Starting phenix.real_space_refine on Thu May 1 01:13:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wce_37439/05_2025/8wce_37439.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wce_37439/05_2025/8wce_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_37439/05_2025/8wce_37439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wce_37439/05_2025/8wce_37439.map" model { file = "/net/cci-nas-00/data/ceres_data/8wce_37439/05_2025/8wce_37439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wce_37439/05_2025/8wce_37439.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 6.43, per 1000 atoms: 0.62 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: 2.50 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 3.61 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: 4.99 Time building geometry restraints manager: 2.98 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=" 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=" CB GLU A 964 " pdb=" CG GLU A 964 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.88e+00 bond pdb=" CA ASN A 169 " pdb=" CB ASN A 169 " ideal model delta sigma weight residual 1.530 1.553 -0.023 1.69e-02 3.50e+03 1.78e+00 bond pdb=" N ASP A1024 " pdb=" CA ASP A1024 " ideal model delta sigma weight residual 1.463 1.479 -0.017 1.31e-02 5.83e+03 1.62e+00 bond pdb=" O5' C T 13 " pdb=" C5' C T 13 " ideal model delta sigma weight residual 1.420 1.438 -0.018 1.50e-02 4.44e+03 1.45e+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=" 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 angle pdb=" CA ARG A 653 " pdb=" CB ARG A 653 " pdb=" CG ARG A 653 " ideal model delta sigma weight residual 114.10 122.10 -8.00 2.00e+00 2.50e-01 1.60e+01 angle pdb=" C GLU A 993 " pdb=" N GLU A 994 " pdb=" CA GLU A 994 " ideal model delta sigma weight residual 121.54 128.94 -7.40 1.91e+00 2.74e-01 1.50e+01 angle pdb=" CA GLU A 263 " pdb=" C GLU A 263 " pdb=" N GLY A 264 " ideal model delta sigma weight residual 119.98 116.79 3.19 8.50e-01 1.38e+00 1.41e+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: 0.880 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 29.740 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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= 0.151 Angle : 0.640 9.114 14954 Z= 0.344 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 : 4.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP A 315 HIS 0.004 0.001 HIS A 101 PHE 0.018 0.001 PHE A 676 TYR 0.012 0.001 TYR A 635 ARG 0.011 0.001 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.14691 ( 488) hydrogen bonds : angle 6.01832 ( 1345) covalent geometry : bond 0.00303 (10773) covalent geometry : angle 0.64011 (14954) *********************** 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 : 1.100 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: 0.2392 time to fit residues: 34.8290 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 : 1.098 ------------------------------------------------------------------------------- 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 91 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 55 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 84 optimal weight: 0.0170 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.151884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.103864 restraints weight = 13391.953| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.98 r_work: 0.3052 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.0839 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= 0.109 Angle : 0.541 7.177 14954 Z= 0.277 Chirality : 0.035 0.160 1692 Planarity : 0.003 0.029 1521 Dihedral : 20.329 174.193 2570 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 2.21 % Allowed : 29.00 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.27), residues: 990 helix: 1.93 (0.22), residues: 537 sheet: -1.06 (0.70), residues: 60 loop : -2.19 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 315 HIS 0.003 0.000 HIS A1019 PHE 0.014 0.001 PHE A 676 TYR 0.010 0.001 TYR A1091 ARG 0.004 0.000 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.04622 ( 488) hydrogen bonds : angle 3.92149 ( 1345) covalent geometry : bond 0.00215 (10773) covalent geometry : angle 0.54128 (14954) *********************** 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 128 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6405 (mt-10) REVERT: A 994 GLU cc_start: 0.5986 (OUTLIER) cc_final: 0.5192 (tm-30) outliers start: 20 outliers final: 11 residues processed: 124 average time/residue: 0.2227 time to fit residues: 39.8880 Evaluate side-chains 110 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 205 HIS Chi-restraints excluded: chain A residue 231 GLU 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 529 THR Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 994 GLU 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 29 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A1105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.149499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.105084 restraints weight = 13653.210| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.06 r_work: 0.3062 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10773 Z= 0.230 Angle : 0.641 7.084 14954 Z= 0.329 Chirality : 0.040 0.182 1692 Planarity : 0.003 0.035 1521 Dihedral : 20.422 167.613 2568 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 3.31 % Allowed : 28.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.27), residues: 990 helix: 1.72 (0.22), residues: 540 sheet: -1.17 (0.70), residues: 60 loop : -2.28 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 891 HIS 0.003 0.001 HIS A 101 PHE 0.015 0.002 PHE A 676 TYR 0.021 0.002 TYR A 968 ARG 0.005 0.000 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.06101 ( 488) hydrogen bonds : angle 3.98019 ( 1345) covalent geometry : bond 0.00524 (10773) covalent geometry : angle 0.64052 (14954) *********************** 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 135 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: A 169 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.8239 (t0) REVERT: A 226 GLU cc_start: 0.7137 (mp0) cc_final: 0.6862 (mp0) REVERT: A 231 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6565 (mt-10) REVERT: A 469 LYS cc_start: 0.6851 (OUTLIER) cc_final: 0.6361 (mptt) REVERT: A 562 ASP cc_start: 0.8424 (p0) cc_final: 0.8184 (p0) REVERT: A 811 MET cc_start: 0.8169 (tpp) cc_final: 0.7922 (tpt) REVERT: A 1077 ILE cc_start: 0.8824 (mm) cc_final: 0.8600 (mm) outliers start: 30 outliers final: 16 residues processed: 127 average time/residue: 0.2149 time to fit residues: 40.0899 Evaluate side-chains 119 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL 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 231 GLU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 324 VAL 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 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 733 MET Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 1021 VAL 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 18 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.154428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.111246 restraints weight = 13419.648| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.68 r_work: 0.3154 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1292 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= 0.116 Angle : 0.552 10.562 14954 Z= 0.284 Chirality : 0.036 0.130 1692 Planarity : 0.003 0.029 1521 Dihedral : 20.351 168.961 2568 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.98 % Allowed : 28.78 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.27), residues: 990 helix: 2.03 (0.22), residues: 533 sheet: -1.08 (0.71), residues: 60 loop : -2.17 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 315 HIS 0.004 0.001 HIS A 101 PHE 0.017 0.001 PHE A 676 TYR 0.016 0.001 TYR A 193 ARG 0.003 0.000 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.04552 ( 488) hydrogen bonds : angle 3.66731 ( 1345) covalent geometry : bond 0.00235 (10773) covalent geometry : angle 0.55222 (14954) *********************** 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 136 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 256 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7310 (mp) REVERT: A 444 MET cc_start: 0.7368 (mmm) cc_final: 0.7058 (mmm) REVERT: A 451 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8303 (mt) REVERT: A 469 LYS cc_start: 0.6827 (OUTLIER) cc_final: 0.6294 (mptt) REVERT: A 562 ASP cc_start: 0.8279 (p0) cc_final: 0.8003 (p0) REVERT: A 686 ARG cc_start: 0.8559 (ttm110) cc_final: 0.8195 (ttm-80) outliers start: 27 outliers final: 14 residues processed: 131 average time/residue: 0.2252 time to fit residues: 42.1321 Evaluate side-chains 117 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 256 LEU 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 512 THR 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 739 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 1108 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 53 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.153511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.112352 restraints weight = 13090.851| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.50 r_work: 0.3162 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10773 Z= 0.130 Angle : 0.559 8.918 14954 Z= 0.285 Chirality : 0.037 0.246 1692 Planarity : 0.003 0.029 1521 Dihedral : 20.328 169.910 2568 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % 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 : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.27), residues: 990 helix: 2.02 (0.22), residues: 537 sheet: -1.17 (0.70), residues: 60 loop : -2.13 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 315 HIS 0.004 0.001 HIS A 101 PHE 0.016 0.001 PHE A 676 TYR 0.013 0.001 TYR A 193 ARG 0.006 0.000 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.04635 ( 488) hydrogen bonds : angle 3.64685 ( 1345) covalent geometry : bond 0.00279 (10773) covalent geometry : angle 0.55879 (14954) *********************** 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 140 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6447 (mt-10) REVERT: A 256 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7357 (mp) REVERT: A 318 MET cc_start: 0.4149 (ttt) cc_final: 0.3872 (ttt) REVERT: A 390 GLU cc_start: 0.7741 (tp30) cc_final: 0.6691 (tm-30) REVERT: A 444 MET cc_start: 0.7432 (mmm) cc_final: 0.7086 (mmm) REVERT: A 451 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8259 (mt) REVERT: A 469 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6435 (mptt) REVERT: A 562 ASP cc_start: 0.8353 (p0) cc_final: 0.8032 (p0) REVERT: A 686 ARG cc_start: 0.8592 (ttm110) cc_final: 0.8213 (ttm-80) REVERT: A 811 MET cc_start: 0.8368 (tpt) cc_final: 0.8037 (tpp) REVERT: A 994 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6471 (pt0) outliers start: 34 outliers final: 21 residues processed: 137 average time/residue: 0.2227 time to fit residues: 43.8356 Evaluate side-chains 127 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 205 HIS 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 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 564 ILE 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 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 1108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 103 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.148409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.106151 restraints weight = 13222.187| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.62 r_work: 0.3069 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10773 Z= 0.244 Angle : 0.660 9.071 14954 Z= 0.338 Chirality : 0.041 0.149 1692 Planarity : 0.003 0.034 1521 Dihedral : 20.382 167.013 2568 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % 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 : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.27), residues: 990 helix: 1.75 (0.22), residues: 536 sheet: -1.40 (0.70), residues: 60 loop : -2.25 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 891 HIS 0.004 0.001 HIS A 101 PHE 0.018 0.002 PHE A 676 TYR 0.021 0.002 TYR A 968 ARG 0.007 0.000 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.06177 ( 488) hydrogen bonds : angle 3.90692 ( 1345) covalent geometry : bond 0.00559 (10773) covalent geometry : angle 0.65982 (14954) *********************** 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 147 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 142 TYR cc_start: 0.6945 (OUTLIER) cc_final: 0.4801 (t80) REVERT: A 231 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6578 (mt-10) REVERT: A 256 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7473 (mp) REVERT: A 318 MET cc_start: 0.4098 (ttt) cc_final: 0.3750 (ttt) REVERT: A 350 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8422 (mp) REVERT: A 451 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8224 (mt) REVERT: A 469 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6460 (mptt) REVERT: A 562 ASP cc_start: 0.8596 (p0) cc_final: 0.8255 (p0) REVERT: A 686 ARG cc_start: 0.8650 (ttm110) cc_final: 0.8246 (ttm-80) REVERT: A 811 MET cc_start: 0.8526 (tpt) cc_final: 0.8168 (tpp) REVERT: A 970 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7010 (mm-40) REVERT: A 994 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7184 (pt0) outliers start: 40 outliers final: 25 residues processed: 138 average time/residue: 0.2208 time to fit residues: 44.8360 Evaluate side-chains 135 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 142 TYR 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 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 324 VAL Chi-restraints excluded: chain A residue 350 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 564 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 711 THR 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 941 LYS Chi-restraints excluded: chain A residue 970 GLN Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1080 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 13 optimal weight: 0.0050 chunk 102 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.153688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.110728 restraints weight = 13556.037| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.59 r_work: 0.3155 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1552 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= 0.117 Angle : 0.560 9.139 14954 Z= 0.288 Chirality : 0.037 0.152 1692 Planarity : 0.003 0.030 1521 Dihedral : 20.356 168.611 2568 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 3.53 % Allowed : 29.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.27), residues: 990 helix: 2.06 (0.22), residues: 534 sheet: -1.24 (0.70), residues: 60 loop : -2.21 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 315 HIS 0.004 0.001 HIS A 101 PHE 0.017 0.001 PHE A 676 TYR 0.015 0.001 TYR A 193 ARG 0.005 0.000 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.04496 ( 488) hydrogen bonds : angle 3.65406 ( 1345) covalent geometry : bond 0.00241 (10773) covalent geometry : angle 0.55953 (14954) *********************** 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 140 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.6867 (OUTLIER) cc_final: 0.4706 (t80) REVERT: A 226 GLU cc_start: 0.7062 (mp0) cc_final: 0.6343 (tp30) REVERT: A 256 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7393 (mp) REVERT: A 318 MET cc_start: 0.3882 (ttt) cc_final: 0.3200 (ttp) REVERT: A 444 MET cc_start: 0.7441 (mmm) cc_final: 0.7022 (mmm) REVERT: A 451 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8263 (mt) REVERT: A 469 LYS cc_start: 0.6885 (OUTLIER) cc_final: 0.6466 (mptt) REVERT: A 509 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7844 (mttt) REVERT: A 562 ASP cc_start: 0.8381 (p0) cc_final: 0.8037 (p0) REVERT: A 811 MET cc_start: 0.8444 (tpt) cc_final: 0.8090 (tpp) REVERT: A 970 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7086 (mm-40) REVERT: A 994 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6579 (pt0) outliers start: 32 outliers final: 18 residues processed: 133 average time/residue: 0.2855 time to fit residues: 54.9470 Evaluate side-chains 126 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 142 TYR Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 223 TYR 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 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 591 ILE Chi-restraints excluded: chain A residue 611 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 780 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 970 GLN Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain A residue 1111 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 92 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 0.0570 chunk 107 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.153712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.112025 restraints weight = 13167.476| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.54 r_work: 0.3157 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1557 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= 0.125 Angle : 0.562 9.128 14954 Z= 0.289 Chirality : 0.036 0.159 1692 Planarity : 0.003 0.030 1521 Dihedral : 20.328 169.715 2568 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 3.64 % Allowed : 29.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.27), residues: 990 helix: 2.10 (0.22), residues: 535 sheet: -1.22 (0.70), residues: 60 loop : -2.16 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 315 HIS 0.004 0.001 HIS A 101 PHE 0.016 0.001 PHE A 676 TYR 0.017 0.001 TYR A 193 ARG 0.008 0.000 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.04492 ( 488) hydrogen bonds : angle 3.64568 ( 1345) covalent geometry : bond 0.00266 (10773) covalent geometry : angle 0.56245 (14954) *********************** 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 141 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.6915 (OUTLIER) cc_final: 0.4723 (t80) REVERT: A 256 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7404 (mp) REVERT: A 318 MET cc_start: 0.3880 (ttt) cc_final: 0.3564 (ttt) REVERT: A 390 GLU cc_start: 0.7830 (tp30) cc_final: 0.6949 (tm-30) REVERT: A 444 MET cc_start: 0.7424 (mmm) cc_final: 0.7014 (mmm) REVERT: A 451 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8260 (mt) REVERT: A 469 LYS cc_start: 0.6882 (OUTLIER) cc_final: 0.6331 (mptt) REVERT: A 473 LEU cc_start: 0.8182 (mm) cc_final: 0.7957 (mm) REVERT: A 509 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7802 (mttt) REVERT: A 562 ASP cc_start: 0.8400 (p0) cc_final: 0.8030 (p0) REVERT: A 752 ASN cc_start: 0.8555 (m-40) cc_final: 0.8237 (t0) REVERT: A 811 MET cc_start: 0.8419 (tpt) cc_final: 0.8066 (tpp) REVERT: A 970 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7134 (mm-40) REVERT: A 994 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6548 (pt0) outliers start: 33 outliers final: 23 residues processed: 133 average time/residue: 0.2341 time to fit residues: 44.7754 Evaluate side-chains 133 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 142 TYR Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 324 VAL 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 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 564 ILE 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 733 MET 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 970 GLN Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain A residue 1111 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 80 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 27 optimal weight: 0.2980 chunk 10 optimal weight: 8.9990 chunk 81 optimal weight: 0.0370 chunk 105 optimal weight: 10.0000 chunk 75 optimal weight: 0.0670 chunk 57 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.154062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105771 restraints weight = 13691.597| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.94 r_work: 0.3155 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1589 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= 0.122 Angle : 0.560 9.100 14954 Z= 0.289 Chirality : 0.036 0.171 1692 Planarity : 0.003 0.033 1521 Dihedral : 20.319 169.899 2568 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 3.75 % Allowed : 29.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.27), residues: 990 helix: 2.14 (0.22), residues: 535 sheet: -1.21 (0.70), residues: 60 loop : -2.13 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 315 HIS 0.004 0.001 HIS A 101 PHE 0.016 0.001 PHE A 676 TYR 0.016 0.001 TYR A 193 ARG 0.008 0.000 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.04418 ( 488) hydrogen bonds : angle 3.62767 ( 1345) covalent geometry : bond 0.00260 (10773) covalent geometry : angle 0.56033 (14954) *********************** 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 139 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.6908 (OUTLIER) cc_final: 0.4681 (t80) REVERT: A 256 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7380 (mp) REVERT: A 318 MET cc_start: 0.3839 (ttt) cc_final: 0.3537 (ttt) REVERT: A 390 GLU cc_start: 0.7804 (tp30) cc_final: 0.6879 (tm-30) REVERT: A 444 MET cc_start: 0.7412 (mmm) cc_final: 0.7076 (mmm) REVERT: A 451 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8213 (mt) REVERT: A 469 LYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6311 (mptt) REVERT: A 473 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7924 (mm) REVERT: A 509 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7811 (mttt) REVERT: A 562 ASP cc_start: 0.8406 (p0) cc_final: 0.8038 (p0) REVERT: A 635 TYR cc_start: 0.8545 (t80) cc_final: 0.8269 (t80) REVERT: A 752 ASN cc_start: 0.8553 (m-40) cc_final: 0.8242 (t0) REVERT: A 755 LYS cc_start: 0.8729 (mmmt) cc_final: 0.8237 (tppt) REVERT: A 811 MET cc_start: 0.8434 (tpt) cc_final: 0.8080 (tpp) REVERT: A 970 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7104 (mm-40) REVERT: A 994 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6525 (pt0) outliers start: 34 outliers final: 20 residues processed: 129 average time/residue: 0.2414 time to fit residues: 43.7574 Evaluate side-chains 128 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 142 TYR Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 324 VAL 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 473 LEU 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 564 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 611 SER 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 970 GLN Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain A residue 1080 LEU 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 6 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.150555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.101882 restraints weight = 13674.876| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.94 r_work: 0.3095 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10773 Z= 0.187 Angle : 0.616 9.020 14954 Z= 0.316 Chirality : 0.038 0.159 1692 Planarity : 0.003 0.032 1521 Dihedral : 20.348 168.541 2568 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 4.08 % Allowed : 29.22 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.27), residues: 990 helix: 1.94 (0.22), residues: 533 sheet: -1.34 (0.70), residues: 60 loop : -2.22 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 891 HIS 0.004 0.001 HIS A1019 PHE 0.016 0.001 PHE A 676 TYR 0.017 0.002 TYR A 968 ARG 0.009 0.000 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.05377 ( 488) hydrogen bonds : angle 3.77724 ( 1345) covalent geometry : bond 0.00421 (10773) covalent geometry : angle 0.61560 (14954) ********************** 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 139 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 102 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.6991 (OUTLIER) cc_final: 0.4786 (t80) REVERT: A 256 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7455 (mp) REVERT: A 318 MET cc_start: 0.3984 (ttt) cc_final: 0.3670 (ttt) REVERT: A 444 MET cc_start: 0.7389 (mmm) cc_final: 0.7151 (mmm) REVERT: A 451 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8221 (mt) REVERT: A 469 LYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6333 (mptt) REVERT: A 473 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7859 (mm) REVERT: A 509 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7876 (mttt) REVERT: A 562 ASP cc_start: 0.8519 (p0) cc_final: 0.8175 (p0) REVERT: A 752 ASN cc_start: 0.8527 (m-40) cc_final: 0.8269 (t0) REVERT: A 811 MET cc_start: 0.8520 (tpt) cc_final: 0.8167 (tpp) REVERT: A 970 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7070 (mm-40) REVERT: A 994 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7013 (pt0) outliers start: 37 outliers final: 24 residues processed: 131 average time/residue: 0.2767 time to fit residues: 52.9397 Evaluate side-chains 134 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 142 TYR 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 223 TYR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 324 VAL 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 473 LEU 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 564 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 733 MET Chi-restraints excluded: chain A residue 739 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 970 GLN Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain A residue 1080 LEU 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 15 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.151797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.108789 restraints weight = 13495.367| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.74 r_work: 0.3106 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1686 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= 0.148 Angle : 0.594 9.145 14954 Z= 0.307 Chirality : 0.037 0.194 1692 Planarity : 0.003 0.033 1521 Dihedral : 20.359 168.375 2568 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 4.08 % Allowed : 28.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.27), residues: 990 helix: 1.99 (0.22), residues: 533 sheet: -1.30 (0.70), residues: 60 loop : -2.21 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 315 HIS 0.004 0.001 HIS A 101 PHE 0.017 0.001 PHE A 676 TYR 0.017 0.001 TYR A 193 ARG 0.009 0.000 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.04969 ( 488) hydrogen bonds : angle 3.73510 ( 1345) covalent geometry : bond 0.00323 (10773) covalent geometry : angle 0.59413 (14954) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6342.28 seconds wall clock time: 111 minutes 18.54 seconds (6678.54 seconds total)