Starting phenix.real_space_refine on Wed Mar 4 14:36:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z4k_14500/03_2026/7z4k_14500.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z4k_14500/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7z4k_14500/03_2026/7z4k_14500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z4k_14500/03_2026/7z4k_14500.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z4k_14500/03_2026/7z4k_14500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z4k_14500/03_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-5986/lib/python3.9/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: 3.07, per 1000 atoms: 0.22 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: 1.01 Conformation dependent library (CDL) restraints added in 531.2 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: 1.81 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: 3.48 Time building geometry restraints manager: 1.40 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 1.414 1.378 0.036 2.00e-02 2.50e+03 3.23e+00 bond pdb=" C5 DT D -12 " pdb=" C6 DT D -12 " ideal model delta sigma weight residual 1.338 1.364 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C2 DT D -13 " pdb=" O2 DT D -13 " ideal model delta sigma weight residual 1.218 1.242 -0.024 2.00e-02 2.50e+03 1.47e+00 bond pdb=" N1 DT D -12 " pdb=" C6 DT D -12 " ideal model delta sigma weight residual 1.380 1.404 -0.024 2.00e-02 2.50e+03 1.45e+00 bond pdb=" C4' DC C 7 " pdb=" C3' DC C 7 " ideal model delta sigma weight residual 1.523 1.501 0.022 2.00e-02 2.50e+03 1.18e+00 ... (remaining 14543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 19814 1.30 - 2.60: 352 2.60 - 3.90: 50 3.90 - 5.20: 3 5.20 - 6.50: 2 Bond angle restraints: 20221 Sorted by residual: angle pdb=" N ARG B1333 " pdb=" CA ARG B1333 " pdb=" C ARG B1333 " ideal model delta sigma weight residual 109.07 115.57 -6.50 1.61e+00 3.86e-01 1.63e+01 angle pdb=" N LYS B 918 " pdb=" CA LYS B 918 " pdb=" C LYS B 918 " ideal model delta sigma weight residual 111.28 108.74 2.54 1.09e+00 8.42e-01 5.41e+00 angle pdb=" C4 DT D -12 " pdb=" C5 DT D -12 " pdb=" C7 DT D -12 " ideal model delta sigma weight residual 122.40 119.08 3.32 1.50e+00 4.44e-01 4.89e+00 angle pdb=" C3' DA D 3 " pdb=" C2' DA D 3 " pdb=" C1' DA D 3 " ideal model delta sigma weight residual 101.60 104.75 -3.15 1.50e+00 4.44e-01 4.40e+00 angle pdb=" N LYS B1130 " pdb=" CA LYS B1130 " pdb=" C LYS B1130 " ideal model delta sigma weight residual 114.04 111.55 2.49 1.24e+00 6.50e-01 4.03e+00 ... (remaining 20216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.18: 7837 18.18 - 36.36: 532 36.36 - 54.54: 289 54.54 - 72.71: 147 72.71 - 90.89: 26 Dihedral angle restraints: 8831 sinusoidal: 4834 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 8828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1626 0.030 - 0.059: 484 0.059 - 0.089: 124 0.089 - 0.119: 64 0.119 - 0.149: 7 Chirality restraints: 2305 Sorted by residual: chirality pdb=" CA VAL B 870 " pdb=" N VAL B 870 " pdb=" C VAL B 870 " pdb=" CB VAL B 870 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.52e-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 5.28e-01 chirality pdb=" CA ILE B 448 " pdb=" N ILE B 448 " pdb=" C ILE B 448 " pdb=" CB ILE B 448 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-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: 4.140 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.210 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 0.036 14548 Z= 0.141 Angle : 0.438 6.496 20221 Z= 0.243 Chirality : 0.034 0.149 2305 Planarity : 0.003 0.038 2089 Dihedral : 17.217 90.892 6247 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 covalent geometry : bond 0.00271 (14548) covalent geometry : angle 0.43789 (20221) hydrogen bonds : bond 0.12980 ( 646) hydrogen bonds : angle 5.22172 ( 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 : 0.495 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: 0.1474 time to fit residues: 61.7186 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 : 0.469 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 99 HIS B 113 HIS B 224 ASN B 228 GLN B 277 ASN B 556 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.081635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.060454 restraints weight = 86304.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.062280 restraints weight = 50715.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.063397 restraints weight = 36211.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.064145 restraints weight = 29078.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.064518 restraints weight = 25277.334| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14548 Z= 0.151 Angle : 0.580 12.366 20221 Z= 0.300 Chirality : 0.037 0.145 2305 Planarity : 0.004 0.065 2089 Dihedral : 20.559 89.972 3361 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.72 % Allowed : 13.30 % Favored : 84.98 % 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: 0.94 (0.22), residues: 1356 helix: 1.66 (0.20), residues: 669 sheet: -0.37 (0.53), residues: 86 loop : -0.37 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1078 TYR 0.028 0.002 TYR B1001 PHE 0.023 0.002 PHE B1258 TRP 0.015 0.001 TRP B 464 HIS 0.013 0.001 HIS B 930 Details of bonding type rmsd covalent geometry : bond 0.00320 (14548) covalent geometry : angle 0.58034 (20221) hydrogen bonds : bond 0.04179 ( 646) hydrogen bonds : angle 4.31940 ( 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 184 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.460 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: B 158 LEU cc_start: 0.8758 (mt) cc_final: 0.8545 (mt) REVERT: B 165 ARG cc_start: 0.8392 (ptt180) cc_final: 0.5713 (ptt180) REVERT: B 321 MET cc_start: 0.8439 (mmp) cc_final: 0.7706 (mmp) REVERT: B 433 LEU cc_start: 0.9394 (mt) cc_final: 0.9156 (tt) REVERT: B 504 ASN cc_start: 0.9243 (m-40) cc_final: 0.9006 (p0) REVERT: B 613 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7955 (tp30) REVERT: B 694 MET cc_start: 0.9629 (tpp) cc_final: 0.8818 (tpp) REVERT: B 698 HIS cc_start: 0.9042 (m90) cc_final: 0.8720 (m90) REVERT: B 930 HIS cc_start: 0.8497 (m-70) cc_final: 0.8163 (m-70) REVERT: B 979 ASN cc_start: 0.8657 (p0) cc_final: 0.8250 (m-40) REVERT: B 980 ASN cc_start: 0.8819 (m-40) cc_final: 0.8454 (p0) REVERT: B 1039 TYR cc_start: 0.9320 (m-10) cc_final: 0.9034 (m-10) REVERT: B 1169 MET cc_start: 0.9088 (mtm) cc_final: 0.8865 (mtt) REVERT: B 1225 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8042 (mm-30) REVERT: B 1262 HIS cc_start: 0.8223 (m-70) cc_final: 0.7992 (t-90) REVERT: B 1276 PHE cc_start: 0.8296 (t80) cc_final: 0.7727 (t80) outliers start: 21 outliers final: 8 residues processed: 178 average time/residue: 0.1400 time to fit residues: 35.1395 Evaluate side-chains 138 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 179 SER 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 1203 LEU 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: 7.9990 chunk 128 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 25 optimal weight: 30.0000 chunk 68 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 881 ASN ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1252 ASN B1297 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.075626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.055092 restraints weight = 90160.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.056676 restraints weight = 53453.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.057654 restraints weight = 38407.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.058276 restraints weight = 31198.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.058613 restraints weight = 27455.727| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14548 Z= 0.310 Angle : 0.706 8.201 20221 Z= 0.372 Chirality : 0.041 0.186 2305 Planarity : 0.005 0.058 2089 Dihedral : 20.602 92.083 3360 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.79 % Allowed : 14.78 % 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: 0.14 (0.21), residues: 1356 helix: 0.85 (0.19), residues: 673 sheet: -0.59 (0.51), residues: 89 loop : -0.59 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 586 TYR 0.023 0.002 TYR B 451 PHE 0.028 0.003 PHE B1008 TRP 0.046 0.004 TRP B 883 HIS 0.009 0.002 HIS B 930 Details of bonding type rmsd covalent geometry : bond 0.00641 (14548) covalent geometry : angle 0.70563 (20221) hydrogen bonds : bond 0.06302 ( 646) hydrogen bonds : angle 4.67203 ( 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 167 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.457 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 161 MET cc_start: 0.7991 (tpp) cc_final: 0.7719 (tpp) REVERT: B 162 ILE cc_start: 0.9104 (pt) cc_final: 0.8897 (pt) REVERT: B 165 ARG cc_start: 0.8470 (ptt180) cc_final: 0.6676 (ptt180) REVERT: B 266 LEU cc_start: 0.7094 (tt) cc_final: 0.6521 (mp) REVERT: B 504 ASN cc_start: 0.9252 (m-40) cc_final: 0.8976 (p0) REVERT: B 596 ASP cc_start: 0.9292 (OUTLIER) cc_final: 0.9049 (m-30) REVERT: B 847 LEU cc_start: 0.9217 (tp) cc_final: 0.8963 (mt) REVERT: B 930 HIS cc_start: 0.8598 (m-70) cc_final: 0.8294 (m-70) REVERT: B 980 ASN cc_start: 0.8801 (m-40) cc_final: 0.8470 (p0) REVERT: B 1046 PHE cc_start: 0.7206 (m-80) cc_final: 0.6956 (m-80) REVERT: B 1169 MET cc_start: 0.9055 (mtm) cc_final: 0.8790 (mtt) REVERT: B 1244 LYS cc_start: 0.7518 (mmtm) cc_final: 0.7198 (pttp) outliers start: 34 outliers final: 20 residues processed: 156 average time/residue: 0.1170 time to fit residues: 27.1841 Evaluate side-chains 131 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN 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 179 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 312 ILE 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 899 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 1175 GLU Chi-restraints excluded: chain B residue 1182 LEU 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 1347 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 132 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 147 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 HIS ** B 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3842 r_free = 0.3842 target = 0.077206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.056497 restraints weight = 86901.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.058161 restraints weight = 51068.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.059190 restraints weight = 36488.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.059879 restraints weight = 29427.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.060113 restraints weight = 25659.746| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14548 Z= 0.151 Angle : 0.555 9.423 20221 Z= 0.292 Chirality : 0.036 0.143 2305 Planarity : 0.004 0.043 2089 Dihedral : 20.337 89.831 3360 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.46 % Allowed : 16.34 % Favored : 81.20 % 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: 0.52 (0.22), residues: 1356 helix: 1.22 (0.20), residues: 668 sheet: -0.48 (0.48), residues: 99 loop : -0.44 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 220 TYR 0.016 0.002 TYR B1039 PHE 0.027 0.001 PHE B1276 TRP 0.020 0.002 TRP B 883 HIS 0.007 0.001 HIS B 930 Details of bonding type rmsd covalent geometry : bond 0.00323 (14548) covalent geometry : angle 0.55494 (20221) hydrogen bonds : bond 0.04015 ( 646) hydrogen bonds : angle 4.35608 ( 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 160 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.462 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: B 161 MET cc_start: 0.8048 (tpp) cc_final: 0.7690 (tpp) REVERT: B 499 ASP cc_start: 0.7360 (t70) cc_final: 0.6472 (t0) REVERT: B 504 ASN cc_start: 0.9258 (m-40) cc_final: 0.8921 (p0) REVERT: B 596 ASP cc_start: 0.9197 (m-30) cc_final: 0.8969 (m-30) REVERT: B 643 PHE cc_start: 0.6435 (p90) cc_final: 0.5683 (p90) REVERT: B 648 MET cc_start: 0.9440 (tmm) cc_final: 0.9094 (tmm) REVERT: B 846 PHE cc_start: 0.9127 (m-80) cc_final: 0.8491 (m-80) REVERT: B 847 LEU cc_start: 0.9091 (tp) cc_final: 0.8797 (mt) REVERT: B 883 TRP cc_start: 0.8326 (m-10) cc_final: 0.7965 (m-10) REVERT: B 908 LEU cc_start: 0.9256 (mm) cc_final: 0.9036 (mm) REVERT: B 930 HIS cc_start: 0.8673 (m-70) cc_final: 0.8218 (m90) REVERT: B 999 LYS cc_start: 0.8661 (mtpt) cc_final: 0.8407 (ptpt) REVERT: B 1169 MET cc_start: 0.9047 (mtm) cc_final: 0.8827 (mtt) REVERT: B 1205 GLU cc_start: 0.8327 (tt0) cc_final: 0.7848 (tp30) REVERT: B 1225 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8369 (mm-30) REVERT: B 1262 HIS cc_start: 0.8273 (m-70) cc_final: 0.8047 (t-90) outliers start: 30 outliers final: 17 residues processed: 151 average time/residue: 0.1006 time to fit residues: 23.4571 Evaluate side-chains 131 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 335 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 899 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 1225 GLU Chi-restraints excluded: chain B residue 1226 LEU 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: 2.9990 chunk 48 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 100 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 544 GLN ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.073851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.053543 restraints weight = 91185.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.055053 restraints weight = 54063.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.056008 restraints weight = 38952.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.056600 restraints weight = 31839.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.056953 restraints weight = 28081.507| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 14548 Z= 0.274 Angle : 0.662 11.083 20221 Z= 0.350 Chirality : 0.040 0.222 2305 Planarity : 0.005 0.051 2089 Dihedral : 20.463 91.483 3360 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.45 % Allowed : 16.42 % Favored : 80.13 % 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: -0.11 (0.21), residues: 1356 helix: 0.65 (0.19), residues: 676 sheet: -0.77 (0.49), residues: 94 loop : -0.72 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 220 TYR 0.022 0.002 TYR B 451 PHE 0.021 0.002 PHE B 518 TRP 0.022 0.003 TRP B 883 HIS 0.010 0.002 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00571 (14548) covalent geometry : angle 0.66234 (20221) hydrogen bonds : bond 0.06163 ( 646) hydrogen bonds : angle 4.72896 ( 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 158 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 116 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ARG cc_start: 0.9420 (OUTLIER) cc_final: 0.9160 (ttm-80) REVERT: B 45 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.6853 (mmmt) REVERT: B 161 MET cc_start: 0.8007 (tpp) cc_final: 0.7786 (tpp) REVERT: B 165 ARG cc_start: 0.8480 (ptt180) cc_final: 0.7899 (ptt180) REVERT: B 499 ASP cc_start: 0.7692 (t70) cc_final: 0.6700 (m-30) REVERT: B 596 ASP cc_start: 0.9375 (m-30) cc_final: 0.9145 (m-30) REVERT: B 656 TYR cc_start: 0.8498 (m-80) cc_final: 0.8082 (m-80) REVERT: B 823 TYR cc_start: 0.6808 (m-80) cc_final: 0.5411 (m-80) REVERT: B 846 PHE cc_start: 0.9070 (m-80) cc_final: 0.8398 (m-80) REVERT: B 847 LEU cc_start: 0.9207 (tp) cc_final: 0.8949 (mt) REVERT: B 858 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.7385 (t) REVERT: B 883 TRP cc_start: 0.8644 (m-10) cc_final: 0.8444 (m-10) REVERT: B 959 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7979 (ptpp) REVERT: B 980 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8385 (p0) REVERT: B 1046 PHE cc_start: 0.7068 (m-80) cc_final: 0.6822 (m-80) REVERT: B 1089 MET cc_start: 0.8585 (mmp) cc_final: 0.8249 (mmp) REVERT: B 1205 GLU cc_start: 0.8311 (tt0) cc_final: 0.7884 (tp30) REVERT: B 1244 LYS cc_start: 0.7620 (mmtm) cc_final: 0.7323 (pttp) REVERT: B 1262 HIS cc_start: 0.8290 (m-70) cc_final: 0.8048 (t-90) outliers start: 42 outliers final: 23 residues processed: 149 average time/residue: 0.1078 time to fit residues: 24.5293 Evaluate side-chains 133 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 ARG 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 335 LEU Chi-restraints excluded: chain B residue 380 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 636 LEU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 858 THR Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 959 LYS 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 1226 LEU Chi-restraints excluded: chain B residue 1263 LYS Chi-restraints excluded: chain B residue 1314 THR 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: 5.9990 chunk 78 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN B1041 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.076221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.055599 restraints weight = 89740.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.057230 restraints weight = 52743.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.058254 restraints weight = 37781.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.058897 restraints weight = 30574.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.059242 restraints weight = 26809.551| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14548 Z= 0.125 Angle : 0.574 12.219 20221 Z= 0.295 Chirality : 0.037 0.152 2305 Planarity : 0.004 0.047 2089 Dihedral : 20.236 87.722 3360 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.79 % Allowed : 17.49 % Favored : 79.72 % 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: 0.36 (0.22), residues: 1356 helix: 1.07 (0.20), residues: 670 sheet: -0.83 (0.50), residues: 95 loop : -0.45 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 220 TYR 0.019 0.002 TYR B 981 PHE 0.022 0.001 PHE B 290 TRP 0.014 0.002 TRP B 883 HIS 0.005 0.001 HIS B 983 Details of bonding type rmsd covalent geometry : bond 0.00267 (14548) covalent geometry : angle 0.57397 (20221) hydrogen bonds : bond 0.03897 ( 646) hydrogen bonds : angle 4.46042 ( 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 156 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.339 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 165 ARG cc_start: 0.8563 (ptt180) cc_final: 0.7961 (ptt180) REVERT: B 504 ASN cc_start: 0.9329 (m-40) cc_final: 0.9042 (p0) REVERT: B 510 LYS cc_start: 0.9524 (ttmm) cc_final: 0.9249 (mtpp) REVERT: B 516 GLU cc_start: 0.9429 (mp0) cc_final: 0.9123 (pm20) REVERT: B 596 ASP cc_start: 0.9246 (m-30) cc_final: 0.9003 (m-30) REVERT: B 648 MET cc_start: 0.9480 (tmm) cc_final: 0.9192 (ppp) REVERT: B 656 TYR cc_start: 0.8293 (m-80) cc_final: 0.7983 (m-80) REVERT: B 846 PHE cc_start: 0.9088 (m-80) cc_final: 0.8140 (m-80) REVERT: B 847 LEU cc_start: 0.9166 (tp) cc_final: 0.8721 (mt) REVERT: B 858 THR cc_start: 0.8010 (OUTLIER) cc_final: 0.5505 (t) REVERT: B 883 TRP cc_start: 0.8666 (m-10) cc_final: 0.8442 (m-10) REVERT: B 999 LYS cc_start: 0.8679 (mtpt) cc_final: 0.8385 (ptpt) REVERT: B 1046 PHE cc_start: 0.7019 (m-80) cc_final: 0.6800 (m-80) REVERT: B 1182 LEU cc_start: 0.9679 (mt) cc_final: 0.9319 (pp) REVERT: B 1205 GLU cc_start: 0.8355 (tt0) cc_final: 0.7840 (tp30) REVERT: B 1244 LYS cc_start: 0.7579 (mmtm) cc_final: 0.7163 (pttp) outliers start: 34 outliers final: 17 residues processed: 149 average time/residue: 0.1054 time to fit residues: 24.0067 Evaluate side-chains 128 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 266 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 858 THR Chi-restraints excluded: chain B residue 899 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 1226 LEU 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: 6.9990 chunk 29 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.073612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.053273 restraints weight = 89994.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.054833 restraints weight = 52928.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.055805 restraints weight = 38115.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.056432 restraints weight = 30797.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.056718 restraints weight = 26960.994| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14548 Z= 0.237 Angle : 0.654 11.607 20221 Z= 0.339 Chirality : 0.040 0.315 2305 Planarity : 0.004 0.057 2089 Dihedral : 20.343 90.191 3360 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.71 % Allowed : 18.47 % 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: 0.12 (0.22), residues: 1356 helix: 0.81 (0.20), residues: 679 sheet: -0.74 (0.52), residues: 92 loop : -0.55 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 220 TYR 0.019 0.002 TYR B1356 PHE 0.027 0.002 PHE B 518 TRP 0.028 0.003 TRP B 464 HIS 0.009 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00496 (14548) covalent geometry : angle 0.65372 (20221) hydrogen bonds : bond 0.05505 ( 646) hydrogen bonds : angle 4.70728 ( 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 142 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.508 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 18 TRP cc_start: 0.8506 (p-90) cc_final: 0.7544 (p-90) REVERT: B 40 ARG cc_start: 0.9422 (OUTLIER) cc_final: 0.9171 (ttm-80) REVERT: B 161 MET cc_start: 0.8113 (tpp) cc_final: 0.7671 (tpp) REVERT: B 165 ARG cc_start: 0.8446 (ptt180) cc_final: 0.8031 (ptt180) REVERT: B 648 MET cc_start: 0.9561 (tmm) cc_final: 0.9152 (ppp) REVERT: B 656 TYR cc_start: 0.8602 (m-80) cc_final: 0.8282 (m-80) REVERT: B 847 LEU cc_start: 0.9178 (tp) cc_final: 0.8822 (mt) REVERT: B 858 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.6885 (t) REVERT: B 883 TRP cc_start: 0.8958 (m-10) cc_final: 0.8459 (m-10) REVERT: B 1089 MET cc_start: 0.8614 (mmp) cc_final: 0.8303 (mmp) REVERT: B 1205 GLU cc_start: 0.8387 (tt0) cc_final: 0.8098 (pp20) REVERT: B 1225 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7875 (mm-30) REVERT: B 1244 LYS cc_start: 0.7627 (mmtm) cc_final: 0.7332 (pttp) REVERT: B 1313 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8065 (t80) outliers start: 33 outliers final: 23 residues processed: 134 average time/residue: 0.1082 time to fit residues: 22.1999 Evaluate side-chains 127 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 335 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 636 LEU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 858 THR Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 927 ILE 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 1225 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 117 optimal weight: 0.0870 chunk 131 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 overall best weight: 2.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 776 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.075045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.054577 restraints weight = 90659.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.056190 restraints weight = 53233.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.057180 restraints weight = 38094.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.057710 restraints weight = 30869.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.058143 restraints weight = 27496.430| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14548 Z= 0.137 Angle : 0.597 12.770 20221 Z= 0.305 Chirality : 0.038 0.294 2305 Planarity : 0.004 0.047 2089 Dihedral : 20.229 88.112 3360 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.38 % Allowed : 19.54 % Favored : 78.08 % 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: 0.32 (0.23), residues: 1356 helix: 0.96 (0.20), residues: 681 sheet: -0.52 (0.51), residues: 97 loop : -0.46 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 220 TYR 0.030 0.002 TYR B 286 PHE 0.022 0.001 PHE B 518 TRP 0.017 0.002 TRP B 464 HIS 0.008 0.001 HIS B1262 Details of bonding type rmsd covalent geometry : bond 0.00297 (14548) covalent geometry : angle 0.59740 (20221) hydrogen bonds : bond 0.04048 ( 646) hydrogen bonds : angle 4.52497 ( 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 141 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.476 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 18 TRP cc_start: 0.8583 (p-90) cc_final: 0.7629 (p-90) REVERT: B 90 MET cc_start: 0.8265 (tpp) cc_final: 0.7885 (mmp) REVERT: B 165 ARG cc_start: 0.8519 (ptt180) cc_final: 0.7873 (ptt180) REVERT: B 596 ASP cc_start: 0.9239 (m-30) cc_final: 0.9030 (m-30) REVERT: B 656 TYR cc_start: 0.8398 (m-80) cc_final: 0.8061 (m-80) REVERT: B 847 LEU cc_start: 0.9082 (tp) cc_final: 0.8756 (mt) REVERT: B 883 TRP cc_start: 0.8864 (m-10) cc_final: 0.8375 (m-10) REVERT: B 999 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8414 (ptpt) REVERT: B 1205 GLU cc_start: 0.8367 (tt0) cc_final: 0.8056 (pp20) REVERT: B 1244 LYS cc_start: 0.7605 (mmtm) cc_final: 0.7189 (pttp) REVERT: B 1313 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.7980 (t80) outliers start: 29 outliers final: 21 residues processed: 133 average time/residue: 0.1055 time to fit residues: 21.7405 Evaluate side-chains 124 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 266 LEU Chi-restraints excluded: chain B residue 335 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 759 ILE Chi-restraints excluded: chain B residue 899 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 1226 LEU Chi-restraints excluded: chain B residue 1263 LYS Chi-restraints excluded: chain B residue 1265 TYR Chi-restraints excluded: chain B residue 1313 PHE 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: 7.9990 chunk 76 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 43 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.073442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.053262 restraints weight = 92490.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.054802 restraints weight = 54193.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.055801 restraints weight = 38803.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.056374 restraints weight = 31453.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.056762 restraints weight = 27786.404| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.6029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14548 Z= 0.196 Angle : 0.646 12.883 20221 Z= 0.328 Chirality : 0.039 0.303 2305 Planarity : 0.004 0.052 2089 Dihedral : 20.291 88.880 3360 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.30 % Allowed : 19.79 % Favored : 77.91 % 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: 0.12 (0.22), residues: 1356 helix: 0.80 (0.20), residues: 681 sheet: -0.55 (0.49), residues: 102 loop : -0.57 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 220 TYR 0.019 0.002 TYR B 812 PHE 0.030 0.002 PHE B 518 TRP 0.013 0.002 TRP B 464 HIS 0.007 0.001 HIS B1264 Details of bonding type rmsd covalent geometry : bond 0.00417 (14548) covalent geometry : angle 0.64556 (20221) hydrogen bonds : bond 0.04754 ( 646) hydrogen bonds : angle 4.61639 ( 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 129 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.380 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 18 TRP cc_start: 0.8597 (p-90) cc_final: 0.7693 (p-90) REVERT: B 161 MET cc_start: 0.8037 (tpp) cc_final: 0.7743 (tpp) REVERT: B 656 TYR cc_start: 0.8490 (m-80) cc_final: 0.8218 (m-80) REVERT: B 846 PHE cc_start: 0.8907 (m-80) cc_final: 0.8168 (m-80) REVERT: B 847 LEU cc_start: 0.9157 (tp) cc_final: 0.8762 (mt) REVERT: B 883 TRP cc_start: 0.8924 (m-10) cc_final: 0.8424 (m-10) REVERT: B 999 LYS cc_start: 0.8769 (mtpt) cc_final: 0.8451 (ptpt) REVERT: B 1089 MET cc_start: 0.8601 (mmp) cc_final: 0.8289 (mmp) REVERT: B 1205 GLU cc_start: 0.8386 (tt0) cc_final: 0.8122 (pp20) REVERT: B 1225 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7973 (tp30) REVERT: B 1244 LYS cc_start: 0.7632 (mmtm) cc_final: 0.7411 (pttp) REVERT: B 1313 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8015 (t80) outliers start: 28 outliers final: 23 residues processed: 123 average time/residue: 0.1160 time to fit residues: 21.6281 Evaluate side-chains 120 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 335 LEU Chi-restraints excluded: chain B residue 507 VAL 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 759 ILE Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 899 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 1225 GLU Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 1263 LYS Chi-restraints excluded: chain B residue 1265 TYR Chi-restraints excluded: chain B residue 1313 PHE 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: 5.9990 chunk 1 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1252 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.074502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.054351 restraints weight = 90654.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.055952 restraints weight = 52621.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.056986 restraints weight = 37262.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.057466 restraints weight = 29971.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.057881 restraints weight = 26700.707| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14548 Z= 0.144 Angle : 0.632 13.259 20221 Z= 0.317 Chirality : 0.039 0.309 2305 Planarity : 0.004 0.050 2089 Dihedral : 20.189 87.202 3360 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.64 % Allowed : 20.61 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.23), residues: 1356 helix: 0.94 (0.20), residues: 674 sheet: -0.70 (0.54), residues: 86 loop : -0.60 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 220 TYR 0.020 0.002 TYR B 812 PHE 0.034 0.002 PHE B 518 TRP 0.015 0.002 TRP B 464 HIS 0.006 0.001 HIS B1264 Details of bonding type rmsd covalent geometry : bond 0.00312 (14548) covalent geometry : angle 0.63234 (20221) hydrogen bonds : bond 0.04177 ( 646) hydrogen bonds : angle 4.54604 ( 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 126 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.542 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: B 18 TRP cc_start: 0.8604 (p-90) cc_final: 0.7600 (p-90) REVERT: B 161 MET cc_start: 0.8031 (tpp) cc_final: 0.7719 (tpp) REVERT: B 656 TYR cc_start: 0.8386 (m-80) cc_final: 0.8051 (m-80) REVERT: B 846 PHE cc_start: 0.8944 (m-80) cc_final: 0.8278 (m-80) REVERT: B 847 LEU cc_start: 0.9125 (tp) cc_final: 0.8735 (mt) REVERT: B 883 TRP cc_start: 0.8925 (m-10) cc_final: 0.8420 (m-10) REVERT: B 930 HIS cc_start: 0.8629 (m-70) cc_final: 0.8382 (m-70) REVERT: B 999 LYS cc_start: 0.8728 (mtpt) cc_final: 0.8418 (ptpt) REVERT: B 1205 GLU cc_start: 0.8382 (tt0) cc_final: 0.8117 (pp20) REVERT: B 1225 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7968 (tp30) REVERT: B 1244 LYS cc_start: 0.7560 (mmtm) cc_final: 0.7243 (pttp) REVERT: B 1313 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.7963 (t80) outliers start: 20 outliers final: 17 residues processed: 121 average time/residue: 0.1111 time to fit residues: 20.8327 Evaluate side-chains 121 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 335 LEU Chi-restraints excluded: chain B residue 516 GLU 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 759 ILE Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 1062 LEU 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 1225 GLU Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 1263 LYS Chi-restraints excluded: chain B residue 1265 TYR Chi-restraints excluded: chain B residue 1313 PHE 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: 9.9990 chunk 112 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 22 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.073029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.053096 restraints weight = 93457.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.054505 restraints weight = 54382.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.055574 restraints weight = 39169.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.056089 restraints weight = 31690.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.056502 restraints weight = 28197.064| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.6393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14548 Z= 0.190 Angle : 0.648 12.913 20221 Z= 0.329 Chirality : 0.040 0.282 2305 Planarity : 0.004 0.052 2089 Dihedral : 20.217 88.624 3360 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.89 % Allowed : 20.36 % Favored : 77.75 % 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: 0.02 (0.22), residues: 1356 helix: 0.79 (0.20), residues: 681 sheet: -0.94 (0.51), residues: 97 loop : -0.65 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 220 TYR 0.023 0.002 TYR B 5 PHE 0.033 0.002 PHE B 518 TRP 0.014 0.002 TRP B 464 HIS 0.007 0.001 HIS B1264 Details of bonding type rmsd covalent geometry : bond 0.00404 (14548) covalent geometry : angle 0.64848 (20221) hydrogen bonds : bond 0.04840 ( 646) hydrogen bonds : angle 4.66305 ( 1748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2827.64 seconds wall clock time: 49 minutes 37.49 seconds (2977.49 seconds total)