Starting phenix.real_space_refine on Sat Sep 12 05:35:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z4l_14501/09_2026/7z4l_14501.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z4l_14501/09_2026/7z4l_14501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z4l_14501/09_2026/7z4l_14501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z4l_14501/09_2026/7z4l_14501.map" model { file = "/net/cci-nas-00/data/ceres_data/7z4l_14501/09_2026/7z4l_14501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z4l_14501/09_2026/7z4l_14501.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7z4l_14501/09_2026/7z4l_14501.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z4l_14501/09_2026/7z4l_14501.cif" } resolution = 2.54 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 133 5.49 5 Mg 1 5.21 5 S 22 5.16 5 C 8289 2.51 5 N 2419 2.21 5 O 2957 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 13823 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 2055 Classifications: {'RNAv2': 96} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 51, 'rna3p_pyr': 33} Link IDs: {'rna2p': 12, 'rna3p': 83} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 10949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10949 Classifications: {'peptide': 1337} Link IDs: {'PTRANS': 35, 'TRANS': 1301} Chain breaks: 3 Chain: "C" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 565 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "D" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 245 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' K': 2, ' MG': 1} Classifications: {'undetermined': 3, 'water': 5} Link IDs: {None: 7} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.43, per 1000 atoms: 0.18 Number of scatterers: 13823 At special positions: 0 Unit cell: (89.1, 122.85, 120.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 S 22 16.00 P 133 15.00 Mg 1 11.99 O 2957 8.00 N 2419 7.00 C 8289 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: 1.25 Conformation dependent library (CDL) restraints added in 496.5 milliseconds 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2546 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 11 sheets defined 53.5% alpha, 9.7% beta 50 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'B' and resid 59 through 94 removed outlier: 4.802A pdb=" N ASN B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLU B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS B 92 " --> pdb=" O ASN B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 104 Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 134 through 145 removed outlier: 3.607A 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: 3.624A pdb=" N LEU B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 217 through 228 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.696A pdb=" N PHE B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 282 Processing helix chain 'B' and resid 286 through 303 Processing helix chain 'B' and resid 315 through 343 Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 368 through 382 Proline residue: B 378 - end of helix Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.937A pdb=" N GLY B 408 " --> pdb=" O PHE B 405 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 removed outlier: 3.922A pdb=" N HIS B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 436 through 446 Processing helix chain 'B' and resid 477 through 481 Processing helix chain 'B' and resid 484 through 494 Processing helix chain 'B' and resid 512 through 525 Processing helix chain 'B' and resid 541 through 552 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.547A 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 604 through 609 Processing helix chain 'B' and resid 612 through 626 removed outlier: 3.631A pdb=" N LEU B 616 " --> pdb=" O ASN B 612 " (cutoff:3.500A) 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 664 through 669 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 714 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 removed outlier: 3.560A pdb=" N HIS B 799 " --> pdb=" O ILE B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 807 Processing helix chain 'B' and resid 808 through 817 Processing helix chain 'B' and resid 851 through 853 No H-bonds generated for 'chain 'B' and resid 851 through 853' Processing helix chain 'B' and resid 860 through 865 Processing helix chain 'B' and resid 872 through 889 removed outlier: 5.945A pdb=" N ASN B 881 " --> pdb=" O LYS B 877 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N TYR B 882 " --> pdb=" O LYS B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 901 Processing helix chain 'B' and resid 909 through 920 Processing helix chain 'B' and resid 925 through 940 Processing helix chain 'B' and resid 959 through 970 removed outlier: 3.974A pdb=" N VAL B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 1001 removed outlier: 3.931A pdb=" N ALA B 984 " --> pdb=" O ASN B 980 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA B 996 " --> pdb=" O VAL B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1009 Processing helix chain 'B' and resid 1032 through 1041 Processing helix chain 'B' and resid 1078 through 1087 Processing helix chain 'B' and resid 1127 through 1132 Processing helix chain 'B' and resid 1170 through 1177 removed outlier: 3.530A pdb=" N ASN B1177 " --> pdb=" O SER B1173 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1186 Processing helix chain 'B' and resid 1229 through 1240 Processing helix chain 'B' and resid 1248 through 1262 Processing helix chain 'B' and resid 1264 through 1280 Processing helix chain 'B' and resid 1283 through 1297 Processing helix chain 'B' and resid 1301 through 1313 Processing helix chain 'B' and resid 1340 through 1344 Processing helix chain 'B' and resid 1363 through 1365 No H-bonds generated for 'chain 'B' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'B' and resid 954 through 957 Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 46 removed outlier: 9.964A pdb=" N GLU B1357 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS B 33 " --> pdb=" O GLU B1357 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ARG B1359 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B 35 " --> pdb=" O ARG B1359 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ASP B1361 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU B1203 " --> pdb=" O ILE B1348 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER B1202 " --> pdb=" O LEU B1214 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLU B1219 " --> pdb=" O ALA B1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 466 through 467 removed outlier: 4.820A pdb=" N THR B 466 " --> pdb=" O ASP B 483 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 507 through 509 removed outlier: 5.243A pdb=" N LEU B 508 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.919A pdb=" N ALA B 538 " --> pdb=" O TYR B 529 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR B 529 " --> pdb=" O ALA B 538 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 837 through 840 Processing sheet with id=AA7, first strand: chain 'B' and resid 1049 through 1050 Processing sheet with id=AA8, first strand: chain 'B' and resid 1063 through 1065 removed outlier: 4.081A pdb=" N TRP B1074 " --> pdb=" O GLU B1064 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1156 through 1163 removed outlier: 7.078A pdb=" N ILE B1166 " --> pdb=" O ALA B1140 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1156 through 1163 Processing sheet with id=AB2, first strand: chain 'B' and resid 1324 through 1326 526 hydrogen bonds defined for protein. 1521 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 124 hydrogen bonds 244 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 3.67 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2190 1.32 - 1.44: 4346 1.44 - 1.57: 7508 1.57 - 1.69: 266 1.69 - 1.81: 42 Bond restraints: 14352 Sorted by residual: bond pdb=" C3' DC C -1 " pdb=" O3' DC C -1 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 9.89e+00 bond pdb=" C ASP B 10 " pdb=" O ASP B 10 " ideal model delta sigma weight residual 1.235 1.199 0.036 1.14e-02 7.69e+03 9.85e+00 bond pdb=" C3' DA D 3 " pdb=" C2' DA D 3 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.65e+00 bond pdb=" C3' DA C 0 " pdb=" O3' DA C 0 " ideal model delta sigma weight residual 1.435 1.395 0.040 1.30e-02 5.92e+03 9.45e+00 bond pdb=" C3' DC C -2 " pdb=" O3' DC C -2 " ideal model delta sigma weight residual 1.435 1.395 0.040 1.30e-02 5.92e+03 9.44e+00 ... (remaining 14347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 18945 1.30 - 2.59: 732 2.59 - 3.89: 232 3.89 - 5.18: 41 5.18 - 6.48: 5 Bond angle restraints: 19955 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 106.00 102.82 3.18 6.00e-01 2.78e+00 2.82e+01 angle pdb=" O4' DC C 5 " pdb=" C4' DC C 5 " pdb=" C3' DC C 5 " ideal model delta sigma weight residual 106.00 103.32 2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT C 11 " pdb=" C4 DT C 11 " pdb=" O4 DT C 11 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT C 13 " pdb=" C4 DT C 13 " pdb=" O4 DT C 13 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT C -3 " pdb=" C4 DT C -3 " pdb=" O4 DT C -3 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 ... (remaining 19950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 7426 17.81 - 35.61: 575 35.61 - 53.42: 303 53.42 - 71.22: 109 71.22 - 89.03: 15 Dihedral angle restraints: 8428 sinusoidal: 4494 harmonic: 3934 Sorted by residual: 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 -38.11 74.45 1 3.10e+00 1.04e-01 7.31e+02 dihedral pdb=" C4' G A 43 " pdb=" C3' G A 43 " pdb=" C2' G A 43 " pdb=" C1' G A 43 " ideal model delta sinusoidal sigma weight residual 36.34 -37.72 74.06 1 3.10e+00 1.04e-01 7.25e+02 dihedral pdb=" C4' A A 88 " pdb=" C3' A A 88 " pdb=" C2' A A 88 " pdb=" C1' A A 88 " ideal model delta sinusoidal sigma weight residual 36.35 -37.47 73.82 1 3.10e+00 1.04e-01 7.21e+02 ... (remaining 8425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1906 0.062 - 0.125: 238 0.125 - 0.187: 26 0.187 - 0.250: 95 0.250 - 0.312: 18 Chirality restraints: 2283 Sorted by residual: 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 -2.48 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C2' G A 43 " pdb=" C3' G A 43 " pdb=" O2' G A 43 " pdb=" C1' G A 43 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C2' G A 89 " pdb=" C3' G A 89 " pdb=" O2' G A 89 " pdb=" C1' G A 89 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 2280 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B1273 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C ILE B1273 " -0.035 2.00e-02 2.50e+03 pdb=" O ILE B1273 " 0.013 2.00e-02 2.50e+03 pdb=" N SER B1274 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 298 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.72e+00 pdb=" C ASP B 298 " -0.033 2.00e-02 2.50e+03 pdb=" O ASP B 298 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA B 299 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 983 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C HIS B 983 " -0.033 2.00e-02 2.50e+03 pdb=" O HIS B 983 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA B 984 " 0.011 2.00e-02 2.50e+03 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.45: 69 2.45 - 3.12: 10515 3.12 - 3.80: 27962 3.80 - 4.47: 43036 4.47 - 5.14: 63090 Nonbonded interactions: 144672 Sorted by model distance: nonbonded pdb="MG MG A 201 " pdb=" O HOH A 301 " model vdw 1.780 2.170 nonbonded pdb="MG MG A 201 " pdb=" O HOH A 302 " model vdw 1.818 2.170 nonbonded pdb="MG MG A 201 " pdb=" O HOH A 304 " model vdw 1.883 2.170 nonbonded pdb="MG MG A 201 " pdb=" O HOH A 305 " model vdw 1.884 2.170 nonbonded pdb="MG MG A 201 " pdb=" O HOH A 303 " model vdw 1.888 2.170 ... (remaining 144667 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.240 Find NCS groups from input model: 0.050 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:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 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 : 0.006 0.074 14352 Z= 0.324 Angle : 0.662 6.476 19955 Z= 0.383 Chirality : 0.066 0.312 2283 Planarity : 0.004 0.031 2055 Dihedral : 16.768 89.030 5882 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.83 % Allowed : 6.82 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.22), residues: 1329 helix: 0.93 (0.20), residues: 661 sheet: -0.89 (0.48), residues: 104 loop : -0.21 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 139 TYR 0.018 0.002 TYR B 155 PHE 0.013 0.002 PHE B 491 TRP 0.008 0.001 TRP B 476 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.32 (14352) covalent geometry : angle 0.66177 / 0.38 (19955) hydrogen bonds : bond 0.11888 / 6.45 ( 642) hydrogen bonds : angle 5.47487 / 2.18 ( 1765) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.520 Fit side-chains REVERT: B 4 LYS cc_start: 0.8640 (mttt) cc_final: 0.8415 (mtmt) REVERT: B 312 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7891 (pp) REVERT: B 629 ARG cc_start: 0.7388 (mmt90) cc_final: 0.6965 (ttp80) REVERT: B 655 ARG cc_start: 0.6628 (mtm-85) cc_final: 0.5866 (ttt90) REVERT: B 682 PHE cc_start: 0.8116 (m-80) cc_final: 0.7581 (m-80) REVERT: B 710 LYS cc_start: 0.8614 (mttt) cc_final: 0.8185 (tptp) REVERT: B 809 GLU cc_start: 0.7772 (tt0) cc_final: 0.7116 (mp0) REVERT: B 855 LYS cc_start: 0.4970 (mttt) cc_final: 0.4319 (mtpt) REVERT: B 881 ASN cc_start: 0.8080 (m-40) cc_final: 0.7683 (p0) REVERT: B 925 ARG cc_start: 0.8023 (mtm-85) cc_final: 0.7736 (mtm180) REVERT: B 976 ARG cc_start: 0.8354 (mtp85) cc_final: 0.8145 (mtt-85) REVERT: B 1069 THR cc_start: 0.7847 (p) cc_final: 0.7492 (p) REVERT: B 1124 LYS cc_start: 0.8872 (mttp) cc_final: 0.8447 (mptm) REVERT: B 1242 TYR cc_start: 0.5207 (OUTLIER) cc_final: 0.4121 (t80) REVERT: B 1256 GLN cc_start: 0.7606 (tp40) cc_final: 0.7157 (mm-40) REVERT: B 1296 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8061 (mptp) outliers start: 34 outliers final: 8 residues processed: 171 average time/residue: 0.7470 time to fit residues: 137.8677 Evaluate side-chains 87 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1190 VAL Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1296 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 ASN B 113 HIS B 116 HIS B 129 HIS B 228 GLN B 805 GLN B 807 GLN ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 885 GLN B 920 GLN B1041 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.133285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.082511 restraints weight = 23135.132| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.06 r_work: 0.3053 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 14352 Z= 0.271 Angle : 0.962 21.216 19955 Z= 0.425 Chirality : 0.083 1.165 2283 Planarity : 0.004 0.045 2055 Dihedral : 17.003 135.829 3058 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.66 % Allowed : 11.97 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.23), residues: 1329 helix: 1.08 (0.20), residues: 675 sheet: -0.73 (0.44), residues: 129 loop : -0.20 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 557 TYR 0.030 0.002 TYR B1001 PHE 0.015 0.002 PHE B1038 TRP 0.010 0.001 TRP B 476 HIS 0.007 0.001 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.27 (14352) covalent geometry : angle 0.96152 / 0.42 (19955) hydrogen bonds : bond 0.04557 / 2.36 ( 642) hydrogen bonds : angle 4.58635 / 1.80 ( 1765) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 0.436 Fit side-chains REVERT: B 4 LYS cc_start: 0.8742 (mttt) cc_final: 0.8444 (mtmt) REVERT: B 228 GLN cc_start: 0.6040 (OUTLIER) cc_final: 0.5814 (mt0) REVERT: B 312 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7794 (pp) REVERT: B 629 ARG cc_start: 0.7442 (mmt90) cc_final: 0.6921 (ttp80) REVERT: B 655 ARG cc_start: 0.6630 (mtm-85) cc_final: 0.5828 (tpt170) REVERT: B 682 PHE cc_start: 0.8072 (m-80) cc_final: 0.7581 (m-80) REVERT: B 694 MET cc_start: 0.8556 (mmt) cc_final: 0.8225 (mmp) REVERT: B 704 PHE cc_start: 0.6539 (m-80) cc_final: 0.6255 (m-10) REVERT: B 706 GLU cc_start: 0.8029 (tp30) cc_final: 0.7775 (pp20) REVERT: B 710 LYS cc_start: 0.8563 (mttt) cc_final: 0.8189 (tptp) REVERT: B 809 GLU cc_start: 0.7836 (tt0) cc_final: 0.7173 (mp0) REVERT: B 855 LYS cc_start: 0.4998 (mttt) cc_final: 0.4302 (mtpp) REVERT: B 879 MET cc_start: 0.4698 (mmt) cc_final: 0.4430 (mmt) REVERT: B 881 ASN cc_start: 0.8027 (m-40) cc_final: 0.7665 (p0) REVERT: B 1124 LYS cc_start: 0.8929 (mttp) cc_final: 0.8467 (mptm) REVERT: B 1219 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8369 (tt0) REVERT: B 1242 TYR cc_start: 0.5224 (OUTLIER) cc_final: 0.4069 (t80) REVERT: B 1256 GLN cc_start: 0.7522 (tp40) cc_final: 0.7048 (mm-40) REVERT: B 1296 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8002 (mptp) outliers start: 32 outliers final: 13 residues processed: 104 average time/residue: 0.7001 time to fit residues: 78.6182 Evaluate side-chains 83 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1190 VAL Chi-restraints excluded: chain B residue 1219 GLU Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1296 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 54 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 807 GLN B 817 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.135031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.085042 restraints weight = 23206.730| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.05 r_work: 0.3098 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14352 Z= 0.165 Angle : 0.721 14.468 19955 Z= 0.335 Chirality : 0.060 0.799 2283 Planarity : 0.004 0.046 2055 Dihedral : 17.118 155.637 3058 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.83 % Allowed : 12.14 % Favored : 85.04 % 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: 0.65 (0.23), residues: 1329 helix: 1.21 (0.20), residues: 675 sheet: -0.62 (0.45), residues: 124 loop : -0.19 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 951 TYR 0.033 0.001 TYR B1001 PHE 0.013 0.001 PHE B 446 TRP 0.009 0.001 TRP B 476 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (14352) covalent geometry : angle 0.72149 / 0.34 (19955) hydrogen bonds : bond 0.03965 / 2.05 ( 642) hydrogen bonds : angle 4.38167 / 1.73 ( 1765) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 68 time to evaluate : 0.492 Fit side-chains REVERT: B 4 LYS cc_start: 0.8726 (mttt) cc_final: 0.8429 (mtmt) REVERT: B 655 ARG cc_start: 0.6605 (mtm-85) cc_final: 0.5957 (tpt170) REVERT: B 664 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.7022 (ttp-110) REVERT: B 682 PHE cc_start: 0.8056 (m-80) cc_final: 0.7547 (m-80) REVERT: B 694 MET cc_start: 0.8545 (mmt) cc_final: 0.8236 (mmm) REVERT: B 706 GLU cc_start: 0.8011 (tp30) cc_final: 0.7771 (pp20) REVERT: B 710 LYS cc_start: 0.8556 (mttt) cc_final: 0.8174 (tptp) REVERT: B 809 GLU cc_start: 0.7828 (tt0) cc_final: 0.7172 (mp0) REVERT: B 855 LYS cc_start: 0.4944 (mttt) cc_final: 0.4239 (mtpp) REVERT: B 881 ASN cc_start: 0.8054 (m-40) cc_final: 0.7704 (p0) REVERT: B 948 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7706 (mtmt) REVERT: B 1069 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7833 (p) REVERT: B 1078 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7680 (ptt90) REVERT: B 1124 LYS cc_start: 0.8907 (mttp) cc_final: 0.8458 (mptm) REVERT: B 1242 TYR cc_start: 0.5128 (OUTLIER) cc_final: 0.3989 (t80) REVERT: B 1256 GLN cc_start: 0.7534 (tp40) cc_final: 0.6973 (mm-40) REVERT: B 1296 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8025 (mptp) outliers start: 34 outliers final: 14 residues processed: 96 average time/residue: 0.6821 time to fit residues: 71.0510 Evaluate side-chains 82 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 664 ARG Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 948 LYS Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1078 ARG Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1129 LYS Chi-restraints excluded: chain B residue 1190 VAL Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1296 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 31 optimal weight: 20.0000 chunk 112 optimal weight: 0.4980 chunk 90 optimal weight: 20.0000 chunk 140 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 459 ASN B 807 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.132772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.082316 restraints weight = 23136.158| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.05 r_work: 0.3029 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 14352 Z= 0.289 Angle : 0.779 14.855 19955 Z= 0.360 Chirality : 0.061 0.613 2283 Planarity : 0.004 0.050 2055 Dihedral : 17.099 156.051 3052 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.74 % Allowed : 11.72 % Favored : 84.54 % 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: 0.57 (0.23), residues: 1329 helix: 1.13 (0.20), residues: 675 sheet: -0.78 (0.44), residues: 129 loop : -0.16 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 139 TYR 0.029 0.002 TYR B1001 PHE 0.019 0.002 PHE B 518 TRP 0.009 0.002 TRP B 476 HIS 0.007 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.29 (14352) covalent geometry : angle 0.77907 / 0.36 (19955) hydrogen bonds : bond 0.04470 / 2.31 ( 642) hydrogen bonds : angle 4.42084 / 1.73 ( 1765) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 66 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: B 4 LYS cc_start: 0.8748 (mttt) cc_final: 0.8438 (mtmt) REVERT: B 629 ARG cc_start: 0.7471 (mmt-90) cc_final: 0.6765 (ttp80) REVERT: B 655 ARG cc_start: 0.6624 (mtm-85) cc_final: 0.5895 (tpt170) REVERT: B 664 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.7090 (ttp-110) REVERT: B 682 PHE cc_start: 0.8094 (m-80) cc_final: 0.7571 (m-80) REVERT: B 694 MET cc_start: 0.8547 (mmt) cc_final: 0.8241 (mmm) REVERT: B 706 GLU cc_start: 0.8020 (tp30) cc_final: 0.7777 (pp20) REVERT: B 710 LYS cc_start: 0.8567 (mttt) cc_final: 0.8186 (tptp) REVERT: B 809 GLU cc_start: 0.7824 (tt0) cc_final: 0.7168 (mp0) REVERT: B 855 LYS cc_start: 0.4967 (mttt) cc_final: 0.4263 (mtpp) REVERT: B 881 ASN cc_start: 0.8058 (m-40) cc_final: 0.7730 (p0) REVERT: B 948 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7729 (mtmt) REVERT: B 1078 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7621 (ptt90) REVERT: B 1124 LYS cc_start: 0.8890 (mttp) cc_final: 0.8421 (mptm) REVERT: B 1219 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8384 (tt0) REVERT: B 1242 TYR cc_start: 0.5123 (OUTLIER) cc_final: 0.3934 (t80) REVERT: B 1256 GLN cc_start: 0.7518 (tp40) cc_final: 0.7048 (mm-40) REVERT: B 1296 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8035 (mptp) outliers start: 45 outliers final: 20 residues processed: 105 average time/residue: 0.7038 time to fit residues: 80.4920 Evaluate side-chains 87 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 664 ARG Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 853 ASP Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 948 LYS Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1078 ARG Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1129 LYS Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1190 VAL Chi-restraints excluded: chain B residue 1219 GLU Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1296 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 36 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 817 GLN ** 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 = 0.4009 r_free = 0.4009 target = 0.134610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.084746 restraints weight = 23240.825| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.03 r_work: 0.3094 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14352 Z= 0.181 Angle : 0.693 11.674 19955 Z= 0.323 Chirality : 0.056 0.538 2283 Planarity : 0.003 0.049 2055 Dihedral : 17.249 156.436 3052 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.66 % Allowed : 13.55 % Favored : 83.79 % 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: 0.71 (0.23), residues: 1329 helix: 1.27 (0.20), residues: 675 sheet: -0.65 (0.44), residues: 124 loop : -0.17 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 395 TYR 0.031 0.001 TYR B1001 PHE 0.022 0.002 PHE B 518 TRP 0.009 0.001 TRP B 476 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (14352) covalent geometry : angle 0.69349 / 0.32 (19955) hydrogen bonds : bond 0.03884 / 2.01 ( 642) hydrogen bonds : angle 4.33206 / 1.69 ( 1765) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 4 LYS cc_start: 0.8735 (mttt) cc_final: 0.8423 (mtmm) REVERT: B 629 ARG cc_start: 0.7478 (mmt-90) cc_final: 0.6771 (ttp80) REVERT: B 631 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.6741 (mtm) REVERT: B 655 ARG cc_start: 0.6580 (mtm-85) cc_final: 0.5894 (tpt170) REVERT: B 664 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.7066 (ttp-110) REVERT: B 682 PHE cc_start: 0.8092 (m-80) cc_final: 0.7596 (m-80) REVERT: B 694 MET cc_start: 0.8532 (mmt) cc_final: 0.8231 (mmm) REVERT: B 706 GLU cc_start: 0.8006 (tp30) cc_final: 0.7780 (pp20) REVERT: B 710 LYS cc_start: 0.8558 (mttt) cc_final: 0.8188 (tptp) REVERT: B 809 GLU cc_start: 0.7862 (tt0) cc_final: 0.7124 (mp0) REVERT: B 855 LYS cc_start: 0.5048 (mttt) cc_final: 0.4255 (mtpp) REVERT: B 881 ASN cc_start: 0.8093 (m-40) cc_final: 0.7791 (p0) REVERT: B 948 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7743 (mtmt) REVERT: B 1069 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7705 (p) REVERT: B 1124 LYS cc_start: 0.8880 (mttp) cc_final: 0.8421 (mptm) REVERT: B 1242 TYR cc_start: 0.5072 (OUTLIER) cc_final: 0.3900 (t80) REVERT: B 1256 GLN cc_start: 0.7520 (tp40) cc_final: 0.6965 (mm-40) REVERT: B 1296 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8036 (mptp) outliers start: 32 outliers final: 15 residues processed: 95 average time/residue: 0.7025 time to fit residues: 72.9403 Evaluate side-chains 85 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 664 ARG Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 948 LYS Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1129 LYS Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1190 VAL Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1296 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 21 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.133942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.084451 restraints weight = 23059.019| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.01 r_work: 0.3065 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 14352 Z= 0.207 Angle : 0.694 12.188 19955 Z= 0.323 Chirality : 0.056 0.608 2283 Planarity : 0.004 0.050 2055 Dihedral : 17.242 156.639 3052 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.83 % Allowed : 13.72 % Favored : 83.46 % 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: 0.75 (0.23), residues: 1329 helix: 1.34 (0.20), residues: 676 sheet: -0.80 (0.43), residues: 129 loop : -0.15 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1303 TYR 0.029 0.001 TYR B1001 PHE 0.022 0.002 PHE B 518 TRP 0.009 0.001 TRP B 476 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.21 (14352) covalent geometry : angle 0.69429 / 0.32 (19955) hydrogen bonds : bond 0.04009 / 2.08 ( 642) hydrogen bonds : angle 4.31870 / 1.68 ( 1765) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 66 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: B 4 LYS cc_start: 0.8729 (mttt) cc_final: 0.8401 (mtmm) REVERT: B 534 MET cc_start: 0.2309 (ptt) cc_final: 0.1294 (mtm) REVERT: B 629 ARG cc_start: 0.7456 (mmt-90) cc_final: 0.6670 (ttp80) REVERT: B 631 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.6718 (mtm) REVERT: B 655 ARG cc_start: 0.6572 (mtm-85) cc_final: 0.5885 (tpt170) REVERT: B 664 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.7071 (ttp-110) REVERT: B 682 PHE cc_start: 0.8113 (m-80) cc_final: 0.7655 (m-80) REVERT: B 694 MET cc_start: 0.8539 (mmt) cc_final: 0.8235 (mmm) REVERT: B 706 GLU cc_start: 0.7998 (tp30) cc_final: 0.7759 (pp20) REVERT: B 710 LYS cc_start: 0.8556 (mttt) cc_final: 0.8180 (tptp) REVERT: B 809 GLU cc_start: 0.7851 (tt0) cc_final: 0.7129 (mp0) REVERT: B 855 LYS cc_start: 0.5029 (mttt) cc_final: 0.4232 (mtpp) REVERT: B 881 ASN cc_start: 0.8133 (m-40) cc_final: 0.7831 (p0) REVERT: B 948 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7736 (mtmt) REVERT: B 1124 LYS cc_start: 0.8873 (mttp) cc_final: 0.8393 (mptm) REVERT: B 1242 TYR cc_start: 0.5024 (OUTLIER) cc_final: 0.3808 (t80) REVERT: B 1256 GLN cc_start: 0.7487 (tp40) cc_final: 0.6945 (mm-40) REVERT: B 1296 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8013 (mptp) outliers start: 34 outliers final: 17 residues processed: 96 average time/residue: 0.6972 time to fit residues: 72.7296 Evaluate side-chains 84 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 664 ARG Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 948 LYS Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1129 LYS Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1296 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 18 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4003 r_free = 0.4003 target = 0.134269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.084195 restraints weight = 23141.448| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.06 r_work: 0.3084 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 14352 Z= 0.195 Angle : 0.684 11.336 19955 Z= 0.318 Chirality : 0.055 0.633 2283 Planarity : 0.004 0.050 2055 Dihedral : 17.253 156.412 3051 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.49 % Allowed : 14.38 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.23), residues: 1329 helix: 1.34 (0.20), residues: 676 sheet: -0.80 (0.43), residues: 129 loop : -0.17 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 557 TYR 0.030 0.001 TYR B1001 PHE 0.023 0.002 PHE B 518 TRP 0.009 0.001 TRP B 476 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (14352) covalent geometry : angle 0.68428 / 0.32 (19955) hydrogen bonds : bond 0.03942 / 2.05 ( 642) hydrogen bonds : angle 4.30058 / 1.68 ( 1765) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: B 4 LYS cc_start: 0.8738 (mttt) cc_final: 0.8423 (mtmm) REVERT: B 228 GLN cc_start: 0.6012 (OUTLIER) cc_final: 0.5812 (mp10) REVERT: B 534 MET cc_start: 0.2488 (ptt) cc_final: 0.1673 (mtm) REVERT: B 631 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.6788 (mtm) REVERT: B 655 ARG cc_start: 0.6623 (mtm-85) cc_final: 0.6021 (tpt170) REVERT: B 661 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7265 (mmm160) REVERT: B 664 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.7085 (ttp-110) REVERT: B 682 PHE cc_start: 0.8126 (m-80) cc_final: 0.7669 (m-80) REVERT: B 694 MET cc_start: 0.8540 (mmt) cc_final: 0.8214 (mmp) REVERT: B 706 GLU cc_start: 0.7993 (tp30) cc_final: 0.7769 (pp20) REVERT: B 710 LYS cc_start: 0.8566 (mttt) cc_final: 0.8193 (tptp) REVERT: B 809 GLU cc_start: 0.7862 (tt0) cc_final: 0.7110 (mp0) REVERT: B 855 LYS cc_start: 0.5048 (mttt) cc_final: 0.4280 (mtpp) REVERT: B 881 ASN cc_start: 0.8163 (m-40) cc_final: 0.7854 (p0) REVERT: B 948 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7746 (mtmt) REVERT: B 1124 LYS cc_start: 0.8881 (mttp) cc_final: 0.8421 (mptm) REVERT: B 1242 TYR cc_start: 0.5028 (OUTLIER) cc_final: 0.3741 (t80) REVERT: B 1256 GLN cc_start: 0.7511 (tp40) cc_final: 0.6965 (mm-40) REVERT: B 1296 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8050 (mptp) outliers start: 30 outliers final: 15 residues processed: 91 average time/residue: 0.6959 time to fit residues: 69.2900 Evaluate side-chains 83 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 664 ARG Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 948 LYS Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1296 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 74 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.133703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.083919 restraints weight = 23063.341| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.01 r_work: 0.3084 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 14352 Z= 0.230 Angle : 0.714 11.624 19955 Z= 0.332 Chirality : 0.057 0.655 2283 Planarity : 0.004 0.050 2055 Dihedral : 17.266 155.877 3051 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.83 % Allowed : 14.55 % Favored : 82.63 % 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: 0.73 (0.23), residues: 1329 helix: 1.32 (0.20), residues: 676 sheet: -0.81 (0.43), residues: 129 loop : -0.17 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1303 TYR 0.029 0.002 TYR B1001 PHE 0.023 0.002 PHE B 518 TRP 0.009 0.001 TRP B 476 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.23 (14352) covalent geometry : angle 0.71357 / 0.33 (19955) hydrogen bonds : bond 0.04132 / 2.14 ( 642) hydrogen bonds : angle 4.32413 / 1.69 ( 1765) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 0.455 Fit side-chains REVERT: B 4 LYS cc_start: 0.8726 (mttt) cc_final: 0.8408 (mtmm) REVERT: B 333 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8463 (p) REVERT: B 631 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.6791 (mtm) REVERT: B 655 ARG cc_start: 0.6645 (mtm-85) cc_final: 0.5988 (tpt170) REVERT: B 661 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7284 (mmm160) REVERT: B 664 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7114 (ttp-170) REVERT: B 694 MET cc_start: 0.8541 (mmt) cc_final: 0.8238 (mmm) REVERT: B 706 GLU cc_start: 0.8015 (tp30) cc_final: 0.7630 (tm-30) REVERT: B 809 GLU cc_start: 0.7968 (tt0) cc_final: 0.7735 (tt0) REVERT: B 855 LYS cc_start: 0.5098 (mttt) cc_final: 0.4617 (mtpt) REVERT: B 881 ASN cc_start: 0.8219 (m-40) cc_final: 0.7901 (p0) REVERT: B 948 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7753 (mtmt) REVERT: B 1124 LYS cc_start: 0.8869 (mttp) cc_final: 0.8398 (mptm) REVERT: B 1242 TYR cc_start: 0.5029 (OUTLIER) cc_final: 0.3731 (t80) REVERT: B 1256 GLN cc_start: 0.7514 (tp40) cc_final: 0.7031 (mm-40) REVERT: B 1296 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8044 (mptp) outliers start: 34 outliers final: 14 residues processed: 90 average time/residue: 0.7196 time to fit residues: 70.7360 Evaluate side-chains 79 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 664 ARG Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 948 LYS Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1129 LYS Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1296 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 123 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 817 GLN ** 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 = 0.4015 r_free = 0.4015 target = 0.134523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.085557 restraints weight = 23056.101| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.03 r_work: 0.3110 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14352 Z= 0.173 Angle : 0.693 11.087 19955 Z= 0.324 Chirality : 0.055 0.615 2283 Planarity : 0.003 0.050 2055 Dihedral : 17.261 155.776 3051 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.41 % Allowed : 15.21 % Favored : 82.38 % 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: 0.73 (0.23), residues: 1329 helix: 1.33 (0.20), residues: 676 sheet: -0.83 (0.43), residues: 129 loop : -0.16 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1303 TYR 0.028 0.001 TYR B1001 PHE 0.025 0.002 PHE B 518 TRP 0.009 0.001 TRP B 476 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (14352) covalent geometry : angle 0.69350 / 0.32 (19955) hydrogen bonds : bond 0.03905 / 2.03 ( 642) hydrogen bonds : angle 4.30260 / 1.67 ( 1765) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 0.535 Fit side-chains REVERT: B 4 LYS cc_start: 0.8707 (mttt) cc_final: 0.8389 (mtmm) REVERT: B 534 MET cc_start: 0.2500 (OUTLIER) cc_final: 0.2128 (ptm) REVERT: B 631 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.6784 (mtm) REVERT: B 655 ARG cc_start: 0.6503 (mtm-85) cc_final: 0.5996 (tpt170) REVERT: B 661 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7265 (mmm160) REVERT: B 664 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7103 (ttp-170) REVERT: B 694 MET cc_start: 0.8532 (mmt) cc_final: 0.8212 (mmp) REVERT: B 809 GLU cc_start: 0.7953 (tt0) cc_final: 0.7718 (tt0) REVERT: B 855 LYS cc_start: 0.5172 (mttt) cc_final: 0.4672 (mtpt) REVERT: B 879 MET cc_start: 0.1157 (OUTLIER) cc_final: 0.0775 (ptt) REVERT: B 881 ASN cc_start: 0.8239 (m-40) cc_final: 0.7926 (p0) REVERT: B 948 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7753 (mtmt) REVERT: B 1124 LYS cc_start: 0.8870 (mttp) cc_final: 0.8387 (mptm) REVERT: B 1242 TYR cc_start: 0.4973 (OUTLIER) cc_final: 0.3665 (t80) REVERT: B 1256 GLN cc_start: 0.7494 (tp40) cc_final: 0.7001 (mm-40) REVERT: B 1296 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8046 (mptp) outliers start: 29 outliers final: 12 residues processed: 81 average time/residue: 0.7132 time to fit residues: 63.1962 Evaluate side-chains 76 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 664 ARG Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 879 MET Chi-restraints excluded: chain B residue 948 LYS Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1129 LYS Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1296 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 124 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 64 optimal weight: 20.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 888 ASN ** B1262 HIS ** 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 = 0.4011 r_free = 0.4011 target = 0.134246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.087336 restraints weight = 23047.977| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.31 r_work: 0.3074 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 14352 Z= 0.187 Angle : 0.701 12.510 19955 Z= 0.327 Chirality : 0.055 0.605 2283 Planarity : 0.004 0.050 2055 Dihedral : 17.218 156.019 3051 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.66 % Allowed : 15.88 % Favored : 82.46 % 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: 0.72 (0.23), residues: 1329 helix: 1.31 (0.20), residues: 676 sheet: -0.80 (0.43), residues: 129 loop : -0.16 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1303 TYR 0.028 0.001 TYR B1001 PHE 0.025 0.002 PHE B 518 TRP 0.008 0.001 TRP B 476 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (14352) covalent geometry : angle 0.70106 / 0.33 (19955) hydrogen bonds : bond 0.03917 / 2.03 ( 642) hydrogen bonds : angle 4.28879 / 1.67 ( 1765) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: B 4 LYS cc_start: 0.8729 (mttt) cc_final: 0.8399 (mtmm) REVERT: B 534 MET cc_start: 0.2644 (OUTLIER) cc_final: 0.2225 (ptm) REVERT: B 557 ARG cc_start: 0.7533 (tpp80) cc_final: 0.7320 (tpp80) REVERT: B 631 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.6778 (mtm) REVERT: B 655 ARG cc_start: 0.6527 (mtm-85) cc_final: 0.6027 (tpt170) REVERT: B 661 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7307 (mmm160) REVERT: B 664 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7113 (ttp-110) REVERT: B 694 MET cc_start: 0.8548 (mmt) cc_final: 0.8217 (mmm) REVERT: B 881 ASN cc_start: 0.8259 (m-40) cc_final: 0.7937 (p0) REVERT: B 948 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7756 (mtmt) REVERT: B 1124 LYS cc_start: 0.8893 (mttp) cc_final: 0.8397 (mptm) REVERT: B 1242 TYR cc_start: 0.4984 (OUTLIER) cc_final: 0.3663 (t80) REVERT: B 1256 GLN cc_start: 0.7480 (tp40) cc_final: 0.6990 (mm-40) REVERT: B 1296 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8047 (mptp) outliers start: 20 outliers final: 12 residues processed: 72 average time/residue: 0.7455 time to fit residues: 58.4705 Evaluate side-chains 76 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 664 ARG Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 948 LYS Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1129 LYS Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1296 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 139 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 140 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 34 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1262 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.135233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.088746 restraints weight = 23034.197| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.22 r_work: 0.3099 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14352 Z= 0.153 Angle : 0.671 12.677 19955 Z= 0.313 Chirality : 0.053 0.565 2283 Planarity : 0.003 0.050 2055 Dihedral : 17.171 156.518 3049 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.58 % Allowed : 16.13 % Favored : 82.29 % 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: 0.85 (0.23), residues: 1329 helix: 1.40 (0.20), residues: 676 sheet: -0.60 (0.44), residues: 124 loop : -0.13 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1303 TYR 0.026 0.001 TYR B1001 PHE 0.025 0.001 PHE B 518 TRP 0.008 0.001 TRP B 476 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (14352) covalent geometry : angle 0.67083 / 0.31 (19955) hydrogen bonds : bond 0.03682 / 1.91 ( 642) hydrogen bonds : angle 4.25753 / 1.66 ( 1765) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6401.18 seconds wall clock time: 109 minutes 38.23 seconds (6578.23 seconds total)