 0.0736 time to fit residues: 15.9944 Evaluate side-chains 149 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 762 ASN Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 25 optimal weight: 0.3980 chunk 74 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 678 GLN A 876 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.159662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.125150 restraints weight = 8295.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.126047 restraints weight = 7670.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.127180 restraints weight = 6751.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.127425 restraints weight = 5031.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.127647 restraints weight = 4733.360| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7339 Z= 0.153 Angle : 0.574 7.527 10064 Z= 0.292 Chirality : 0.043 0.232 1164 Planarity : 0.003 0.041 1158 Dihedral : 11.612 165.656 1216 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.01 % Allowed : 22.32 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.30), residues: 805 helix: 1.76 (0.29), residues: 303 sheet: -0.07 (0.43), residues: 159 loop : -0.32 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 637 TYR 0.016 0.002 TYR A 303 PHE 0.012 0.001 PHE B 414 TRP 0.013 0.001 TRP B 257 HIS 0.004 0.001 HIS B 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 7335) covalent geometry : angle 0.56454 / 0.29 (10058) hydrogen bonds : bond 0.04726 / 3.18 ( 319) hydrogen bonds : angle 4.31950 / 3.09 ( 886) metal coordination : bond 0.00225 / 0.11 ( 4) metal coordination : angle 4.32399 / 2.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.163 Fit side-chains REVERT: A 283 LYS cc_start: 0.8656 (tppt) cc_final: 0.7983 (tttp) REVERT: A 387 MET cc_start: 0.9028 (mmp) cc_final: 0.8725 (mmt) REVERT: A 612 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7749 (tm-30) REVERT: A 657 LYS cc_start: 0.8650 (tptm) cc_final: 0.8161 (tppt) REVERT: A 756 TYR cc_start: 0.7529 (t80) cc_final: 0.7211 (t80) REVERT: A 761 MET cc_start: 0.7541 (ttp) cc_final: 0.7300 (ttp) REVERT: A 822 ASP cc_start: 0.8342 (m-30) cc_final: 0.7552 (t0) outliers start: 28 outliers final: 23 residues processed: 148 average time/residue: 0.0750 time to fit residues: 15.2874 Evaluate side-chains 153 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 762 ASN Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 14 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 83 optimal weight: 0.0050 chunk 42 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 overall best weight: 2.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 678 GLN A 876 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.159414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.124180 restraints weight = 8168.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.124344 restraints weight = 7910.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.125562 restraints weight = 7562.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.125975 restraints weight = 5568.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.126371 restraints weight = 5070.880| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7339 Z= 0.158 Angle : 0.583 7.911 10064 Z= 0.295 Chirality : 0.043 0.233 1164 Planarity : 0.003 0.041 1158 Dihedral : 11.591 165.802 1216 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.86 % Allowed : 22.89 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.29), residues: 805 helix: 1.75 (0.29), residues: 303 sheet: -0.06 (0.43), residues: 158 loop : -0.38 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 296 TYR 0.016 0.002 TYR A 303 PHE 0.010 0.001 PHE A 911 TRP 0.010 0.001 TRP B 257 HIS 0.004 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 7335) covalent geometry : angle 0.57294 / 0.29 (10058) hydrogen bonds : bond 0.04773 / 3.23 ( 319) hydrogen bonds : angle 4.30654 / 3.08 ( 886) metal coordination : bond 0.00206 / 0.10 ( 4) metal coordination : angle 4.42281 / 2.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.251 Fit side-chains REVERT: A 283 LYS cc_start: 0.8654 (tppt) cc_final: 0.7986 (tttp) REVERT: A 387 MET cc_start: 0.9041 (mmt) cc_final: 0.8737 (mmt) REVERT: A 612 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7771 (tm-30) REVERT: A 657 LYS cc_start: 0.8644 (tptm) cc_final: 0.8139 (tppt) REVERT: A 756 TYR cc_start: 0.7502 (t80) cc_final: 0.7195 (t80) REVERT: A 761 MET cc_start: 0.7540 (ttp) cc_final: 0.7287 (ttp) REVERT: A 822 ASP cc_start: 0.8375 (m-30) cc_final: 0.7472 (t0) outliers start: 27 outliers final: 24 residues processed: 144 average time/residue: 0.0704 time to fit residues: 14.3167 Evaluate side-chains 149 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 762 ASN Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 0.0980 chunk 65 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 678 GLN A 876 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.161495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.127344 restraints weight = 8175.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.128242 restraints weight = 7621.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.129423 restraints weight = 6605.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.129620 restraints weight = 5008.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.130132 restraints weight = 4652.707| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7339 Z= 0.119 Angle : 0.561 8.510 10064 Z= 0.280 Chirality : 0.042 0.217 1164 Planarity : 0.003 0.041 1158 Dihedral : 11.533 165.373 1216 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.58 % Allowed : 23.32 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.30), residues: 805 helix: 1.89 (0.29), residues: 303 sheet: 0.12 (0.44), residues: 155 loop : -0.40 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 296 TYR 0.029 0.002 TYR A 541 PHE 0.013 0.001 PHE B 414 TRP 0.011 0.001 TRP B 257 HIS 0.003 0.001 HIS B 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 7335) covalent geometry : angle 0.55254 / 0.28 (10058) hydrogen bonds : bond 0.04269 / 2.88 ( 319) hydrogen bonds : angle 4.14175 / 2.97 ( 886) metal coordination : bond 0.00196 / 0.10 ( 4) metal coordination : angle 3.89936 / 1.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.164 Fit side-chains REVERT: A 283 LYS cc_start: 0.8622 (tppt) cc_final: 0.8005 (tttp) REVERT: A 387 MET cc_start: 0.8977 (mmt) cc_final: 0.8669 (mmt) REVERT: A 612 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7665 (tm-30) REVERT: A 756 TYR cc_start: 0.7515 (t80) cc_final: 0.7199 (t80) REVERT: A 822 ASP cc_start: 0.8307 (m-30) cc_final: 0.7447 (t0) REVERT: B 297 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.6967 (m-80) outliers start: 25 outliers final: 21 residues processed: 149 average time/residue: 0.0684 time to fit residues: 14.4439 Evaluate side-chains 150 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 77 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 71 optimal weight: 0.0970 chunk 74 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 678 GLN A 876 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.161646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.127718 restraints weight = 8020.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.128632 restraints weight = 7545.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.129715 restraints weight = 6668.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.130445 restraints weight = 5049.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.130642 restraints weight = 4617.245| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7339 Z= 0.119 Angle : 0.558 8.073 10064 Z= 0.278 Chirality : 0.042 0.217 1164 Planarity : 0.003 0.041 1158 Dihedral : 11.495 165.246 1216 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.72 % Allowed : 23.89 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.29), residues: 805 helix: 1.87 (0.29), residues: 304 sheet: 0.19 (0.44), residues: 155 loop : -0.40 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 296 TYR 0.030 0.002 TYR A 541 PHE 0.010 0.001 PHE A 911 TRP 0.009 0.001 TRP B 257 HIS 0.006 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 7335) covalent geometry : angle 0.55024 / 0.28 (10058) hydrogen bonds : bond 0.04212 / 2.84 ( 319) hydrogen bonds : angle 4.09518 / 2.93 ( 886) metal coordination : bond 0.00193 / 0.10 ( 4) metal coordination : angle 3.84231 / 1.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.275 Fit side-chains REVERT: A 283 LYS cc_start: 0.8607 (tppt) cc_final: 0.7997 (tttp) REVERT: A 387 MET cc_start: 0.8981 (mmt) cc_final: 0.8670 (mmt) REVERT: A 612 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7669 (tm-30) REVERT: A 652 LYS cc_start: 0.8243 (mttt) cc_final: 0.7715 (mttt) REVERT: A 756 TYR cc_start: 0.7526 (t80) cc_final: 0.7207 (t80) REVERT: A 822 ASP cc_start: 0.8288 (m-30) cc_final: 0.7472 (t0) REVERT: B 297 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.6903 (m-80) outliers start: 26 outliers final: 22 residues processed: 147 average time/residue: 0.0640 time to fit residues: 13.3466 Evaluate side-chains 153 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 678 GLN A 876 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.158219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.123243 restraints weight = 8186.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.124528 restraints weight = 7652.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.125544 restraints weight = 6521.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.125767 restraints weight = 4921.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.126258 restraints weight = 4627.410| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7339 Z= 0.198 Angle : 0.627 8.818 10064 Z= 0.314 Chirality : 0.044 0.247 1164 Planarity : 0.003 0.041 1158 Dihedral : 11.541 165.973 1216 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.43 % Allowed : 24.03 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.29), residues: 805 helix: 1.70 (0.29), residues: 303 sheet: -0.03 (0.43), residues: 156 loop : -0.49 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 296 TYR 0.025 0.002 TYR A 541 PHE 0.014 0.002 PHE A 911 TRP 0.010 0.001 TRP B 379 HIS 0.005 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 ( 7335) covalent geometry : angle 0.61553 / 0.31 (10058) hydrogen bonds : bond 0.05073 / 3.41 ( 319) hydrogen bonds : angle 4.32535 / 3.09 ( 886) metal coordination : bond 0.00259 / 0.12 ( 4) metal coordination : angle 4.84215 / 2.26 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.240 Fit side-chains REVERT: A 283 LYS cc_start: 0.8651 (tppt) cc_final: 0.7979 (tttp) REVERT: A 387 MET cc_start: 0.9090 (mmt) cc_final: 0.8789 (mmt) REVERT: A 612 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7769 (tm-30) REVERT: A 756 TYR cc_start: 0.7547 (t80) cc_final: 0.7219 (t80) REVERT: A 822 ASP cc_start: 0.8315 (m-30) cc_final: 0.7461 (t0) REVERT: B 297 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.7098 (m-80) outliers start: 24 outliers final: 18 residues processed: 138 average time/residue: 0.0703 time to fit residues: 13.7324 Evaluate side-chains 141 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 30 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 678 GLN A 876 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.160734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.126337 restraints weight = 8137.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.127309 restraints weight = 7573.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.128465 restraints weight = 6773.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.128687 restraints weight = 4983.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.128994 restraints weight = 4748.938| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7339 Z= 0.122 Angle : 0.572 8.628 10064 Z= 0.284 Chirality : 0.042 0.217 1164 Planarity : 0.003 0.041 1158 Dihedral : 11.491 165.455 1216 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.00 % Allowed : 25.18 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.29), residues: 805 helix: 1.87 (0.29), residues: 303 sheet: 0.11 (0.44), residues: 155 loop : -0.46 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 296 TYR 0.028 0.002 TYR A 541 PHE 0.011 0.001 PHE A 911 TRP 0.009 0.001 TRP B 257 HIS 0.003 0.001 HIS B 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 7335) covalent geometry : angle 0.56423 / 0.28 (10058) hydrogen bonds : bond 0.04330 / 2.92 ( 319) hydrogen bonds : angle 4.11031 / 2.94 ( 886) metal coordination : bond 0.00164 / 0.08 ( 4) metal coordination : angle 3.87506 / 1.86 ( 6) =============================================================================== Job complete usr+sys time: 1068.91 seconds wall clock time: 19 minutes 9.70 seconds (1149.70 seconds total)