Starting phenix.real_space_refine on Sat Sep 12 06:43:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z4k_14500/09_2026/7z4k_14500.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z4k_14500/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7z4k_14500/09_2026/7z4k_14500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z4k_14500/09_2026/7z4k_14500.map" model { file = "/net/cci-nas-00/data/ceres_data/7z4k_14500/09_2026/7z4k_14500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z4k_14500/09_2026/7z4k_14500.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7z4k_14500/09_2026/7z4k_14500.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z4k_14500/09_2026/7z4k_14500.cif" } 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14005 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 11109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1360, 11109 Classifications: {'peptide': 1360} Link IDs: {'PTRANS': 35, 'TRANS': 1324} Chain breaks: 1 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1884 Classifications: {'RNAv2': 88} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 46, 'rna3p_pyr': 30} Link IDs: {'rna2p': 12, 'rna3p': 75} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 3.08, 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: 1.26 Conformation dependent library (CDL) restraints added in 511.3 milliseconds 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2584 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 10 sheets defined 53.9% alpha, 7.9% beta 51 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 2.00 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: 3.59 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2627 1.33 - 1.45: 4055 1.45 - 1.57: 7554 1.57 - 1.69: 268 1.69 - 1.81: 44 Bond restraints: 14548 Sorted by residual: bond pdb=" O4' DT D -13 " pdb=" C1' DT D -13 " ideal model delta sigma weight residual 1.420 1.378 0.042 1.10e-02 8.26e+03 1.46e+01 bond pdb=" N1 DT D -12 " pdb=" C6 DT D -12 " ideal model delta sigma weight residual 1.378 1.404 -0.026 7.00e-03 2.04e+04 1.39e+01 bond pdb=" C5 DT D -12 " pdb=" C6 DT D -12 " ideal model delta sigma weight residual 1.339 1.364 -0.025 7.00e-03 2.04e+04 1.31e+01 bond pdb=" C5' DT D -12 " pdb=" C4' DT D -12 " ideal model delta sigma weight residual 1.512 1.534 -0.022 7.00e-03 2.04e+04 9.55e+00 bond pdb=" C3' DC C 7 " pdb=" O3' DC C 7 " ideal model delta sigma weight residual 1.435 1.398 0.037 1.30e-02 5.92e+03 8.02e+00 ... (remaining 14543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 19414 1.30 - 2.60: 573 2.60 - 3.90: 203 3.90 - 5.20: 28 5.20 - 6.50: 3 Bond angle restraints: 20221 Sorted by residual: angle pdb=" O4' DC C 7 " pdb=" C4' DC C 7 " pdb=" C3' DC C 7 " ideal model delta sigma weight residual 106.00 103.00 3.00 6.00e-01 2.78e+00 2.50e+01 angle pdb=" N3 DT D -13 " pdb=" C4 DT D -13 " pdb=" O4 DT D -13 " ideal model delta sigma weight residual 119.90 122.81 -2.91 6.00e-01 2.78e+00 2.36e+01 angle pdb=" O4' DG C 17 " pdb=" C4' DG C 17 " pdb=" C3' DG C 17 " ideal model delta sigma weight residual 106.00 103.17 2.83 6.00e-01 2.78e+00 2.23e+01 angle pdb=" O4 DT D -12 " pdb=" C4 DT D -12 " pdb=" C5 DT D -12 " ideal model delta sigma weight residual 124.90 121.67 3.23 7.00e-01 2.04e+00 2.12e+01 angle pdb=" N3 DT C 9 " pdb=" C4 DT C 9 " pdb=" O4 DT C 9 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.04e+01 ... (remaining 20216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 7561 17.37 - 34.75: 520 34.75 - 52.12: 306 52.12 - 69.49: 142 69.49 - 86.86: 22 Dihedral angle restraints: 8551 sinusoidal: 4554 harmonic: 3997 Sorted by residual: dihedral pdb=" C4' U A 63 " pdb=" C3' U A 63 " pdb=" C2' U A 63 " pdb=" C1' U A 63 " ideal model delta sinusoidal sigma weight residual 36.34 -36.32 72.66 1 3.10e+00 1.04e-01 7.01e+02 dihedral pdb=" C4' A A 28 " pdb=" C3' A A 28 " pdb=" C2' A A 28 " pdb=" C1' A A 28 " ideal model delta sinusoidal sigma weight residual 36.34 -36.30 72.65 1 3.10e+00 1.04e-01 7.01e+02 dihedral pdb=" C4' G A 89 " pdb=" C3' G A 89 " pdb=" C2' G A 89 " pdb=" C1' G A 89 " ideal model delta sinusoidal sigma weight residual 36.35 -36.14 72.49 1 3.10e+00 1.04e-01 6.98e+02 ... (remaining 8548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1943 0.059 - 0.118: 232 0.118 - 0.177: 21 0.177 - 0.236: 83 0.236 - 0.295: 26 Chirality restraints: 2305 Sorted by residual: chirality pdb=" C2' G A 81 " pdb=" C3' G A 81 " pdb=" O2' G A 81 " pdb=" C1' G A 81 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C2' U A 59 " pdb=" C3' U A 59 " pdb=" O2' U A 59 " pdb=" C1' U A 59 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C2' C A 55 " pdb=" C3' C A 55 " pdb=" O2' C A 55 " pdb=" C1' C A 55 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 2302 not shown) Planarity restraints: 2089 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 991 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.97e+00 pdb=" C ALA B 991 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA B 991 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL B 992 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 992 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C VAL B 992 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL B 992 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL B 993 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 995 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.28e+00 pdb=" C THR B 995 " -0.036 2.00e-02 2.50e+03 pdb=" O THR B 995 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA B 996 " 0.012 2.00e-02 2.50e+03 ... (remaining 2086 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1153 2.74 - 3.28: 14104 3.28 - 3.82: 25732 3.82 - 4.36: 30178 4.36 - 4.90: 47525 Nonbonded interactions: 118692 Sorted by model distance: nonbonded pdb=" OG1 THR B 474 " pdb=" OD1 ASN B 477 " model vdw 2.200 3.040 nonbonded pdb=" OG SER B 512 " pdb=" OE1 GLU B 617 " model vdw 2.222 3.040 nonbonded pdb=" OG SER B1109 " pdb=" OP2 DG C 1 " model vdw 2.235 3.040 nonbonded pdb=" O LYS B 209 " pdb=" OG SER B 213 " model vdw 2.271 3.040 nonbonded pdb=" N2 G A 33 " pdb=" OP2 A A 36 " model vdw 2.277 3.120 ... (remaining 118687 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.160 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14548 Z= 0.274 Angle : 0.587 6.496 20221 Z= 0.367 Chirality : 0.063 0.295 2305 Planarity : 0.003 0.038 2089 Dihedral : 16.731 86.864 5967 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.99 % Allowed : 4.68 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.23), residues: 1356 helix: 1.88 (0.21), residues: 659 sheet: -0.56 (0.49), residues: 118 loop : -0.25 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1333 TYR 0.008 0.001 TYR B 882 PHE 0.006 0.001 PHE B1008 TRP 0.007 0.001 TRP B 464 HIS 0.003 0.000 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.27 (14548) covalent geometry : angle 0.58671 / 0.37 (20221) hydrogen bonds : bond 0.12980 / 8.98 ( 646) hydrogen bonds : angle 5.22172 / 3.66 ( 1748) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 294 time to evaluate : 0.490 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: 0.1465 time to fit residues: 61.8303 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 : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1018 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 HIS B 113 HIS ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN B 277 ASN B 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.082378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.061290 restraints weight = 86387.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.063105 restraints weight = 50848.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.064230 restraints weight = 36307.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.064980 restraints weight = 29230.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.065236 restraints weight = 25417.971| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2378 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= 0.193 Angle : 0.967 19.356 20221 Z= 0.430 Chirality : 0.082 1.100 2305 Planarity : 0.005 0.064 2089 Dihedral : 18.991 132.845 3081 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.05 % Allowed : 13.46 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.22), residues: 1356 helix: 1.61 (0.20), residues: 663 sheet: -0.39 (0.54), residues: 86 loop : -0.36 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 220 TYR 0.025 0.002 TYR B 981 PHE 0.023 0.002 PHE B1258 TRP 0.016 0.001 TRP B 464 HIS 0.015 0.002 HIS B 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 (14548) covalent geometry : angle 0.96669 / 0.43 (20221) hydrogen bonds : bond 0.04676 / 3.16 ( 646) hydrogen bonds : angle 4.43890 / 3.17 ( 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 186 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 LEU cc_start: 0.8718 (mt) cc_final: 0.8516 (mt) REVERT: B 165 ARG cc_start: 0.8294 (ptt180) cc_final: 0.5736 (ptt180) REVERT: B 433 LEU cc_start: 0.9388 (mt) cc_final: 0.9165 (tt) REVERT: B 504 ASN cc_start: 0.9219 (m-40) cc_final: 0.8979 (p0) REVERT: B 694 MET cc_start: 0.9629 (tpp) cc_final: 0.8798 (tpp) REVERT: B 698 HIS cc_start: 0.9034 (m90) cc_final: 0.8713 (m90) REVERT: B 930 HIS cc_start: 0.8492 (m-70) cc_final: 0.8032 (m90) REVERT: B 979 ASN cc_start: 0.8571 (p0) cc_final: 0.8240 (m110) REVERT: B 1039 TYR cc_start: 0.9338 (m-10) cc_final: 0.9130 (m-10) REVERT: B 1262 HIS cc_start: 0.8075 (m-70) cc_final: 0.7837 (t-90) REVERT: B 1276 PHE cc_start: 0.8261 (t80) cc_final: 0.7653 (t80) outliers start: 25 outliers final: 11 residues processed: 177 average time/residue: 0.1354 time to fit residues: 34.2662 Evaluate side-chains 138 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1156 LYS Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1313 PHE Chi-restraints excluded: chain B residue 1347 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 87 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 25 optimal weight: 30.0000 chunk 68 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 HIS B 175 ASN ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 HIS ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.079321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.058553 restraints weight = 88715.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.060237 restraints weight = 52663.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.061294 restraints weight = 37791.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.061992 restraints weight = 30613.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.062239 restraints weight = 26738.650| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14548 Z= 0.216 Angle : 0.822 14.501 20221 Z= 0.381 Chirality : 0.065 0.818 2305 Planarity : 0.005 0.054 2089 Dihedral : 18.978 149.469 3080 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.96 % Allowed : 14.37 % Favored : 82.68 % 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: 0.69 (0.22), residues: 1356 helix: 1.39 (0.20), residues: 662 sheet: -0.19 (0.53), residues: 87 loop : -0.43 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 220 TYR 0.023 0.002 TYR B 823 PHE 0.016 0.002 PHE B 518 TRP 0.027 0.002 TRP B 464 HIS 0.009 0.002 HIS B 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.22 (14548) covalent geometry : angle 0.82215 / 0.38 (20221) hydrogen bonds : bond 0.04927 / 3.36 ( 646) hydrogen bonds : angle 4.35471 / 3.12 ( 1748) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 165 ARG cc_start: 0.8463 (ptt180) cc_final: 0.5894 (ptt180) REVERT: B 321 MET cc_start: 0.8364 (mmp) cc_final: 0.8108 (mmp) REVERT: B 433 LEU cc_start: 0.9420 (mt) cc_final: 0.9165 (tt) REVERT: B 504 ASN cc_start: 0.9225 (m-40) cc_final: 0.8995 (p0) REVERT: B 596 ASP cc_start: 0.9095 (OUTLIER) cc_final: 0.8818 (t0) REVERT: B 648 MET cc_start: 0.9349 (tmm) cc_final: 0.8669 (tmm) REVERT: B 694 MET cc_start: 0.9628 (tpp) cc_final: 0.9004 (tmm) REVERT: B 698 HIS cc_start: 0.9058 (m90) cc_final: 0.8815 (m90) REVERT: B 908 LEU cc_start: 0.8848 (mm) cc_final: 0.8456 (mm) REVERT: B 930 HIS cc_start: 0.8540 (m-70) cc_final: 0.8111 (m-70) REVERT: B 1046 PHE cc_start: 0.7401 (m-80) cc_final: 0.7182 (m-80) REVERT: B 1262 HIS cc_start: 0.8281 (m-70) cc_final: 0.8018 (t-90) outliers start: 36 outliers final: 22 residues processed: 158 average time/residue: 0.1176 time to fit residues: 27.5777 Evaluate side-chains 143 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 980 ASN Chi-restraints excluded: chain B residue 1043 MET Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1089 MET Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 1314 THR Chi-restraints excluded: chain B residue 1316 THR Chi-restraints excluded: chain B residue 1347 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 132 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 147 optimal weight: 30.0000 chunk 1 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN B 224 ASN B 544 GLN ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.075803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.055060 restraints weight = 90656.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.056621 restraints weight = 54141.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.057546 restraints weight = 39230.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.058201 restraints weight = 32352.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.058544 restraints weight = 28524.976| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 14548 Z= 0.325 Angle : 0.901 15.444 20221 Z= 0.428 Chirality : 0.063 0.720 2305 Planarity : 0.005 0.055 2089 Dihedral : 18.967 140.759 3080 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.96 % Allowed : 15.76 % Favored : 81.28 % 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: 0.09 (0.21), residues: 1356 helix: 0.83 (0.19), residues: 666 sheet: -0.63 (0.50), residues: 89 loop : -0.62 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 165 TYR 0.036 0.003 TYR B 286 PHE 0.028 0.003 PHE B 290 TRP 0.038 0.003 TRP B 464 HIS 0.007 0.002 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.33 (14548) covalent geometry : angle 0.90132 / 0.43 (20221) hydrogen bonds : bond 0.06389 / 4.34 ( 646) hydrogen bonds : angle 4.73769 / 3.43 ( 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 161 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.563 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: B 161 MET cc_start: 0.7818 (mtm) cc_final: 0.7421 (mmm) REVERT: B 165 ARG cc_start: 0.8483 (ptt180) cc_final: 0.5938 (ptt180) REVERT: B 504 ASN cc_start: 0.9228 (m-40) cc_final: 0.8984 (p0) REVERT: B 596 ASP cc_start: 0.9260 (OUTLIER) cc_final: 0.9017 (m-30) REVERT: B 643 PHE cc_start: 0.6770 (p90) cc_final: 0.5865 (p90) REVERT: B 648 MET cc_start: 0.9558 (tmm) cc_final: 0.9226 (tmm) REVERT: B 846 PHE cc_start: 0.9056 (m-80) cc_final: 0.8588 (m-80) REVERT: B 879 MET cc_start: 0.3159 (mpp) cc_final: 0.2899 (mpp) REVERT: B 930 HIS cc_start: 0.8611 (m-70) cc_final: 0.8201 (m90) REVERT: B 1175 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8869 (mm-30) outliers start: 36 outliers final: 23 residues processed: 149 average time/residue: 0.1200 time to fit residues: 26.5160 Evaluate side-chains 134 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 635 ARG Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 980 ASN Chi-restraints excluded: chain B residue 1043 MET Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 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 1313 PHE Chi-restraints excluded: chain B residue 1314 THR Chi-restraints excluded: chain B residue 1347 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 56 optimal weight: 0.4980 chunk 89 optimal weight: 30.0000 chunk 100 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 HIS ** 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 = 0.3864 r_free = 0.3864 target = 0.078285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.057342 restraints weight = 88561.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.059021 restraints weight = 52364.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.060077 restraints weight = 37428.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.060571 restraints weight = 30394.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.061070 restraints weight = 27127.702| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14548 Z= 0.144 Angle : 0.756 19.918 20221 Z= 0.351 Chirality : 0.057 0.602 2305 Planarity : 0.004 0.051 2089 Dihedral : 18.776 137.851 3080 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.87 % Allowed : 16.58 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.22), residues: 1356 helix: 1.12 (0.20), residues: 666 sheet: -0.57 (0.48), residues: 99 loop : -0.47 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 220 TYR 0.019 0.002 TYR B 823 PHE 0.024 0.002 PHE B 518 TRP 0.015 0.002 TRP B 464 HIS 0.007 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (14548) covalent geometry : angle 0.75578 / 0.35 (20221) hydrogen bonds : bond 0.04209 / 2.85 ( 646) hydrogen bonds : angle 4.42291 / 3.19 ( 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 160 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 0.451 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: 0.7794 (mtm) cc_final: 0.7346 (mmm) REVERT: B 165 ARG cc_start: 0.8600 (ptt180) cc_final: 0.6671 (ptt180) REVERT: B 499 ASP cc_start: 0.7272 (t70) cc_final: 0.6114 (t0) REVERT: B 504 ASN cc_start: 0.9233 (m-40) cc_final: 0.8925 (p0) REVERT: B 596 ASP cc_start: 0.9173 (m-30) cc_final: 0.8913 (m-30) REVERT: B 631 MET cc_start: 0.8618 (tpp) cc_final: 0.8390 (tpp) REVERT: B 643 PHE cc_start: 0.6636 (p90) cc_final: 0.6045 (p90) REVERT: B 648 MET cc_start: 0.9494 (tmm) cc_final: 0.9151 (tmm) REVERT: B 846 PHE cc_start: 0.9025 (m-80) cc_final: 0.8463 (m-80) REVERT: B 847 LEU cc_start: 0.9071 (tp) cc_final: 0.8749 (mt) REVERT: B 883 TRP cc_start: 0.8198 (m-10) cc_final: 0.7927 (m-10) REVERT: B 930 HIS cc_start: 0.8601 (m-70) cc_final: 0.8174 (m90) REVERT: B 949 LEU cc_start: 0.7533 (tp) cc_final: 0.7203 (pp) REVERT: B 1001 TYR cc_start: 0.8850 (m-80) cc_final: 0.8366 (m-80) outliers start: 35 outliers final: 20 residues processed: 147 average time/residue: 0.1167 time to fit residues: 25.9472 Evaluate side-chains 129 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 635 ARG Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 980 ASN Chi-restraints excluded: chain B residue 1043 MET Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1089 MET Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1145 VAL 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 1290 VAL Chi-restraints excluded: chain B residue 1313 PHE 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: 7.9990 chunk 78 optimal weight: 0.8980 chunk 67 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 53 optimal weight: 30.0000 chunk 132 optimal weight: 0.5980 chunk 128 optimal weight: 10.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.077553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.056840 restraints weight = 88556.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.058465 restraints weight = 52295.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.059431 restraints weight = 37555.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.060116 restraints weight = 30709.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.060349 restraints weight = 26878.382| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14548 Z= 0.157 Angle : 0.737 13.806 20221 Z= 0.343 Chirality : 0.055 0.550 2305 Planarity : 0.004 0.046 2089 Dihedral : 18.718 141.033 3080 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.13 % Allowed : 17.98 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.22), residues: 1356 helix: 1.20 (0.20), residues: 667 sheet: -0.62 (0.49), residues: 97 loop : -0.44 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 220 TYR 0.032 0.002 TYR B 812 PHE 0.029 0.002 PHE B 290 TRP 0.009 0.001 TRP B 464 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (14548) covalent geometry : angle 0.73720 / 0.34 (20221) hydrogen bonds : bond 0.04460 / 3.04 ( 646) hydrogen bonds : angle 4.44005 / 3.19 ( 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 141 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: 0.7815 (mtm) cc_final: 0.7400 (mmm) REVERT: B 499 ASP cc_start: 0.7353 (t70) cc_final: 0.6245 (t0) REVERT: B 504 ASN cc_start: 0.9248 (m-40) cc_final: 0.9027 (p0) REVERT: B 596 ASP cc_start: 0.9182 (m-30) cc_final: 0.8932 (m-30) REVERT: B 631 MET cc_start: 0.8717 (tpp) cc_final: 0.8477 (tpp) REVERT: B 763 MET cc_start: 0.7974 (mmt) cc_final: 0.7352 (mmm) REVERT: B 846 PHE cc_start: 0.9052 (m-80) cc_final: 0.8461 (m-80) REVERT: B 847 LEU cc_start: 0.9118 (tp) cc_final: 0.8795 (mt) REVERT: B 883 TRP cc_start: 0.8496 (m-10) cc_final: 0.7990 (m-10) REVERT: B 930 HIS cc_start: 0.8624 (m-70) cc_final: 0.8386 (m-70) outliers start: 26 outliers final: 17 residues processed: 134 average time/residue: 0.1104 time to fit residues: 22.9544 Evaluate side-chains 125 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 530 VAL 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 980 ASN Chi-restraints excluded: chain B residue 1043 MET Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1203 LEU 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: 2.9990 chunk 29 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 43 optimal weight: 0.1980 chunk 15 optimal weight: 7.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.076406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.055810 restraints weight = 89044.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.057416 restraints weight = 52575.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.058412 restraints weight = 37780.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.058944 restraints weight = 30731.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.059384 restraints weight = 27347.638| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4731 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= 0.192 Angle : 0.751 12.525 20221 Z= 0.353 Chirality : 0.053 0.564 2305 Planarity : 0.004 0.042 2089 Dihedral : 18.691 137.867 3080 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.38 % Allowed : 18.14 % Favored : 79.47 % 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: 0.38 (0.22), residues: 1356 helix: 1.14 (0.20), residues: 668 sheet: -0.65 (0.50), residues: 97 loop : -0.55 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 220 TYR 0.028 0.002 TYR B 823 PHE 0.029 0.002 PHE B 518 TRP 0.009 0.001 TRP B 659 HIS 0.009 0.001 HIS B1264 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (14548) covalent geometry : angle 0.75063 / 0.35 (20221) hydrogen bonds : bond 0.04804 / 3.31 ( 646) hydrogen bonds : angle 4.45301 / 3.19 ( 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 138 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: 0.7829 (mtm) cc_final: 0.7237 (tpp) REVERT: B 504 ASN cc_start: 0.9276 (m-40) cc_final: 0.9023 (p0) REVERT: B 596 ASP cc_start: 0.9216 (m-30) cc_final: 0.8977 (m-30) REVERT: B 656 TYR cc_start: 0.8233 (m-80) cc_final: 0.7813 (m-80) REVERT: B 763 MET cc_start: 0.7914 (mmt) cc_final: 0.7524 (mmm) REVERT: B 846 PHE cc_start: 0.9103 (m-80) cc_final: 0.8514 (m-80) REVERT: B 847 LEU cc_start: 0.9159 (tp) cc_final: 0.8856 (mt) REVERT: B 883 TRP cc_start: 0.8669 (m-10) cc_final: 0.8136 (m-10) outliers start: 29 outliers final: 22 residues processed: 127 average time/residue: 0.1111 time to fit residues: 21.9233 Evaluate side-chains 126 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 635 ARG Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 980 ASN Chi-restraints excluded: chain B residue 1043 MET Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 1265 TYR Chi-restraints excluded: chain B residue 1347 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 117 optimal weight: 0.2980 chunk 131 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.078082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.057472 restraints weight = 88316.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.059117 restraints weight = 51959.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.060150 restraints weight = 37312.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.060809 restraints weight = 30227.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.061174 restraints weight = 26473.938| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14548 Z= 0.130 Angle : 0.737 19.866 20221 Z= 0.341 Chirality : 0.052 0.522 2305 Planarity : 0.004 0.044 2089 Dihedral : 18.570 137.261 3080 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.22 % Allowed : 19.38 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.23), residues: 1356 helix: 1.26 (0.20), residues: 667 sheet: -0.73 (0.51), residues: 95 loop : -0.52 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 220 TYR 0.016 0.002 TYR B 823 PHE 0.025 0.001 PHE B 518 TRP 0.009 0.001 TRP B 464 HIS 0.007 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (14548) covalent geometry : angle 0.73725 / 0.34 (20221) hydrogen bonds : bond 0.03981 / 2.71 ( 646) hydrogen bonds : angle 4.34458 / 3.09 ( 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 138 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: 0.7864 (mtm) cc_final: 0.7437 (mmm) REVERT: B 499 ASP cc_start: 0.7438 (t70) cc_final: 0.6511 (t0) REVERT: B 504 ASN cc_start: 0.9263 (m-40) cc_final: 0.8939 (p0) REVERT: B 596 ASP cc_start: 0.9176 (m-30) cc_final: 0.8920 (m-30) REVERT: B 656 TYR cc_start: 0.8047 (m-80) cc_final: 0.7691 (m-80) REVERT: B 763 MET cc_start: 0.7840 (mmt) cc_final: 0.7488 (mmm) REVERT: B 846 PHE cc_start: 0.9201 (m-80) cc_final: 0.8552 (m-80) REVERT: B 847 LEU cc_start: 0.9125 (tp) cc_final: 0.8806 (mt) REVERT: B 879 MET cc_start: 0.2860 (mtm) cc_final: 0.2613 (mtt) REVERT: B 883 TRP cc_start: 0.8723 (m-10) cc_final: 0.8290 (m-10) REVERT: B 930 HIS cc_start: 0.8616 (m-70) cc_final: 0.8215 (m90) REVERT: B 939 MET cc_start: 0.8871 (mmt) cc_final: 0.8538 (mmm) REVERT: B 1001 TYR cc_start: 0.8891 (m-80) cc_final: 0.8420 (m-80) REVERT: B 1177 ASN cc_start: 0.9151 (t0) cc_final: 0.8813 (t0) REVERT: B 1205 GLU cc_start: 0.8340 (tt0) cc_final: 0.7807 (mm-30) outliers start: 27 outliers final: 22 residues processed: 128 average time/residue: 0.1089 time to fit residues: 21.8607 Evaluate side-chains 131 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 635 ARG Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 980 ASN Chi-restraints excluded: chain B residue 1043 MET Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1175 GLU Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 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: 0.1980 chunk 76 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1044 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 = 0.3824 r_free = 0.3824 target = 0.076182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.055635 restraints weight = 90544.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.057233 restraints weight = 53513.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.058232 restraints weight = 38551.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.058704 restraints weight = 31476.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.059188 restraints weight = 28136.574| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14548 Z= 0.189 Angle : 0.752 17.392 20221 Z= 0.349 Chirality : 0.052 0.544 2305 Planarity : 0.004 0.051 2089 Dihedral : 18.603 137.418 3080 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.13 % Allowed : 19.79 % 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: 0.46 (0.23), residues: 1356 helix: 1.26 (0.20), residues: 668 sheet: -0.61 (0.50), residues: 97 loop : -0.57 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 220 TYR 0.032 0.002 TYR B 823 PHE 0.035 0.002 PHE B 518 TRP 0.030 0.002 TRP B 659 HIS 0.006 0.001 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (14548) covalent geometry : angle 0.75217 / 0.35 (20221) hydrogen bonds : bond 0.04767 / 3.28 ( 646) hydrogen bonds : angle 4.43529 / 3.17 ( 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 132 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: 0.7826 (mtm) cc_final: 0.7238 (tpp) REVERT: B 499 ASP cc_start: 0.7593 (t70) cc_final: 0.6768 (t0) REVERT: B 504 ASN cc_start: 0.9274 (m-40) cc_final: 0.9011 (p0) REVERT: B 596 ASP cc_start: 0.9230 (m-30) cc_final: 0.9008 (m-30) REVERT: B 648 MET cc_start: 0.9478 (tmm) cc_final: 0.9000 (ppp) REVERT: B 763 MET cc_start: 0.7868 (mmt) cc_final: 0.7483 (mmm) REVERT: B 846 PHE cc_start: 0.9183 (m-80) cc_final: 0.8506 (m-80) REVERT: B 847 LEU cc_start: 0.9132 (tp) cc_final: 0.8802 (mt) REVERT: B 879 MET cc_start: 0.2998 (mtm) cc_final: 0.2734 (mtt) REVERT: B 883 TRP cc_start: 0.8821 (m-10) cc_final: 0.8383 (m-10) REVERT: B 930 HIS cc_start: 0.8656 (m-70) cc_final: 0.8260 (m90) REVERT: B 1205 GLU cc_start: 0.8301 (tt0) cc_final: 0.8021 (pp20) outliers start: 26 outliers final: 23 residues processed: 124 average time/residue: 0.1117 time to fit residues: 21.2623 Evaluate side-chains 126 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 635 ARG Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 855 LYS Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 980 ASN Chi-restraints excluded: chain B residue 1043 MET Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1175 GLU Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 1265 TYR 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: 6.9990 chunk 1 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 36 optimal weight: 0.0970 chunk 128 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 ASN ** B1044 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 = 0.3869 r_free = 0.3869 target = 0.077884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.057566 restraints weight = 88771.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.059160 restraints weight = 53955.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.060115 restraints weight = 39084.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.060532 restraints weight = 32064.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.061047 restraints weight = 28922.386| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5122 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= 0.124 Angle : 0.732 15.326 20221 Z= 0.338 Chirality : 0.051 0.511 2305 Planarity : 0.004 0.043 2089 Dihedral : 18.472 135.608 3080 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.64 % Allowed : 20.28 % 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: 0.54 (0.23), residues: 1356 helix: 1.35 (0.20), residues: 672 sheet: -0.73 (0.51), residues: 95 loop : -0.57 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 220 TYR 0.029 0.002 TYR B 823 PHE 0.024 0.001 PHE B 518 TRP 0.009 0.001 TRP B 464 HIS 0.006 0.001 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (14548) covalent geometry : angle 0.73172 / 0.34 (20221) hydrogen bonds : bond 0.03890 / 2.65 ( 646) hydrogen bonds : angle 4.34936 / 3.08 ( 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 134 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: 0.7671 (mtm) cc_final: 0.7328 (mmm) REVERT: B 499 ASP cc_start: 0.7490 (t70) cc_final: 0.6642 (t0) REVERT: B 504 ASN cc_start: 0.9245 (m-40) cc_final: 0.8986 (p0) REVERT: B 510 LYS cc_start: 0.9165 (mtpt) cc_final: 0.8948 (mtmt) REVERT: B 596 ASP cc_start: 0.9163 (m-30) cc_final: 0.8919 (m-30) REVERT: B 648 MET cc_start: 0.9453 (tmm) cc_final: 0.8986 (ppp) REVERT: B 763 MET cc_start: 0.7754 (mmt) cc_final: 0.7404 (mmm) REVERT: B 846 PHE cc_start: 0.9231 (m-80) cc_final: 0.8605 (m-80) REVERT: B 847 LEU cc_start: 0.9167 (tp) cc_final: 0.8844 (mt) REVERT: B 879 MET cc_start: 0.3176 (mtm) cc_final: 0.2881 (mtt) REVERT: B 883 TRP cc_start: 0.8810 (m-10) cc_final: 0.8353 (m-10) REVERT: B 930 HIS cc_start: 0.8651 (m-70) cc_final: 0.8236 (m90) REVERT: B 939 MET cc_start: 0.8811 (mmt) cc_final: 0.8489 (mmm) REVERT: B 1177 ASN cc_start: 0.9135 (t0) cc_final: 0.8824 (t0) outliers start: 20 outliers final: 20 residues processed: 127 average time/residue: 0.1072 time to fit residues: 21.2456 Evaluate side-chains 124 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 855 LYS Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 980 ASN Chi-restraints excluded: chain B residue 1043 MET Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1094 ILE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1175 GLU Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1226 LEU Chi-restraints excluded: chain B residue 1265 TYR 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: 4.9990 chunk 112 optimal weight: 0.0770 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 36 optimal weight: 0.0030 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.4152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.077447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.057286 restraints weight = 88478.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.058860 restraints weight = 53603.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.059847 restraints weight = 38956.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.060507 restraints weight = 31774.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.060729 restraints weight = 27912.198| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14548 Z= 0.134 Angle : 0.734 16.435 20221 Z= 0.340 Chirality : 0.050 0.506 2305 Planarity : 0.004 0.055 2089 Dihedral : 18.439 135.205 3080 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.64 % Allowed : 20.77 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.23), residues: 1356 helix: 1.40 (0.20), residues: 670 sheet: -0.82 (0.52), residues: 97 loop : -0.52 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 832 TYR 0.028 0.002 TYR B 812 PHE 0.037 0.002 PHE B 518 TRP 0.035 0.002 TRP B 464 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (14548) covalent geometry : angle 0.73442 / 0.34 (20221) hydrogen bonds : bond 0.04131 / 2.83 ( 646) hydrogen bonds : angle 4.36134 / 3.10 ( 1748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2906.12 seconds wall clock time: 51 minutes 7.08 seconds (3067.08 seconds total)