Starting phenix.real_space_refine on Wed Aug 5 13:39:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wce_37439/08_2026/8wce_37439.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wce_37439/08_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_37439/08_2026/8wce_37439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wce_37439/08_2026/8wce_37439.map" model { file = "/net/cci-nas-00/data/ceres_data/8wce_37439/08_2026/8wce_37439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wce_37439/08_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-2.2rc3-6140/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: 2.35, per 1000 atoms: 0.23 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: 0.73 Conformation dependent library (CDL) restraints added in 309.9 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: 1.22 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: 2.51 Time building geometry restraints manager: 1.04 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: 14383 1.82 - 3.65: 505 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: 1423 0.062 - 0.125: 183 0.125 - 0.187: 81 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: 1.620 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: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.190 Find NCS groups from input model: 0.050 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.410 ------------------------------------------------------------------------------- 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= 0.194 Angle : 0.712 9.114 14954 Z= 0.516 Chirality : 0.050 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 0.00310 / 0.19 (10773) covalent geometry : angle 0.71220 / 0.52 (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 : 0.290 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: 0.0967 time to fit residues: 14.1926 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 : 0.382 ------------------------------------------------------------------------------- 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: 9.9990 chunk 106 optimal weight: 9.9990 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 = 0.3709 r_free = 0.3709 target = 0.145187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.097571 restraints weight = 13589.041| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.90 r_work: 0.2942 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10773 Z= 0.252 Angle : 0.636 6.781 14954 Z= 0.355 Chirality : 0.043 0.201 1692 Planarity : 0.004 0.034 1521 Dihedral : 20.245 173.582 2570 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 3.09 % Allowed : 29.33 % 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: -0.23 (0.27), residues: 990 helix: 1.43 (0.22), residues: 546 sheet: -1.39 (0.69), residues: 60 loop : -2.40 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 709 TYR 0.023 0.002 TYR A 968 PHE 0.014 0.002 PHE A 676 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 0.00577 / 0.25 (10773) covalent geometry : angle 0.63636 / 0.36 (14954) hydrogen bonds : bond 0.06926 / 4.64 ( 488) hydrogen bonds : angle 4.29727 / 3.07 ( 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 135 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 ASP cc_start: 0.8515 (m-30) cc_final: 0.8302 (m-30) REVERT: A 469 LYS cc_start: 0.6806 (OUTLIER) cc_final: 0.6277 (mptt) REVERT: A 562 ASP cc_start: 0.8644 (p0) cc_final: 0.8408 (p0) REVERT: A 758 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: A 811 MET cc_start: 0.8153 (tpp) cc_final: 0.7894 (tpt) outliers start: 28 outliers final: 16 residues processed: 127 average time/residue: 0.0971 time to fit residues: 17.9488 Evaluate side-chains 118 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 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 564 ILE 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 1080 LEU 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: 8.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN A 795 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.148592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.100664 restraints weight = 13710.673| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.93 r_work: 0.3032 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.0974 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= 0.128 Angle : 0.513 6.971 14954 Z= 0.295 Chirality : 0.037 0.152 1692 Planarity : 0.003 0.032 1521 Dihedral : 20.313 172.010 2568 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 3.20 % Allowed : 29.22 % Favored : 67.59 % 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: 0.05 (0.27), residues: 990 helix: 1.76 (0.22), residues: 542 sheet: -1.37 (0.68), residues: 60 loop : -2.37 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 674 TYR 0.014 0.001 TYR A 968 PHE 0.015 0.001 PHE A 676 TRP 0.007 0.001 TRP A 315 HIS 0.004 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (10773) covalent geometry : angle 0.51339 / 0.29 (14954) hydrogen bonds : bond 0.05943 / 3.93 ( 488) hydrogen bonds : angle 3.96297 / 2.83 ( 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 133 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 469 LYS cc_start: 0.6781 (OUTLIER) cc_final: 0.6192 (mptt) REVERT: A 562 ASP cc_start: 0.8636 (p0) cc_final: 0.8308 (p0) REVERT: A 811 MET cc_start: 0.8049 (tpp) cc_final: 0.7805 (tpt) REVERT: A 882 MET cc_start: 0.9103 (mmm) cc_final: 0.8763 (mmm) outliers start: 29 outliers final: 16 residues processed: 126 average time/residue: 0.0967 time to fit residues: 17.9125 Evaluate side-chains 114 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 189 GLU 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 529 THR 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: 1.9990 chunk 35 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.146936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.099014 restraints weight = 13772.356| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.93 r_work: 0.3017 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10773 Z= 0.169 Angle : 0.547 9.850 14954 Z= 0.308 Chirality : 0.039 0.255 1692 Planarity : 0.003 0.033 1521 Dihedral : 20.259 172.715 2568 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 4.30 % Allowed : 28.11 % 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: 0.00 (0.27), residues: 990 helix: 1.71 (0.22), residues: 546 sheet: -1.44 (0.68), residues: 60 loop : -2.41 (0.28), residues: 384 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 0.016 0.001 PHE A 676 TRP 0.009 0.001 TRP A 315 HIS 0.004 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (10773) covalent geometry : angle 0.54659 / 0.31 (14954) hydrogen bonds : bond 0.06029 / 4.03 ( 488) hydrogen bonds : angle 3.93128 / 2.80 ( 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 140 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 101 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.8118 (t0) REVERT: A 226 GLU cc_start: 0.7128 (mp0) cc_final: 0.6880 (mp0) REVERT: A 231 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6560 (mt-10) REVERT: A 256 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7317 (mp) REVERT: A 469 LYS cc_start: 0.6818 (OUTLIER) cc_final: 0.6328 (mptt) REVERT: A 562 ASP cc_start: 0.8676 (p0) cc_final: 0.8303 (p0) REVERT: A 811 MET cc_start: 0.8055 (tpp) cc_final: 0.7820 (tpt) outliers start: 39 outliers final: 25 residues processed: 132 average time/residue: 0.0999 time to fit residues: 19.3213 Evaluate side-chains 125 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 169 ASN 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 231 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 337 LEU 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 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 758 GLN 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 1108 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 70 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.148798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.100964 restraints weight = 13703.703| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.92 r_work: 0.3041 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10773 Z= 0.118 Angle : 0.508 9.125 14954 Z= 0.290 Chirality : 0.036 0.159 1692 Planarity : 0.003 0.032 1521 Dihedral : 20.284 172.580 2568 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 4.52 % Allowed : 28.34 % Favored : 67.14 % 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: 0.23 (0.27), residues: 990 helix: 1.96 (0.22), residues: 537 sheet: -1.37 (0.69), residues: 60 loop : -2.31 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 674 TYR 0.013 0.001 TYR A1091 PHE 0.016 0.001 PHE A 676 TRP 0.007 0.001 TRP A 315 HIS 0.004 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (10773) covalent geometry : angle 0.50759 / 0.29 (14954) hydrogen bonds : bond 0.05481 / 3.65 ( 488) hydrogen bonds : angle 3.80915 / 2.72 ( 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 : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 226 GLU cc_start: 0.7032 (mp0) cc_final: 0.6788 (mp0) REVERT: A 231 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6532 (mt-10) REVERT: A 256 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7318 (mp) REVERT: A 469 LYS cc_start: 0.6861 (OUTLIER) cc_final: 0.6416 (mptt) REVERT: A 562 ASP cc_start: 0.8637 (p0) cc_final: 0.8265 (p0) REVERT: A 811 MET cc_start: 0.8062 (tpp) cc_final: 0.7839 (tpt) REVERT: A 882 MET cc_start: 0.9131 (mmm) cc_final: 0.8769 (mmm) REVERT: A 994 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6712 (pt0) outliers start: 41 outliers final: 30 residues processed: 134 average time/residue: 0.0938 time to fit residues: 18.1965 Evaluate side-chains 129 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 189 GLU 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 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 702 LEU 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 994 GLU 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: 1.9990 chunk 46 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 88 optimal weight: 0.0010 chunk 2 optimal weight: 0.0070 chunk 74 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.0008 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.149715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.102026 restraints weight = 13749.997| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.91 r_work: 0.3059 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10773 Z= 0.114 Angle : 0.490 9.224 14954 Z= 0.281 Chirality : 0.036 0.160 1692 Planarity : 0.003 0.030 1521 Dihedral : 20.249 173.681 2568 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % 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: 0.37 (0.27), residues: 990 helix: 2.05 (0.22), residues: 535 sheet: -1.34 (0.69), residues: 60 loop : -2.19 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 674 TYR 0.013 0.001 TYR A1091 PHE 0.018 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 0.00231 / 0.11 (10773) covalent geometry : angle 0.49047 / 0.28 (14954) hydrogen bonds : bond 0.05101 / 3.40 ( 488) hydrogen bonds : angle 3.71951 / 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 145 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 106 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 226 GLU cc_start: 0.7082 (mp0) cc_final: 0.6804 (mp0) REVERT: A 231 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6468 (mt-10) REVERT: A 256 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7320 (mp) REVERT: A 562 ASP cc_start: 0.8604 (p0) cc_final: 0.8227 (p0) REVERT: A 882 MET cc_start: 0.9129 (mmm) cc_final: 0.8767 (mmm) REVERT: A 994 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6593 (pt0) outliers start: 39 outliers final: 28 residues processed: 138 average time/residue: 0.0909 time to fit residues: 18.2260 Evaluate side-chains 130 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 451 LEU 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 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 994 GLU Chi-restraints excluded: chain A residue 1091 TYR Chi-restraints excluded: chain A residue 1093 ILE 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: 0.8980 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 2 optimal weight: 0.0020 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 82 optimal weight: 0.0050 chunk 28 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.7806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1054 ASN A1073 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.150915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.103316 restraints weight = 13581.427| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.91 r_work: 0.3074 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10773 Z= 0.107 Angle : 0.494 9.233 14954 Z= 0.280 Chirality : 0.036 0.306 1692 Planarity : 0.003 0.029 1521 Dihedral : 20.236 173.242 2568 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.97 % Allowed : 28.67 % 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: 0.45 (0.27), residues: 990 helix: 2.13 (0.22), residues: 535 sheet: -1.30 (0.69), residues: 60 loop : -2.17 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 674 TYR 0.013 0.001 TYR A1101 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 0.00211 / 0.11 (10773) covalent geometry : angle 0.49405 / 0.28 (14954) hydrogen bonds : bond 0.04837 / 3.23 ( 488) hydrogen bonds : angle 3.67036 / 2.62 ( 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 144 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 ASN cc_start: 0.8243 (t0) cc_final: 0.8016 (t0) REVERT: A 231 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6453 (mt-10) REVERT: A 256 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7310 (mp) REVERT: A 469 LYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6447 (mptt) REVERT: A 562 ASP cc_start: 0.8605 (p0) cc_final: 0.8217 (p0) REVERT: A 811 MET cc_start: 0.8345 (tpt) cc_final: 0.7997 (tpp) REVERT: A 882 MET cc_start: 0.9121 (mmm) cc_final: 0.8763 (mmm) REVERT: A 994 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6473 (pt0) outliers start: 36 outliers final: 26 residues processed: 137 average time/residue: 0.0885 time to fit residues: 17.6712 Evaluate side-chains 129 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 573 GLU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 611 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 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 1080 LEU Chi-restraints excluded: chain A residue 1091 TYR Chi-restraints excluded: chain A residue 1093 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 87 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 99 optimal weight: 30.0000 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.142581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.093737 restraints weight = 13778.105| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.94 r_work: 0.2908 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 10773 Z= 0.272 Angle : 0.662 9.025 14954 Z= 0.362 Chirality : 0.044 0.195 1692 Planarity : 0.004 0.036 1521 Dihedral : 20.283 171.308 2568 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 4.19 % Allowed : 28.78 % Favored : 67.03 % 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: -0.07 (0.27), residues: 990 helix: 1.61 (0.22), residues: 538 sheet: -1.63 (0.69), residues: 60 loop : -2.26 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 875 TYR 0.022 0.002 TYR A 968 PHE 0.022 0.002 PHE A 676 TRP 0.013 0.002 TRP A 891 HIS 0.006 0.001 HIS A 991 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.27 (10773) covalent geometry : angle 0.66202 / 0.36 (14954) hydrogen bonds : bond 0.06945 / 4.69 ( 488) hydrogen bonds : angle 4.05476 / 2.89 ( 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 146 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 231 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6535 (mt-10) REVERT: A 256 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7463 (mp) REVERT: A 390 GLU cc_start: 0.8021 (tp30) cc_final: 0.7020 (tm-30) REVERT: A 469 LYS cc_start: 0.6978 (OUTLIER) cc_final: 0.6475 (mptt) REVERT: A 562 ASP cc_start: 0.8761 (p0) cc_final: 0.8325 (p0) REVERT: A 811 MET cc_start: 0.8558 (tpt) cc_final: 0.8204 (tpp) REVERT: A 994 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7167 (pt0) outliers start: 38 outliers final: 28 residues processed: 137 average time/residue: 0.0899 time to fit residues: 18.1768 Evaluate side-chains 138 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 189 GLU 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 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 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 611 SER Chi-restraints excluded: chain A residue 708 TYR 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 912 ASN 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 1091 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 63 optimal weight: 0.0980 chunk 32 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.148844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.101095 restraints weight = 13515.949| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.89 r_work: 0.3044 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1456 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 : 0.518 9.557 14954 Z= 0.296 Chirality : 0.036 0.185 1692 Planarity : 0.003 0.031 1521 Dihedral : 20.299 170.734 2568 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 3.42 % Allowed : 29.55 % Favored : 67.03 % 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: 0.29 (0.27), residues: 990 helix: 2.00 (0.22), residues: 534 sheet: -1.50 (0.68), residues: 60 loop : -2.22 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 686 TYR 0.016 0.001 TYR A 769 PHE 0.015 0.001 PHE A 676 TRP 0.007 0.001 TRP A 315 HIS 0.004 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.12 (10773) covalent geometry : angle 0.51794 / 0.30 (14954) hydrogen bonds : bond 0.05269 / 3.52 ( 488) hydrogen bonds : angle 3.79199 / 2.70 ( 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 137 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 ASN cc_start: 0.8183 (t0) cc_final: 0.7931 (t0) REVERT: A 231 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6484 (mt-10) REVERT: A 256 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7340 (mp) REVERT: A 390 GLU cc_start: 0.7780 (tp30) cc_final: 0.6720 (tm-30) REVERT: A 469 LYS cc_start: 0.6912 (OUTLIER) cc_final: 0.6472 (mptt) REVERT: A 562 ASP cc_start: 0.8650 (p0) cc_final: 0.8245 (p0) REVERT: A 635 TYR cc_start: 0.8514 (t80) cc_final: 0.8275 (t80) REVERT: A 811 MET cc_start: 0.8440 (tpt) cc_final: 0.8073 (tpp) REVERT: A 882 MET cc_start: 0.9106 (mmm) cc_final: 0.8724 (mmm) REVERT: A 994 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6742 (pt0) outliers start: 31 outliers final: 25 residues processed: 131 average time/residue: 0.0900 time to fit residues: 17.3608 Evaluate side-chains 131 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 223 TYR 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 337 LEU 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 512 THR Chi-restraints excluded: chain A residue 529 THR 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 611 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 994 GLU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1091 TYR Chi-restraints excluded: chain A residue 1111 MET 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: 0.7980 chunk 64 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 84 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.148224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.100092 restraints weight = 13519.262| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.91 r_work: 0.3030 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10773 Z= 0.133 Angle : 0.524 9.206 14954 Z= 0.296 Chirality : 0.037 0.206 1692 Planarity : 0.003 0.031 1521 Dihedral : 20.186 172.375 2568 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 2.98 % Allowed : 30.10 % Favored : 66.92 % 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: 0.31 (0.27), residues: 990 helix: 2.02 (0.22), residues: 534 sheet: -1.44 (0.69), residues: 60 loop : -2.22 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 686 TYR 0.017 0.001 TYR A 769 PHE 0.018 0.001 PHE A 676 TRP 0.007 0.001 TRP A 315 HIS 0.012 0.001 HIS A 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (10773) covalent geometry : angle 0.52382 / 0.30 (14954) hydrogen bonds : bond 0.05269 / 3.54 ( 488) hydrogen bonds : angle 3.77885 / 2.69 ( 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 132 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 ASN cc_start: 0.8250 (t0) cc_final: 0.8005 (t0) REVERT: A 231 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6489 (mt-10) REVERT: A 256 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7350 (mp) REVERT: A 390 GLU cc_start: 0.7869 (tp30) cc_final: 0.6861 (tm-30) REVERT: A 469 LYS cc_start: 0.6942 (OUTLIER) cc_final: 0.6497 (mptt) REVERT: A 562 ASP cc_start: 0.8665 (p0) cc_final: 0.8241 (p0) REVERT: A 635 TYR cc_start: 0.8553 (t80) cc_final: 0.8320 (t80) REVERT: A 811 MET cc_start: 0.8453 (tpt) cc_final: 0.8094 (tpp) REVERT: A 994 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6759 (pt0) outliers start: 27 outliers final: 23 residues processed: 126 average time/residue: 0.0953 time to fit residues: 17.3745 Evaluate side-chains 130 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 223 TYR 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 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 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 611 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 775 VAL Chi-restraints excluded: chain A residue 835 SER 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 1111 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.146026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.097054 restraints weight = 13687.220| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.96 r_work: 0.2960 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10773 Z= 0.163 Angle : 0.549 9.210 14954 Z= 0.307 Chirality : 0.039 0.208 1692 Planarity : 0.003 0.031 1521 Dihedral : 20.233 171.989 2568 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 3.20 % Allowed : 29.77 % Favored : 67.03 % 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: 0.24 (0.27), residues: 990 helix: 1.95 (0.22), residues: 534 sheet: -1.48 (0.69), residues: 60 loop : -2.23 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 589 TYR 0.018 0.002 TYR A 193 PHE 0.017 0.001 PHE A 676 TRP 0.009 0.001 TRP A 315 HIS 0.004 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (10773) covalent geometry : angle 0.54855 / 0.31 (14954) hydrogen bonds : bond 0.05553 / 3.74 ( 488) hydrogen bonds : angle 3.81674 / 2.72 ( 1345) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3040.59 seconds wall clock time: 52 minutes 37.37 seconds (3157.37 seconds total)