Starting phenix.real_space_refine on Fri Jul 3 13:12:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z4k_14500/07_2026/7z4k_14500.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z4k_14500/07_2026/7z4k_14500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7z4k_14500/07_2026/7z4k_14500.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z4k_14500/07_2026/7z4k_14500.cif" model { file = "/net/cci-nas-00/data/ceres_data/7z4k_14500/07_2026/7z4k_14500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z4k_14500/07_2026/7z4k_14500.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z4k_14500/07_2026/7z4k_14500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z4k_14500/07_2026/7z4k_14500.map" } resolution = 3.81 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= 0.001 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 134 5.49 5 S 23 5.16 5 C 8405 2.51 5 N 2455 2.21 5 O 2988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14005 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 11109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1360, 11109 Classifications: {'peptide': 1360} Link IDs: {'PTRANS': 35, 'TRANS': 1324} Chain breaks: 1 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1884 Classifications: {'RNA': 88} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 46, 'rna3p_pyr': 30} Link IDs: {'rna2p': 12, 'rna3p': 75} Chain: "C" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 586 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 426 Inner-chain residues flagged as termini: ['pdbres=" DA D -2 "'] Classifications: {'DNA': 21} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 20} Time building chain proxies: 3.31, per 1000 atoms: 0.24 Number of scatterers: 14005 At special positions: 0 Unit cell: (96.2, 124.15, 124.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 134 15.00 O 2988 8.00 N 2455 7.00 C 8405 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: 1.38 Conformation dependent library (CDL) restraints added in 401.3 milliseconds 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2584 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 10 sheets defined 53.9% alpha, 7.9% beta 51 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'B' and resid 59 through 86 Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 96 through 103 Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 134 through 145 removed outlier: 3.661A pdb=" N LEU B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.524A pdb=" N LEU B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 removed outlier: 3.571A pdb=" N ILE B 211 " --> pdb=" O ASP B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 229 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 273 through 283 removed outlier: 3.587A pdb=" N GLN B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 306 removed outlier: 4.645A pdb=" N LEU B 289 " --> pdb=" O GLN B 285 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 343 Processing helix chain 'B' and resid 343 through 353 removed outlier: 3.535A pdb=" N TYR B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 368 through 383 Proline residue: B 378 - end of helix Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.741A pdb=" N SER B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 410 " --> pdb=" O ASN B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 410' Processing helix chain 'B' and resid 411 through 427 removed outlier: 4.087A pdb=" N HIS B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 446 removed outlier: 5.276A pdb=" N GLU B 438 " --> pdb=" O LYS B 434 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LYS B 439 " --> pdb=" O ASP B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 476 No H-bonds generated for 'chain 'B' and resid 474 through 476' Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 483 through 494 Processing helix chain 'B' and resid 512 through 526 removed outlier: 4.020A pdb=" N LYS B 526 " --> pdb=" O ASN B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 552 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.836A pdb=" N TYR B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 603 through 609 Processing helix chain 'B' and resid 612 through 626 Processing helix chain 'B' and resid 628 through 637 Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 644 through 654 Processing helix chain 'B' and resid 663 through 668 Processing helix chain 'B' and resid 678 through 685 Processing helix chain 'B' and resid 692 through 698 Processing helix chain 'B' and resid 703 through 713 Processing helix chain 'B' and resid 719 through 726 Processing helix chain 'B' and resid 730 through 751 Processing helix chain 'B' and resid 776 through 792 Processing helix chain 'B' and resid 794 through 799 Processing helix chain 'B' and resid 803 through 807 Processing helix chain 'B' and resid 808 through 817 Processing helix chain 'B' and resid 829 through 833 Processing helix chain 'B' and resid 861 through 865 removed outlier: 4.226A pdb=" N ARG B 864 " --> pdb=" O ASP B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 889 removed outlier: 4.959A pdb=" N ASN B 881 " --> pdb=" O LYS B 877 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N TYR B 882 " --> pdb=" O LYS B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 902 Processing helix chain 'B' and resid 903 through 905 No H-bonds generated for 'chain 'B' and resid 903 through 905' Processing helix chain 'B' and resid 909 through 922 removed outlier: 3.588A pdb=" N LYS B 913 " --> pdb=" O SER B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 940 removed outlier: 3.892A pdb=" N LYS B 929 " --> pdb=" O ARG B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 970 removed outlier: 3.836A pdb=" N VAL B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 1001 removed outlier: 4.171A pdb=" N ALA B 984 " --> pdb=" O ASN B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1009 removed outlier: 3.651A pdb=" N PHE B1008 " --> pdb=" O LEU B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1026 through 1031 removed outlier: 4.402A pdb=" N LYS B1031 " --> pdb=" O GLN B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1088 Processing helix chain 'B' and resid 1127 through 1132 Processing helix chain 'B' and resid 1170 through 1177 Processing helix chain 'B' and resid 1177 through 1186 Processing helix chain 'B' and resid 1191 through 1195 Processing helix chain 'B' and resid 1229 through 1241 Processing helix chain 'B' and resid 1248 through 1262 Processing helix chain 'B' and resid 1263 through 1280 removed outlier: 4.262A pdb=" N ASP B1267 " --> pdb=" O LYS B1263 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1297 Processing helix chain 'B' and resid 1301 through 1313 Processing helix chain 'B' and resid 1314 through 1317 Processing helix chain 'B' and resid 1341 through 1344 Processing sheet with id=AA1, first strand: chain 'B' and resid 954 through 957 removed outlier: 6.527A pdb=" N ILE B 759 " --> pdb=" O ILE B 956 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 46 removed outlier: 9.881A pdb=" N GLU B1357 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS B 33 " --> pdb=" O GLU B1357 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ARG B1359 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU B 35 " --> pdb=" O ARG B1359 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASP B1361 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU B1203 " --> pdb=" O ILE B1348 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B1202 " --> pdb=" O LEU B1214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.514A pdb=" N ALA B 538 " --> pdb=" O TYR B 529 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 837 through 840 Processing sheet with id=AA5, first strand: chain 'B' and resid 943 through 944 removed outlier: 3.817A pdb=" N LYS B 948 " --> pdb=" O ASP B 944 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1049 through 1052 removed outlier: 4.087A pdb=" N GLU B1056 " --> pdb=" O LEU B1052 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1063 through 1065 Processing sheet with id=AA8, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AA9, first strand: chain 'B' and resid 1156 through 1167 removed outlier: 3.720A pdb=" N GLU B1162 " --> pdb=" O VAL B1145 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B1145 " --> pdb=" O GLU B1162 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR B1141 " --> pdb=" O ILE B1166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1324 through 1326 520 hydrogen bonds defined for protein. 1500 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 126 hydrogen bonds 248 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 3.73 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2627 1.33 - 1.45: 4055 1.45 - 1.57: 7554 1.57 - 1.69: 268 1.69 - 1.81: 44 Bond restraints: 14548 Sorted by residual: bond pdb=" O4' DT D -13 " pdb=" C1' DT D -13 " ideal model delta sigma weight residual 1.420 1.378 0.042 1.10e-02 8.26e+03 1.46e+01 bond pdb=" N1 DT D -12 " pdb=" C6 DT D -12 " ideal model delta sigma weight residual 1.378 1.404 -0.026 7.00e-03 2.04e+04 1.39e+01 bond pdb=" C5 DT D -12 " pdb=" C6 DT D -12 " ideal model delta sigma weight residual 1.339 1.364 -0.025 7.00e-03 2.04e+04 1.31e+01 bond pdb=" C5' DT D -12 " pdb=" C4' DT D -12 " ideal model delta sigma weight residual 1.512 1.534 -0.022 7.00e-03 2.04e+04 9.55e+00 bond pdb=" C3' DC C 7 " pdb=" O3' DC C 7 " ideal model delta sigma weight residual 1.435 1.398 0.037 1.30e-02 5.92e+03 8.02e+00 ... (remaining 14543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 19672 1.30 - 2.60: 465 2.60 - 3.90: 79 3.90 - 5.20: 3 5.20 - 6.50: 2 Bond angle restraints: 20221 Sorted by residual: angle pdb=" O4' DC C 7 " pdb=" C4' DC C 7 " pdb=" C3' DC C 7 " ideal model delta sigma weight residual 106.00 103.00 3.00 6.00e-01 2.78e+00 2.50e+01 angle pdb=" N3 DT D -13 " pdb=" C4 DT D -13 " pdb=" O4 DT D -13 " ideal model delta sigma weight residual 119.90 122.81 -2.91 6.00e-01 2.78e+00 2.36e+01 angle pdb=" O4' DG C 17 " pdb=" C4' DG C 17 " pdb=" C3' DG C 17 " ideal model delta sigma weight residual 106.00 103.17 2.83 6.00e-01 2.78e+00 2.23e+01 angle pdb=" O4 DT D -12 " pdb=" C4 DT D -12 " pdb=" C5 DT D -12 " ideal model delta sigma weight residual 124.90 121.67 3.23 7.00e-01 2.04e+00 2.12e+01 angle pdb=" N3 DT C 9 " pdb=" C4 DT C 9 " pdb=" O4 DT C 9 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.04e+01 ... (remaining 20216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.18: 7741 18.18 - 36.36: 486 36.36 - 54.54: 249 54.54 - 72.71: 62 72.71 - 90.89: 13 Dihedral angle restraints: 8551 sinusoidal: 4554 harmonic: 3997 Sorted by residual: dihedral pdb=" O4' U A 59 " pdb=" C1' U A 59 " pdb=" N1 U A 59 " pdb=" C2 U A 59 " ideal model delta sinusoidal sigma weight residual -128.00 -62.39 -65.61 1 1.70e+01 3.46e-03 1.95e+01 dihedral pdb=" O5' G A 89 " pdb=" C5' G A 89 " pdb=" C4' G A 89 " pdb=" C3' G A 89 " ideal model delta sinusoidal sigma weight residual 175.00 116.38 58.62 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA GLN B1272 " pdb=" CB GLN B1272 " pdb=" CG GLN B1272 " pdb=" CD GLN B1272 " ideal model delta sinusoidal sigma weight residual -60.00 -117.64 57.64 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 8548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1645 0.032 - 0.064: 455 0.064 - 0.096: 123 0.096 - 0.128: 72 0.128 - 0.160: 10 Chirality restraints: 2305 Sorted by residual: chirality pdb=" C3' DA D 4 " pdb=" C4' DA D 4 " pdb=" O3' DA D 4 " pdb=" C2' DA D 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.40e-01 chirality pdb=" C3' DA C 8 " pdb=" C4' DA C 8 " pdb=" O3' DA C 8 " pdb=" C2' DA C 8 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" C4' DT D -12 " pdb=" C5' DT D -12 " pdb=" O4' DT D -12 " pdb=" C3' DT D -12 " both_signs ideal model delta sigma weight residual False -2.53 -2.38 -0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 2302 not shown) Planarity restraints: 2089 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 991 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.97e+00 pdb=" C ALA B 991 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA B 991 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL B 992 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 992 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C VAL B 992 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL B 992 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL B 993 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 995 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.28e+00 pdb=" C THR B 995 " -0.036 2.00e-02 2.50e+03 pdb=" O THR B 995 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA B 996 " 0.012 2.00e-02 2.50e+03 ... (remaining 2086 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1153 2.74 - 3.28: 14104 3.28 - 3.82: 25732 3.82 - 4.36: 30178 4.36 - 4.90: 47525 Nonbonded interactions: 118692 Sorted by model distance: nonbonded pdb=" OG1 THR B 474 " pdb=" OD1 ASN B 477 " model vdw 2.200 3.040 nonbonded pdb=" OG SER B 512 " pdb=" OE1 GLU B 617 " model vdw 2.222 3.040 nonbonded pdb=" OG SER B1109 " pdb=" OP2 DG C 1 " model vdw 2.235 3.040 nonbonded pdb=" O LYS B 209 " pdb=" OG SER B 213 " model vdw 2.271 3.040 nonbonded pdb=" N2 G A 33 " pdb=" OP2 A A 36 " model vdw 2.277 3.120 ... (remaining 118687 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.030 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: 0.380 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.580 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 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 0.042 14548 Z= 0.272 Angle : 0.481 6.496 20221 Z= 0.351 Chirality : 0.037 0.160 2305 Planarity : 0.003 0.038 2089 Dihedral : 14.983 90.892 5967 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.99 % Allowed : 4.68 % Favored : 94.33 % 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: 1.12 (0.23), residues: 1356 helix: 1.88 (0.21), residues: 659 sheet: -0.56 (0.49), residues: 118 loop : -0.25 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1333 TYR 0.008 0.001 TYR B 882 PHE 0.006 0.001 PHE B1008 TRP 0.007 0.001 TRP B 464 HIS 0.003 0.000 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.27 (14548) covalent geometry : angle 0.48126 / 0.35 (20221) hydrogen bonds : bond 0.12980 / 8.98 ( 646) hydrogen bonds : angle 5.22172 / 3.66 ( 1748) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 294 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 ILE cc_start: 0.7762 (tt) cc_final: 0.7105 (pt) REVERT: B 60 GLU cc_start: 0.9065 (tt0) cc_final: 0.8856 (pp20) REVERT: B 158 LEU cc_start: 0.8742 (mt) cc_final: 0.8407 (mt) REVERT: B 335 LEU cc_start: 0.9351 (tp) cc_final: 0.9071 (tt) REVERT: B 415 HIS cc_start: 0.9023 (m-70) cc_final: 0.8435 (m-70) REVERT: B 433 LEU cc_start: 0.9307 (mt) cc_final: 0.9071 (tt) REVERT: B 489 GLN cc_start: 0.9181 (tt0) cc_final: 0.8849 (pp30) REVERT: B 504 ASN cc_start: 0.9127 (m-40) cc_final: 0.8817 (p0) REVERT: B 613 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7629 (tp30) REVERT: B 616 LEU cc_start: 0.9683 (mt) cc_final: 0.9440 (mt) REVERT: B 648 MET cc_start: 0.8923 (ttp) cc_final: 0.8474 (ttt) REVERT: B 949 LEU cc_start: 0.7192 (tp) cc_final: 0.6933 (tp) REVERT: B 959 LYS cc_start: 0.8633 (mtpp) cc_final: 0.8185 (pttt) REVERT: B 979 ASN cc_start: 0.8231 (p0) cc_final: 0.7656 (m-40) REVERT: B 1004 LEU cc_start: 0.9017 (mt) cc_final: 0.8760 (mt) REVERT: B 1018 VAL cc_start: 0.6456 (OUTLIER) cc_final: 0.6216 (p) REVERT: B 1046 PHE cc_start: 0.7091 (m-10) cc_final: 0.6321 (m-80) REVERT: B 1086 VAL cc_start: 0.8346 (t) cc_final: 0.7770 (t) REVERT: B 1095 VAL cc_start: 0.7857 (t) cc_final: 0.7163 (m) REVERT: B 1177 ASN cc_start: 0.9254 (t0) cc_final: 0.8823 (t0) REVERT: B 1180 ASP cc_start: 0.9152 (m-30) cc_final: 0.8790 (m-30) REVERT: B 1190 VAL cc_start: 0.7155 (m) cc_final: 0.6950 (m) outliers start: 12 outliers final: 0 residues processed: 304 average time/residue: 0.1468 time to fit residues: 61.6829 Evaluate side-chains 163 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1018 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 HIS B 113 HIS ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN B 277 ASN ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 ASN B 983 HIS ** B1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1091 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.082754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.061864 restraints weight = 85607.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.063703 restraints weight = 49842.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.064807 restraints weight = 35278.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.065373 restraints weight = 28320.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.065927 restraints weight = 25042.506| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14548 Z= 0.165 Angle : 0.635 12.349 20221 Z= 0.329 Chirality : 0.039 0.207 2305 Planarity : 0.005 0.054 2089 Dihedral : 17.458 90.714 3081 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.05 % Allowed : 13.30 % Favored : 84.65 % 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: 0.90 (0.22), residues: 1356 helix: 1.61 (0.20), residues: 663 sheet: -0.39 (0.54), residues: 86 loop : -0.34 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 220 TYR 0.024 0.002 TYR B 981 PHE 0.021 0.002 PHE B1258 TRP 0.016 0.001 TRP B 464 HIS 0.015 0.002 HIS B 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (14548) covalent geometry : angle 0.63530 / 0.33 (20221) hydrogen bonds : bond 0.04661 / 3.16 ( 646) hydrogen bonds : angle 4.41549 / 3.14 ( 1748) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 165 ARG cc_start: 0.8299 (ptt180) cc_final: 0.5727 (ptt180) REVERT: B 321 MET cc_start: 0.8551 (mmp) cc_final: 0.7692 (mmp) REVERT: B 433 LEU cc_start: 0.9387 (mt) cc_final: 0.9163 (tt) REVERT: B 504 ASN cc_start: 0.9208 (m-40) cc_final: 0.8964 (p0) REVERT: B 613 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7719 (tp30) REVERT: B 694 MET cc_start: 0.9618 (tpp) cc_final: 0.8735 (tpp) REVERT: B 698 HIS cc_start: 0.9003 (m90) cc_final: 0.8683 (m90) REVERT: B 930 HIS cc_start: 0.8474 (m-70) cc_final: 0.8086 (m-70) REVERT: B 979 ASN cc_start: 0.8546 (p0) cc_final: 0.8286 (m110) REVERT: B 1039 TYR cc_start: 0.9339 (m-10) cc_final: 0.9047 (m-10) REVERT: B 1262 HIS cc_start: 0.8061 (m-70) cc_final: 0.7822 (t-90) REVERT: B 1276 PHE cc_start: 0.8288 (t80) cc_final: 0.7666 (t80) outliers start: 25 outliers final: 11 residues processed: 177 average time/residue: 0.1241 time to fit residues: 31.2199 Evaluate side-chains 142 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1156 LYS Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1347 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 87 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 25 optimal weight: 30.0000 chunk 68 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 HIS B 175 ASN ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 HIS ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.079620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.058808 restraints weight = 87094.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.060527 restraints weight = 50672.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.061599 restraints weight = 35989.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.062115 restraints weight = 29048.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.062598 restraints weight = 25868.089| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14548 Z= 0.196 Angle : 0.619 9.797 20221 Z= 0.325 Chirality : 0.039 0.206 2305 Planarity : 0.004 0.064 2089 Dihedral : 17.362 90.650 3080 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.55 % Allowed : 15.02 % Favored : 82.43 % 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: 0.67 (0.22), residues: 1356 helix: 1.32 (0.20), residues: 670 sheet: -0.19 (0.53), residues: 87 loop : -0.40 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 69 TYR 0.024 0.002 TYR B 823 PHE 0.016 0.002 PHE B 518 TRP 0.026 0.002 TRP B 464 HIS 0.009 0.002 HIS B 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.20 (14548) covalent geometry : angle 0.61937 / 0.33 (20221) hydrogen bonds : bond 0.04803 / 3.26 ( 646) hydrogen bonds : angle 4.36415 / 3.12 ( 1748) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 165 ARG cc_start: 0.8464 (ptt180) cc_final: 0.5874 (ptt180) REVERT: B 433 LEU cc_start: 0.9411 (mt) cc_final: 0.9163 (tt) REVERT: B 504 ASN cc_start: 0.9220 (m-40) cc_final: 0.8988 (p0) REVERT: B 596 ASP cc_start: 0.9075 (OUTLIER) cc_final: 0.8797 (t0) REVERT: B 613 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7795 (tp30) REVERT: B 694 MET cc_start: 0.9629 (tpp) cc_final: 0.9006 (tmm) REVERT: B 698 HIS cc_start: 0.9050 (m90) cc_final: 0.8810 (m90) REVERT: B 908 LEU cc_start: 0.8872 (mm) cc_final: 0.8459 (mm) REVERT: B 930 HIS cc_start: 0.8535 (m-70) cc_final: 0.8134 (m-70) REVERT: B 1046 PHE cc_start: 0.7394 (m-80) cc_final: 0.7181 (m-80) REVERT: B 1262 HIS cc_start: 0.8259 (m-70) cc_final: 0.8001 (t-90) outliers start: 31 outliers final: 18 residues processed: 156 average time/residue: 0.1181 time to fit residues: 27.5967 Evaluate side-chains 138 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 823 TYR Chi-restraints excluded: chain B residue 980 ASN Chi-restraints excluded: chain B residue 1043 MET Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 1314 THR Chi-restraints excluded: chain B residue 1316 THR Chi-restraints excluded: chain B residue 1347 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 132 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 147 optimal weight: 30.0000 chunk 1 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN B 224 ASN B 544 GLN ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 ASN ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1252 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.077107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.056478 restraints weight = 88488.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.058095 restraints weight = 52099.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.059112 restraints weight = 37509.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.059735 restraints weight = 30431.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.060124 restraints weight = 26698.195| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 14548 Z= 0.276 Angle : 0.699 15.460 20221 Z= 0.366 Chirality : 0.041 0.368 2305 Planarity : 0.005 0.056 2089 Dihedral : 17.446 91.403 3080 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.96 % Allowed : 16.34 % Favored : 80.71 % 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: 0.27 (0.22), residues: 1356 helix: 1.00 (0.19), residues: 665 sheet: -0.47 (0.48), residues: 99 loop : -0.57 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 220 TYR 0.032 0.003 TYR B 286 PHE 0.028 0.002 PHE B 290 TRP 0.033 0.003 TRP B 464 HIS 0.007 0.002 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.28 (14548) covalent geometry : angle 0.69902 / 0.37 (20221) hydrogen bonds : bond 0.05795 / 3.93 ( 646) hydrogen bonds : angle 4.63722 / 3.35 ( 1748) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: 0.7988 (tpp) cc_final: 0.7682 (tpp) REVERT: B 165 ARG cc_start: 0.8518 (ptt180) cc_final: 0.5923 (ptt180) REVERT: B 504 ASN cc_start: 0.9222 (m-40) cc_final: 0.8986 (p0) REVERT: B 596 ASP cc_start: 0.9226 (OUTLIER) cc_final: 0.8985 (m-30) REVERT: B 613 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8048 (tp30) REVERT: B 846 PHE cc_start: 0.9078 (m-80) cc_final: 0.8591 (m-80) REVERT: B 879 MET cc_start: 0.3035 (mpp) cc_final: 0.2822 (mpp) REVERT: B 930 HIS cc_start: 0.8612 (m-70) cc_final: 0.8177 (m90) outliers start: 36 outliers final: 20 residues processed: 149 average time/residue: 0.1165 time to fit residues: 25.7487 Evaluate side-chains 129 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 823 TYR Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 980 ASN Chi-restraints excluded: chain B residue 1043 MET Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1314 THR Chi-restraints excluded: chain B residue 1347 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1297 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.077802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.056982 restraints weight = 88060.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.058635 restraints weight = 51790.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.059670 restraints weight = 37220.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.060308 restraints weight = 30183.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.060532 restraints weight = 26543.498| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14548 Z= 0.175 Angle : 0.607 11.075 20221 Z= 0.320 Chirality : 0.039 0.201 2305 Planarity : 0.004 0.049 2089 Dihedral : 17.367 91.301 3080 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.38 % Allowed : 17.08 % Favored : 80.54 % 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: 0.39 (0.22), residues: 1356 helix: 1.12 (0.20), residues: 666 sheet: -0.54 (0.48), residues: 99 loop : -0.53 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 220 TYR 0.018 0.002 TYR B 814 PHE 0.022 0.002 PHE B 518 TRP 0.016 0.002 TRP B 659 HIS 0.005 0.001 HIS B 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (14548) covalent geometry : angle 0.60673 / 0.32 (20221) hydrogen bonds : bond 0.04579 / 3.12 ( 646) hydrogen bonds : angle 4.50848 / 3.27 ( 1748) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: 0.7991 (tpp) cc_final: 0.7739 (tpp) REVERT: B 165 ARG cc_start: 0.8570 (ptt180) cc_final: 0.6703 (ptt180) REVERT: B 499 ASP cc_start: 0.7251 (t70) cc_final: 0.6049 (t0) REVERT: B 504 ASN cc_start: 0.9225 (m-40) cc_final: 0.9009 (p0) REVERT: B 596 ASP cc_start: 0.9217 (m-30) cc_final: 0.8945 (m-30) REVERT: B 613 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8050 (tp30) REVERT: B 631 MET cc_start: 0.8627 (tpp) cc_final: 0.8418 (tpp) REVERT: B 846 PHE cc_start: 0.9056 (m-80) cc_final: 0.8699 (m-80) REVERT: B 930 HIS cc_start: 0.8619 (m-70) cc_final: 0.8401 (m-70) REVERT: B 949 LEU cc_start: 0.7567 (tp) cc_final: 0.7194 (pp) REVERT: B 1262 HIS cc_start: 0.8240 (m-70) cc_final: 0.8015 (t-90) outliers start: 29 outliers final: 20 residues processed: 139 average time/residue: 0.1066 time to fit residues: 22.7107 Evaluate side-chains 131 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 635 ARG Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 980 ASN Chi-restraints excluded: chain B residue 1043 MET Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1175 GLU Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 1290 VAL Chi-restraints excluded: chain B residue 1347 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 41 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 53 optimal weight: 30.0000 chunk 132 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 ASN ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.076648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.055847 restraints weight = 89195.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.057451 restraints weight = 53012.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.058460 restraints weight = 38322.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.059083 restraints weight = 31227.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.059447 restraints weight = 27476.314| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14548 Z= 0.215 Angle : 0.647 10.569 20221 Z= 0.340 Chirality : 0.040 0.320 2305 Planarity : 0.004 0.048 2089 Dihedral : 17.353 90.770 3080 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.04 % Allowed : 17.73 % Favored : 79.23 % 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: 0.26 (0.22), residues: 1356 helix: 1.00 (0.19), residues: 668 sheet: -0.71 (0.49), residues: 99 loop : -0.55 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 220 TYR 0.022 0.002 TYR B 812 PHE 0.032 0.002 PHE B 290 TRP 0.033 0.003 TRP B 883 HIS 0.005 0.001 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 (14548) covalent geometry : angle 0.64663 / 0.34 (20221) hydrogen bonds : bond 0.05127 / 3.50 ( 646) hydrogen bonds : angle 4.55695 / 3.31 ( 1748) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: 0.8037 (tpp) cc_final: 0.7752 (tpp) REVERT: B 165 ARG cc_start: 0.8567 (ptt180) cc_final: 0.6645 (ptt180) REVERT: B 504 ASN cc_start: 0.9233 (m-40) cc_final: 0.9005 (p0) REVERT: B 510 LYS cc_start: 0.9477 (ttmm) cc_final: 0.9210 (mtpp) REVERT: B 596 ASP cc_start: 0.9244 (m-30) cc_final: 0.8977 (m-30) REVERT: B 613 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8220 (tp30) REVERT: B 631 MET cc_start: 0.8738 (tpp) cc_final: 0.8519 (tpp) REVERT: B 763 MET cc_start: 0.7370 (tpt) cc_final: 0.7147 (mmm) REVERT: B 846 PHE cc_start: 0.9045 (m-80) cc_final: 0.8419 (m-80) REVERT: B 847 LEU cc_start: 0.9166 (tp) cc_final: 0.8860 (mt) REVERT: B 1046 PHE cc_start: 0.7190 (m-80) cc_final: 0.6988 (m-80) REVERT: B 1262 HIS cc_start: 0.8241 (m-70) cc_final: 0.8032 (t-90) outliers start: 37 outliers final: 27 residues processed: 138 average time/residue: 0.1083 time to fit residues: 23.0894 Evaluate side-chains 137 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 635 ARG Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 980 ASN Chi-restraints excluded: chain B residue 1043 MET Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1175 GLU Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 1314 THR Chi-restraints excluded: chain B residue 1330 THR Chi-restraints excluded: chain B residue 1347 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.076679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.055857 restraints weight = 89244.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.057441 restraints weight = 52712.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.058444 restraints weight = 37917.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.059096 restraints weight = 30832.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.059510 restraints weight = 26969.915| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14548 Z= 0.175 Angle : 0.619 11.757 20221 Z= 0.322 Chirality : 0.039 0.261 2305 Planarity : 0.004 0.056 2089 Dihedral : 17.302 90.306 3080 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.30 % Allowed : 19.29 % Favored : 78.41 % 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: 0.33 (0.22), residues: 1356 helix: 1.08 (0.20), residues: 669 sheet: -0.67 (0.50), residues: 99 loop : -0.55 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 220 TYR 0.014 0.002 TYR B1039 PHE 0.027 0.002 PHE B 518 TRP 0.021 0.002 TRP B 883 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (14548) covalent geometry : angle 0.61944 / 0.32 (20221) hydrogen bonds : bond 0.04609 / 3.17 ( 646) hydrogen bonds : angle 4.55493 / 3.28 ( 1748) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: 0.8113 (tpp) cc_final: 0.7845 (tpp) REVERT: B 504 ASN cc_start: 0.9257 (m-40) cc_final: 0.8932 (p0) REVERT: B 596 ASP cc_start: 0.9255 (m-30) cc_final: 0.8987 (m-30) REVERT: B 613 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8144 (tp30) REVERT: B 631 MET cc_start: 0.8758 (tpp) cc_final: 0.8531 (tpp) REVERT: B 846 PHE cc_start: 0.9062 (m-80) cc_final: 0.8426 (m-80) REVERT: B 847 LEU cc_start: 0.9161 (tp) cc_final: 0.8859 (mt) REVERT: B 930 HIS cc_start: 0.8634 (m-70) cc_final: 0.8236 (m90) outliers start: 28 outliers final: 25 residues processed: 129 average time/residue: 0.1120 time to fit residues: 22.2468 Evaluate side-chains 133 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 635 ARG Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 980 ASN Chi-restraints excluded: chain B residue 1043 MET Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1175 GLU Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 1263 LYS Chi-restraints excluded: chain B residue 1347 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 76 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 117 optimal weight: 0.0170 chunk 131 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 overall best weight: 3.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 ASN ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.076455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.055593 restraints weight = 89850.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.057227 restraints weight = 53304.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.058231 restraints weight = 38308.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.058876 restraints weight = 31169.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.059298 restraints weight = 27342.404| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14548 Z= 0.165 Angle : 0.613 11.298 20221 Z= 0.319 Chirality : 0.039 0.234 2305 Planarity : 0.004 0.045 2089 Dihedral : 17.208 89.106 3080 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.05 % Allowed : 19.13 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.23), residues: 1356 helix: 1.23 (0.20), residues: 668 sheet: -0.67 (0.52), residues: 97 loop : -0.54 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 220 TYR 0.028 0.002 TYR B 812 PHE 0.028 0.002 PHE B 518 TRP 0.012 0.002 TRP B 883 HIS 0.007 0.001 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (14548) covalent geometry : angle 0.61272 / 0.32 (20221) hydrogen bonds : bond 0.04502 / 3.08 ( 646) hydrogen bonds : angle 4.48230 / 3.21 ( 1748) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: 0.8106 (tpp) cc_final: 0.7853 (tpp) REVERT: B 165 ARG cc_start: 0.8572 (ptt180) cc_final: 0.7774 (ptt180) REVERT: B 499 ASP cc_start: 0.7571 (t70) cc_final: 0.6754 (t0) REVERT: B 504 ASN cc_start: 0.9270 (m-40) cc_final: 0.9016 (p0) REVERT: B 596 ASP cc_start: 0.9278 (m-30) cc_final: 0.9025 (m-30) REVERT: B 656 TYR cc_start: 0.8197 (m-80) cc_final: 0.7845 (m-80) REVERT: B 846 PHE cc_start: 0.9075 (m-80) cc_final: 0.8417 (m-80) REVERT: B 847 LEU cc_start: 0.9185 (tp) cc_final: 0.8873 (mt) REVERT: B 1205 GLU cc_start: 0.8281 (tt0) cc_final: 0.8014 (pp20) REVERT: B 1244 LYS cc_start: 0.7562 (mmtm) cc_final: 0.6962 (pptt) outliers start: 25 outliers final: 19 residues processed: 133 average time/residue: 0.1123 time to fit residues: 22.9259 Evaluate side-chains 129 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 980 ASN Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1175 GLU Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 1347 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 47 optimal weight: 0.0270 chunk 76 optimal weight: 0.0060 chunk 38 optimal weight: 9.9990 chunk 24 optimal weight: 0.0870 chunk 45 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.2234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.077538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.056765 restraints weight = 87533.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.058435 restraints weight = 51339.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.059471 restraints weight = 36607.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.060119 restraints weight = 29509.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.060558 restraints weight = 25795.556| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14548 Z= 0.122 Angle : 0.610 13.716 20221 Z= 0.311 Chirality : 0.038 0.284 2305 Planarity : 0.004 0.048 2089 Dihedral : 17.081 87.919 3080 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.72 % Allowed : 19.79 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.23), residues: 1356 helix: 1.33 (0.20), residues: 669 sheet: -0.64 (0.51), residues: 97 loop : -0.41 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 220 TYR 0.033 0.002 TYR B 814 PHE 0.038 0.002 PHE B 518 TRP 0.013 0.001 TRP B 659 HIS 0.006 0.001 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (14548) covalent geometry : angle 0.60963 / 0.31 (20221) hydrogen bonds : bond 0.04086 / 2.78 ( 646) hydrogen bonds : angle 4.43155 / 3.14 ( 1748) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: 0.8075 (tpp) cc_final: 0.7849 (tpp) REVERT: B 165 ARG cc_start: 0.8591 (ptt180) cc_final: 0.8056 (ptt180) REVERT: B 499 ASP cc_start: 0.7527 (t70) cc_final: 0.6648 (t0) REVERT: B 504 ASN cc_start: 0.9265 (m-40) cc_final: 0.8942 (p0) REVERT: B 596 ASP cc_start: 0.9244 (m-30) cc_final: 0.8971 (m-30) REVERT: B 656 TYR cc_start: 0.8012 (m-80) cc_final: 0.7770 (m-80) REVERT: B 846 PHE cc_start: 0.9101 (m-80) cc_final: 0.8446 (m-80) REVERT: B 847 LEU cc_start: 0.9204 (tp) cc_final: 0.8876 (mt) REVERT: B 930 HIS cc_start: 0.8652 (m-70) cc_final: 0.8286 (m90) REVERT: B 1205 GLU cc_start: 0.8275 (tt0) cc_final: 0.7739 (mm-30) outliers start: 21 outliers final: 17 residues processed: 123 average time/residue: 0.1100 time to fit residues: 21.0372 Evaluate side-chains 122 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 635 ARG Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 763 MET Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 980 ASN Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1175 GLU Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 1347 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 75 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 128 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 115 optimal weight: 0.0770 chunk 88 optimal weight: 3.9990 chunk 47 optimal weight: 0.0570 overall best weight: 1.2058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.077788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.056951 restraints weight = 89218.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.058626 restraints weight = 53157.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.059676 restraints weight = 37960.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.060334 restraints weight = 30760.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.060706 restraints weight = 26927.463| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14548 Z= 0.124 Angle : 0.602 14.056 20221 Z= 0.308 Chirality : 0.038 0.266 2305 Planarity : 0.004 0.052 2089 Dihedral : 16.951 88.133 3080 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.40 % Allowed : 20.20 % Favored : 78.41 % 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: 0.66 (0.23), residues: 1356 helix: 1.39 (0.20), residues: 668 sheet: -0.71 (0.53), residues: 95 loop : -0.39 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 220 TYR 0.023 0.002 TYR B 812 PHE 0.031 0.002 PHE B 290 TRP 0.008 0.001 TRP B 464 HIS 0.005 0.001 HIS B1264 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (14548) covalent geometry : angle 0.60249 / 0.31 (20221) hydrogen bonds : bond 0.04049 / 2.77 ( 646) hydrogen bonds : angle 4.42517 / 3.14 ( 1748) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 MET cc_start: 0.8198 (tpp) cc_final: 0.7750 (mmp) REVERT: B 161 MET cc_start: 0.8032 (tpp) cc_final: 0.7819 (tpp) REVERT: B 165 ARG cc_start: 0.8593 (ptt180) cc_final: 0.8284 (ptt180) REVERT: B 499 ASP cc_start: 0.7531 (t70) cc_final: 0.6713 (t0) REVERT: B 504 ASN cc_start: 0.9259 (m-40) cc_final: 0.9007 (p0) REVERT: B 596 ASP cc_start: 0.9223 (m-30) cc_final: 0.8945 (m-30) REVERT: B 656 TYR cc_start: 0.7968 (m-80) cc_final: 0.7730 (m-80) REVERT: B 846 PHE cc_start: 0.9105 (m-80) cc_final: 0.8482 (m-80) REVERT: B 847 LEU cc_start: 0.9191 (tp) cc_final: 0.8896 (mt) REVERT: B 930 HIS cc_start: 0.8653 (m-70) cc_final: 0.8282 (m90) REVERT: B 1177 ASN cc_start: 0.9155 (t0) cc_final: 0.8827 (t0) outliers start: 17 outliers final: 16 residues processed: 123 average time/residue: 0.1098 time to fit residues: 21.1953 Evaluate side-chains 121 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 635 ARG Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 763 MET Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 980 ASN Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1175 GLU Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 1347 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 776 ASN ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.076344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.055764 restraints weight = 88652.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.057380 restraints weight = 52708.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.058413 restraints weight = 37748.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.058953 restraints weight = 30540.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.059383 restraints weight = 27132.644| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14548 Z= 0.171 Angle : 0.629 13.853 20221 Z= 0.323 Chirality : 0.039 0.273 2305 Planarity : 0.004 0.048 2089 Dihedral : 16.987 88.951 3080 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.72 % Allowed : 20.11 % Favored : 78.16 % 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: 0.64 (0.23), residues: 1356 helix: 1.36 (0.20), residues: 666 sheet: -0.60 (0.52), residues: 97 loop : -0.42 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 220 TYR 0.022 0.002 TYR B 812 PHE 0.039 0.002 PHE B 518 TRP 0.041 0.002 TRP B 464 HIS 0.006 0.001 HIS B1264 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (14548) covalent geometry : angle 0.62877 / 0.32 (20221) hydrogen bonds : bond 0.04692 / 3.24 ( 646) hydrogen bonds : angle 4.48132 / 3.18 ( 1748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2845.08 seconds wall clock time: 50 minutes 9.02 seconds (3009.02 seconds total)