Starting phenix.real_space_refine on Thu Jul 2 20:11:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wce_37439/07_2026/8wce_37439.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wce_37439/07_2026/8wce_37439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wce_37439/07_2026/8wce_37439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wce_37439/07_2026/8wce_37439.map" model { file = "/net/cci-nas-00/data/ceres_data/8wce_37439/07_2026/8wce_37439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wce_37439/07_2026/8wce_37439.cif" } resolution = 3.09 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= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 97 5.49 5 Mg 2 5.21 5 S 31 5.16 5 C 6271 2.51 5 N 1738 2.21 5 O 2211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 10350 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 8275 Classifications: {'peptide': 994} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 972} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1410 Classifications: {'RNA': 66} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p_pur': 32, 'rna3p_pyr': 26} Link IDs: {'rna2p': 8, 'rna3p': 57} Chain: "T" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 663 Classifications: {'RNA': 31} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 16, 'rna3p_pyr': 13} Link IDs: {'rna2p': 2, 'rna3p': 28} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.75, per 1000 atoms: 0.17 Number of scatterers: 10350 At special positions: 0 Unit cell: (92.65, 91.8, 143.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 31 16.00 P 97 15.00 Mg 2 11.99 O 2211 8.00 N 1738 7.00 C 6271 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: 0.68 Conformation dependent library (CDL) restraints added in 284.4 milliseconds 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 6 sheets defined 60.4% alpha, 3.9% beta 37 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 98 through 121 removed outlier: 3.624A pdb=" N TYR A 102 " --> pdb=" O PRO A 98 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 120 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 121 " --> pdb=" O TYR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 163 Processing helix chain 'A' and resid 178 through 204 removed outlier: 5.574A pdb=" N LYS A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 262 removed outlier: 3.702A pdb=" N VAL A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 280 removed outlier: 3.680A pdb=" N GLU A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 275 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 302 removed outlier: 3.901A pdb=" N PHE A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 316 removed outlier: 4.154A pdb=" N THR A 316 " --> pdb=" O THR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 removed outlier: 3.751A pdb=" N THR A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 4.160A pdb=" N ASP A 334 " --> pdb=" O PHE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 361 Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.603A pdb=" N TYR A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 413 through 425 removed outlier: 4.022A pdb=" N TRP A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 451 through 455 removed outlier: 4.177A pdb=" N GLN A 454 " --> pdb=" O LEU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 477 Processing helix chain 'A' and resid 489 through 504 removed outlier: 4.198A pdb=" N LYS A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 496 " --> pdb=" O LYS A 492 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU A 497 " --> pdb=" O LYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 560 removed outlier: 3.729A pdb=" N LEU A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 593 Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'A' and resid 623 through 646 removed outlier: 4.480A pdb=" N ILE A 627 " --> pdb=" O ASP A 623 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 628 " --> pdb=" O LYS A 624 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 679 removed outlier: 3.624A pdb=" N ASP A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 688 Processing helix chain 'A' and resid 691 through 704 Processing helix chain 'A' and resid 711 through 720 removed outlier: 3.588A pdb=" N LYS A 715 " --> pdb=" O THR A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 728 No H-bonds generated for 'chain 'A' and resid 726 through 728' Processing helix chain 'A' and resid 729 through 735 removed outlier: 3.900A pdb=" N GLN A 735 " --> pdb=" O LYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 758 removed outlier: 3.653A pdb=" N GLN A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 774 removed outlier: 3.951A pdb=" N TYR A 769 " --> pdb=" O ASN A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 782 No H-bonds generated for 'chain 'A' and resid 780 through 782' Processing helix chain 'A' and resid 783 through 792 Processing helix chain 'A' and resid 798 through 802 removed outlier: 3.818A pdb=" N LEU A 801 " --> pdb=" O PRO A 798 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 802 " --> pdb=" O GLN A 799 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 798 through 802' Processing helix chain 'A' and resid 809 through 818 removed outlier: 3.633A pdb=" N LYS A 818 " --> pdb=" O LYS A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 836 removed outlier: 4.260A pdb=" N PHE A 828 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 829 " --> pdb=" O ASP A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 849 removed outlier: 3.835A pdb=" N TYR A 844 " --> pdb=" O SER A 840 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 853 Processing helix chain 'A' and resid 865 through 896 removed outlier: 3.751A pdb=" N MET A 869 " --> pdb=" O GLY A 865 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 870 " --> pdb=" O ASN A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 922 Processing helix chain 'A' and resid 957 through 961 removed outlier: 3.828A pdb=" N PHE A 961 " --> pdb=" O PRO A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 980 Processing helix chain 'A' and resid 991 through 1024 removed outlier: 4.059A pdb=" N LEU A 995 " --> pdb=" O HIS A 991 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LYS A 997 " --> pdb=" O GLU A 993 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A1023 " --> pdb=" O HIS A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1029 Processing helix chain 'A' and resid 1052 through 1060 Processing helix chain 'A' and resid 1068 through 1082 Processing helix chain 'A' and resid 1089 through 1106 removed outlier: 3.807A pdb=" N ILE A1093 " --> pdb=" O GLU A1089 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE A1094 " --> pdb=" O LYS A1090 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 139 removed outlier: 5.517A pdb=" N ILE A 138 " --> pdb=" O VAL A 174 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 363 through 364 removed outlier: 6.604A pdb=" N MET A 363 " --> pdb=" O ARG A 409 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 433 through 436 Processing sheet with id=AA4, first strand: chain 'A' and resid 525 through 532 removed outlier: 8.503A pdb=" N HIS A 795 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLN A 541 " --> pdb=" O HIS A 795 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL A 797 " --> pdb=" O GLN A 541 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER A 543 " --> pdb=" O VAL A 797 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 563 through 565 Processing sheet with id=AA6, first strand: chain 'A' and resid 932 through 936 393 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 95 hydrogen bonds 190 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2741 1.34 - 1.46: 2626 1.46 - 1.58: 5158 1.58 - 1.70: 192 1.70 - 1.82: 56 Bond restraints: 10773 Sorted by residual: bond pdb=" N1 U G -26 " pdb=" C2 U G -26 " ideal model delta sigma weight residual 1.381 1.397 -0.016 9.00e-03 1.23e+04 3.05e+00 bond pdb=" N ASP A 562 " pdb=" CA ASP A 562 " ideal model delta sigma weight residual 1.462 1.484 -0.022 1.31e-02 5.83e+03 2.84e+00 bond pdb=" N9 A T 28 " pdb=" C4 A T 28 " ideal model delta sigma weight residual 1.374 1.384 -0.010 6.00e-03 2.78e+04 2.75e+00 bond pdb=" N9 G G -6 " pdb=" C4 G G -6 " ideal model delta sigma weight residual 1.375 1.388 -0.013 8.00e-03 1.56e+04 2.73e+00 bond pdb=" N9 G G -17 " pdb=" C4 G G -17 " ideal model delta sigma weight residual 1.375 1.387 -0.012 8.00e-03 1.56e+04 2.41e+00 ... (remaining 10768 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 14615 1.82 - 3.65: 273 3.65 - 5.47: 51 5.47 - 7.29: 8 7.29 - 9.11: 7 Bond angle restraints: 14954 Sorted by residual: angle pdb=" C GLU A 263 " pdb=" CA GLU A 263 " pdb=" CB GLU A 263 " ideal model delta sigma weight residual 117.23 110.22 7.01 1.36e+00 5.41e-01 2.66e+01 angle pdb=" C1' U G -26 " pdb=" N1 U G -26 " pdb=" C2 U G -26 " ideal model delta sigma weight residual 117.70 123.32 -5.62 1.20e+00 6.94e-01 2.20e+01 angle pdb=" O2 U G 5 " pdb=" C2 U G 5 " pdb=" N3 U G 5 " ideal model delta sigma weight residual 122.20 119.21 2.99 7.00e-01 2.04e+00 1.82e+01 angle pdb=" N9 G G -17 " pdb=" C4 G G -17 " pdb=" N3 G G -17 " ideal model delta sigma weight residual 126.00 128.55 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" C ARG A 648 " pdb=" N LYS A 649 " pdb=" CA LYS A 649 " ideal model delta sigma weight residual 121.54 129.63 -8.09 1.91e+00 2.74e-01 1.79e+01 ... (remaining 14949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 6079 34.93 - 69.86: 504 69.86 - 104.79: 44 104.79 - 139.72: 0 139.72 - 174.65: 1 Dihedral angle restraints: 6628 sinusoidal: 3670 harmonic: 2958 Sorted by residual: dihedral pdb=" O4' U G 18 " pdb=" C1' U G 18 " pdb=" N1 U G 18 " pdb=" C2 U G 18 " ideal model delta sinusoidal sigma weight residual -128.00 46.65 -174.65 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" CA ALA A 604 " pdb=" C ALA A 604 " pdb=" N SER A 605 " pdb=" CA SER A 605 " ideal model delta harmonic sigma weight residual 180.00 154.39 25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA GLU A 603 " pdb=" C GLU A 603 " pdb=" N ALA A 604 " pdb=" CA ALA A 604 " ideal model delta harmonic sigma weight residual -180.00 -154.75 -25.25 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 6625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1517 0.062 - 0.125: 156 0.125 - 0.187: 14 0.187 - 0.249: 4 0.249 - 0.312: 1 Chirality restraints: 1692 Sorted by residual: chirality pdb=" CG LEU A 473 " pdb=" CB LEU A 473 " pdb=" CD1 LEU A 473 " pdb=" CD2 LEU A 473 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C3' C T 13 " pdb=" C4' C T 13 " pdb=" O3' C T 13 " pdb=" C2' C T 13 " both_signs ideal model delta sigma weight residual False -2.48 -2.69 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C3' C T 14 " pdb=" C4' C T 14 " pdb=" O3' C T 14 " pdb=" C2' C T 14 " both_signs ideal model delta sigma weight residual False -2.48 -2.68 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1689 not shown) Planarity restraints: 1521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 994 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.10e+00 pdb=" C GLU A 994 " 0.052 2.00e-02 2.50e+03 pdb=" O GLU A 994 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU A 995 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 169 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.94e+00 pdb=" C ASN A 169 " -0.042 2.00e-02 2.50e+03 pdb=" O ASN A 169 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE A 170 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 877 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.53e+00 pdb=" C LYS A 877 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS A 877 " -0.015 2.00e-02 2.50e+03 pdb=" N THR A 878 " -0.014 2.00e-02 2.50e+03 ... (remaining 1518 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2388 2.79 - 3.32: 9157 3.32 - 3.84: 17666 3.84 - 4.37: 19845 4.37 - 4.90: 32930 Nonbonded interactions: 81986 Sorted by model distance: nonbonded pdb=" OH TYR A 968 " pdb=" OD1 ASN A 996 " model vdw 2.259 3.040 nonbonded pdb=" O LYS A 606 " pdb=" O2' C G 8 " model vdw 2.264 3.040 nonbonded pdb=" OD2 ASP A 963 " pdb="MG MG A1201 " model vdw 2.276 2.170 nonbonded pdb=" OH TYR A 117 " pdb=" OH TYR A 185 " model vdw 2.290 3.040 nonbonded pdb=" O LYS A 492 " pdb=" OG1 THR A 496 " model vdw 2.291 3.040 ... (remaining 81981 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.500 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 : 0.003 0.041 10773 Z= 0.183 Angle : 0.640 9.114 14954 Z= 0.451 Chirality : 0.040 0.312 1692 Planarity : 0.004 0.042 1521 Dihedral : 21.714 174.653 4720 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 0.33 % Allowed : 31.86 % Favored : 67.81 % 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: -0.41 (0.26), residues: 990 helix: 1.21 (0.22), residues: 534 sheet: -0.38 (0.77), residues: 51 loop : -2.40 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 709 TYR 0.012 0.001 TYR A 635 PHE 0.018 0.001 PHE A 676 TRP 0.005 0.001 TRP A 315 HIS 0.004 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.18 (10773) covalent geometry : angle 0.64019 / 0.45 (14954) hydrogen bonds : bond 0.14691 / 9.14 ( 488) hydrogen bonds : angle 6.01832 / 4.29 ( 1345) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 226 GLU cc_start: 0.6336 (mp0) cc_final: 0.5890 (mp0) outliers start: 3 outliers final: 2 residues processed: 101 average time/residue: 0.0792 time to fit residues: 11.6215 Evaluate side-chains 97 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 451 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.144783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.096312 restraints weight = 13561.856| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.01 r_work: 0.2940 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10773 Z= 0.254 Angle : 0.606 6.852 14954 Z= 0.344 Chirality : 0.042 0.179 1692 Planarity : 0.004 0.034 1521 Dihedral : 20.371 173.786 2570 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.65 % Allowed : 29.00 % Favored : 68.36 % 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: -0.19 (0.27), residues: 990 helix: 1.51 (0.22), residues: 541 sheet: -1.34 (0.69), residues: 60 loop : -2.41 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 709 TYR 0.020 0.002 TYR A 968 PHE 0.014 0.002 PHE A 992 TRP 0.011 0.001 TRP A 315 HIS 0.004 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.25 (10773) covalent geometry : angle 0.60590 / 0.34 (14954) hydrogen bonds : bond 0.06874 / 4.59 ( 488) hydrogen bonds : angle 4.33583 / 3.10 ( 1345) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 469 LYS cc_start: 0.6759 (OUTLIER) cc_final: 0.6204 (mptt) REVERT: A 562 ASP cc_start: 0.8635 (p0) cc_final: 0.8405 (p0) REVERT: A 758 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: A 811 MET cc_start: 0.8182 (tpp) cc_final: 0.7898 (tpt) outliers start: 24 outliers final: 15 residues processed: 123 average time/residue: 0.0743 time to fit residues: 13.3255 Evaluate side-chains 118 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 758 GLN Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.147815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.099849 restraints weight = 13709.101| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.93 r_work: 0.3022 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10773 Z= 0.151 Angle : 0.521 6.911 14954 Z= 0.300 Chirality : 0.038 0.156 1692 Planarity : 0.003 0.032 1521 Dihedral : 20.461 171.783 2568 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 3.09 % Allowed : 28.89 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.27), residues: 990 helix: 1.72 (0.22), residues: 542 sheet: -1.35 (0.68), residues: 60 loop : -2.38 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 674 TYR 0.016 0.001 TYR A 968 PHE 0.015 0.001 PHE A 676 TRP 0.008 0.001 TRP A 315 HIS 0.004 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (10773) covalent geometry : angle 0.52145 / 0.30 (14954) hydrogen bonds : bond 0.05957 / 3.96 ( 488) hydrogen bonds : angle 3.99151 / 2.85 ( 1345) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 469 LYS cc_start: 0.6785 (OUTLIER) cc_final: 0.6182 (mptt) REVERT: A 562 ASP cc_start: 0.8660 (p0) cc_final: 0.8327 (p0) REVERT: A 811 MET cc_start: 0.8047 (tpp) cc_final: 0.7804 (tpt) REVERT: A 882 MET cc_start: 0.9099 (mmm) cc_final: 0.8754 (mmm) outliers start: 28 outliers final: 16 residues processed: 125 average time/residue: 0.0714 time to fit residues: 13.0332 Evaluate side-chains 116 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1080 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 48 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 36 optimal weight: 0.0980 chunk 68 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.149124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.101470 restraints weight = 13732.246| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.92 r_work: 0.3037 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10773 Z= 0.125 Angle : 0.501 9.442 14954 Z= 0.288 Chirality : 0.037 0.268 1692 Planarity : 0.003 0.033 1521 Dihedral : 20.417 171.916 2568 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 4.41 % Allowed : 28.11 % Favored : 67.48 % 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: 0.20 (0.27), residues: 990 helix: 1.91 (0.22), residues: 536 sheet: -1.27 (0.69), residues: 60 loop : -2.30 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 674 TYR 0.015 0.001 TYR A 193 PHE 0.016 0.001 PHE A 676 TRP 0.006 0.001 TRP A 315 HIS 0.004 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (10773) covalent geometry : angle 0.50134 / 0.29 (14954) hydrogen bonds : bond 0.05438 / 3.62 ( 488) hydrogen bonds : angle 3.85548 / 2.75 ( 1345) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.8093 (t0) REVERT: A 226 GLU cc_start: 0.7181 (mp0) cc_final: 0.6918 (mp0) REVERT: A 231 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6539 (mt-10) REVERT: A 256 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7279 (mp) REVERT: A 469 LYS cc_start: 0.6832 (OUTLIER) cc_final: 0.6367 (mptt) REVERT: A 562 ASP cc_start: 0.8615 (p0) cc_final: 0.8264 (p0) REVERT: A 811 MET cc_start: 0.8035 (tpp) cc_final: 0.7805 (tpt) REVERT: A 882 MET cc_start: 0.9116 (mmm) cc_final: 0.8773 (mmm) outliers start: 40 outliers final: 24 residues processed: 132 average time/residue: 0.0748 time to fit residues: 14.7639 Evaluate side-chains 124 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 70 optimal weight: 0.0470 chunk 89 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 overall best weight: 1.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.147838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.100497 restraints weight = 13730.330| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.85 r_work: 0.3036 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10773 Z= 0.156 Angle : 0.519 9.003 14954 Z= 0.297 Chirality : 0.038 0.177 1692 Planarity : 0.003 0.033 1521 Dihedral : 20.394 171.974 2568 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 4.52 % Allowed : 28.67 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.27), residues: 990 helix: 1.89 (0.22), residues: 537 sheet: -1.34 (0.69), residues: 60 loop : -2.31 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 653 TYR 0.014 0.001 TYR A 968 PHE 0.016 0.001 PHE A 676 TRP 0.008 0.001 TRP A 315 HIS 0.004 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (10773) covalent geometry : angle 0.51874 / 0.30 (14954) hydrogen bonds : bond 0.05572 / 3.72 ( 488) hydrogen bonds : angle 3.83436 / 2.74 ( 1345) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 101 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 226 GLU cc_start: 0.7112 (mp0) cc_final: 0.6843 (mp0) REVERT: A 231 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6546 (mt-10) REVERT: A 256 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7332 (mp) REVERT: A 469 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6431 (mptt) REVERT: A 562 ASP cc_start: 0.8651 (p0) cc_final: 0.8279 (p0) REVERT: A 811 MET cc_start: 0.8048 (tpp) cc_final: 0.7826 (tpt) REVERT: A 994 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6755 (pt0) outliers start: 41 outliers final: 26 residues processed: 134 average time/residue: 0.0739 time to fit residues: 14.6907 Evaluate side-chains 128 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1091 TYR Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 2 optimal weight: 0.0370 chunk 74 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.150287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.102611 restraints weight = 13730.587| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.91 r_work: 0.3066 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10773 Z= 0.105 Angle : 0.483 9.273 14954 Z= 0.278 Chirality : 0.036 0.174 1692 Planarity : 0.003 0.030 1521 Dihedral : 20.411 171.996 2568 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 4.30 % Allowed : 28.34 % Favored : 67.36 % 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: 0.35 (0.27), residues: 990 helix: 2.04 (0.22), residues: 538 sheet: -1.21 (0.70), residues: 60 loop : -2.27 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 674 TYR 0.015 0.001 TYR A 472 PHE 0.017 0.001 PHE A 676 TRP 0.006 0.001 TRP A 315 HIS 0.004 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.11 (10773) covalent geometry : angle 0.48304 / 0.28 (14954) hydrogen bonds : bond 0.04963 / 3.29 ( 488) hydrogen bonds : angle 3.70724 / 2.65 ( 1345) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 226 GLU cc_start: 0.7079 (mp0) cc_final: 0.6815 (mp0) REVERT: A 231 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6492 (mt-10) REVERT: A 256 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7301 (mp) REVERT: A 562 ASP cc_start: 0.8584 (p0) cc_final: 0.8217 (p0) REVERT: A 811 MET cc_start: 0.8042 (tpp) cc_final: 0.7841 (tpt) REVERT: A 882 MET cc_start: 0.9103 (mmm) cc_final: 0.8752 (mmm) REVERT: A 994 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6558 (pt0) outliers start: 39 outliers final: 28 residues processed: 138 average time/residue: 0.0766 time to fit residues: 15.3447 Evaluate side-chains 134 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 758 GLN Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1091 TYR Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 0.9980 chunk 30 optimal weight: 0.0270 chunk 62 optimal weight: 10.0000 chunk 53 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 2 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 795 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.152163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.104700 restraints weight = 13574.753| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.91 r_work: 0.3096 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10773 Z= 0.102 Angle : 0.493 9.301 14954 Z= 0.280 Chirality : 0.037 0.307 1692 Planarity : 0.003 0.029 1521 Dihedral : 20.349 173.440 2568 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 3.64 % Allowed : 29.11 % Favored : 67.25 % 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: 0.50 (0.27), residues: 990 helix: 2.16 (0.22), residues: 537 sheet: -1.18 (0.70), residues: 60 loop : -2.16 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 393 TYR 0.012 0.001 TYR A1091 PHE 0.017 0.001 PHE A 676 TRP 0.005 0.001 TRP A 315 HIS 0.004 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.10 (10773) covalent geometry : angle 0.49292 / 0.28 (14954) hydrogen bonds : bond 0.04556 / 3.04 ( 488) hydrogen bonds : angle 3.62470 / 2.58 ( 1345) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 226 GLU cc_start: 0.7003 (mp0) cc_final: 0.6722 (mp0) REVERT: A 231 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6388 (mt-10) REVERT: A 256 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7294 (mp) REVERT: A 469 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6513 (mptt) REVERT: A 562 ASP cc_start: 0.8591 (p0) cc_final: 0.8203 (p0) REVERT: A 635 TYR cc_start: 0.8517 (t80) cc_final: 0.8300 (t80) REVERT: A 757 ILE cc_start: 0.8120 (tp) cc_final: 0.7728 (tp) REVERT: A 882 MET cc_start: 0.9090 (mmm) cc_final: 0.8750 (mmm) REVERT: A 994 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6389 (pt0) outliers start: 33 outliers final: 23 residues processed: 136 average time/residue: 0.0833 time to fit residues: 16.4735 Evaluate side-chains 129 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain A residue 1091 TYR Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 87 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 99 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.141773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.093371 restraints weight = 13734.435| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.99 r_work: 0.2880 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 10773 Z= 0.314 Angle : 0.675 9.075 14954 Z= 0.376 Chirality : 0.045 0.203 1692 Planarity : 0.004 0.033 1521 Dihedral : 20.386 170.713 2568 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer: Outliers : 3.75 % Allowed : 28.67 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.26), residues: 990 helix: 1.53 (0.22), residues: 538 sheet: -1.59 (0.69), residues: 60 loop : -2.28 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 709 TYR 0.024 0.002 TYR A 968 PHE 0.018 0.003 PHE A 676 TRP 0.014 0.002 TRP A 891 HIS 0.007 0.001 HIS A 991 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.31 (10773) covalent geometry : angle 0.67510 / 0.38 (14954) hydrogen bonds : bond 0.07165 / 4.84 ( 488) hydrogen bonds : angle 4.08423 / 2.91 ( 1345) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 231 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6599 (mt-10) REVERT: A 256 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7463 (mp) REVERT: A 469 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.6396 (mptt) REVERT: A 509 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8117 (mttt) REVERT: A 562 ASP cc_start: 0.8786 (p0) cc_final: 0.8348 (p0) REVERT: A 811 MET cc_start: 0.8577 (tpt) cc_final: 0.8224 (tpp) REVERT: A 994 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7218 (pt0) outliers start: 34 outliers final: 24 residues processed: 135 average time/residue: 0.0721 time to fit residues: 14.3688 Evaluate side-chains 133 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 63 optimal weight: 0.0040 chunk 32 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.148684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.100783 restraints weight = 13524.112| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.90 r_work: 0.3033 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10773 Z= 0.116 Angle : 0.524 9.719 14954 Z= 0.299 Chirality : 0.037 0.208 1692 Planarity : 0.003 0.032 1521 Dihedral : 20.486 169.411 2568 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 2.76 % Allowed : 29.55 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.27), residues: 990 helix: 2.00 (0.22), residues: 532 sheet: -1.50 (0.68), residues: 60 loop : -2.25 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 709 TYR 0.021 0.001 TYR A 193 PHE 0.017 0.001 PHE A 676 TRP 0.007 0.001 TRP A 315 HIS 0.004 0.001 HIS A1019 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.12 (10773) covalent geometry : angle 0.52384 / 0.30 (14954) hydrogen bonds : bond 0.05274 / 3.52 ( 488) hydrogen bonds : angle 3.78382 / 2.69 ( 1345) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 ASN cc_start: 0.8181 (t0) cc_final: 0.7930 (t0) REVERT: A 231 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6482 (mt-10) REVERT: A 256 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7341 (mp) REVERT: A 469 LYS cc_start: 0.6870 (OUTLIER) cc_final: 0.6364 (mptt) REVERT: A 562 ASP cc_start: 0.8666 (p0) cc_final: 0.8241 (p0) REVERT: A 635 TYR cc_start: 0.8531 (t80) cc_final: 0.8284 (t80) REVERT: A 811 MET cc_start: 0.8427 (tpt) cc_final: 0.8067 (tpp) REVERT: A 994 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6810 (pt0) outliers start: 25 outliers final: 17 residues processed: 129 average time/residue: 0.0750 time to fit residues: 14.2484 Evaluate side-chains 123 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain A residue 1091 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 83 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 448 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.145028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.096174 restraints weight = 13575.615| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.95 r_work: 0.2947 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10773 Z= 0.194 Angle : 0.572 10.122 14954 Z= 0.320 Chirality : 0.040 0.321 1692 Planarity : 0.003 0.032 1521 Dihedral : 20.382 171.110 2568 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 2.54 % Allowed : 30.21 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.27), residues: 990 helix: 1.88 (0.22), residues: 533 sheet: -1.51 (0.69), residues: 60 loop : -2.28 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 709 TYR 0.017 0.002 TYR A 968 PHE 0.019 0.002 PHE A 676 TRP 0.009 0.001 TRP A 315 HIS 0.012 0.001 HIS A 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (10773) covalent geometry : angle 0.57240 / 0.32 (14954) hydrogen bonds : bond 0.05785 / 3.89 ( 488) hydrogen bonds : angle 3.87296 / 2.75 ( 1345) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 169 ASN cc_start: 0.8276 (t0) cc_final: 0.8047 (t0) REVERT: A 231 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6522 (mt-10) REVERT: A 256 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7412 (mp) REVERT: A 469 LYS cc_start: 0.6935 (OUTLIER) cc_final: 0.6447 (mptt) REVERT: A 562 ASP cc_start: 0.8708 (p0) cc_final: 0.8272 (p0) REVERT: A 635 TYR cc_start: 0.8584 (t80) cc_final: 0.8340 (t80) REVERT: A 811 MET cc_start: 0.8544 (tpt) cc_final: 0.8195 (tpp) REVERT: A 994 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6973 (pt0) outliers start: 23 outliers final: 17 residues processed: 124 average time/residue: 0.0833 time to fit residues: 14.9524 Evaluate side-chains 125 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 994 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 97 optimal weight: 0.0000 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 overall best weight: 0.6784 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.148954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.100097 restraints weight = 13677.615| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.96 r_work: 0.3007 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10773 Z= 0.111 Angle : 0.522 9.832 14954 Z= 0.295 Chirality : 0.037 0.293 1692 Planarity : 0.003 0.030 1521 Dihedral : 20.447 171.480 2568 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 2.65 % Allowed : 29.88 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.27), residues: 990 helix: 2.09 (0.22), residues: 533 sheet: -1.37 (0.69), residues: 60 loop : -2.23 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 709 TYR 0.020 0.001 TYR A1101 PHE 0.017 0.001 PHE A 676 TRP 0.006 0.001 TRP A 652 HIS 0.004 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (10773) covalent geometry : angle 0.52195 / 0.29 (14954) hydrogen bonds : bond 0.04894 / 3.27 ( 488) hydrogen bonds : angle 3.73867 / 2.66 ( 1345) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2460.04 seconds wall clock time: 42 minutes 39.17 seconds (2559.17 seconds total)