Starting phenix.real_space_refine on Sun Apr 5 22:33:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z4l_14501/04_2026/7z4l_14501.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z4l_14501/04_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 { model { file = "/net/cci-nas-00/data/ceres_data/7z4l_14501/04_2026/7z4l_14501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z4l_14501/04_2026/7z4l_14501.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z4l_14501/04_2026/7z4l_14501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z4l_14501/04_2026/7z4l_14501.map" } 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-2.1rc1-6017/lib/python3.9/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: {'RNA': 96} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 51, 'rna3p_pyr': 33} Link IDs: {'rna2p': 12, 'rna3p': 83} 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: 3.11, per 1000 atoms: 0.22 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: 1.46 Conformation dependent library (CDL) restraints added in 422.5 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: 2.25 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: 3.60 Time building geometry restraints manager: 1.79 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=" 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=" N THR B 555 " pdb=" CA THR B 555 " ideal model delta sigma weight residual 1.454 1.477 -0.023 1.42e-02 4.96e+03 2.56e+00 bond pdb=" C GLY B 687 " pdb=" O GLY B 687 " ideal model delta sigma weight residual 1.236 1.228 0.008 5.30e-03 3.56e+04 2.47e+00 bond pdb=" CA ASP B 10 " pdb=" C ASP B 10 " ideal model delta sigma weight residual 1.526 1.508 0.017 1.20e-02 6.94e+03 2.09e+00 bond pdb=" C ILE B1110 " pdb=" N LEU B1111 " ideal model delta sigma weight residual 1.340 1.267 0.074 5.87e-02 2.90e+02 1.57e+00 ... (remaining 14347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 19345 1.30 - 2.59: 520 2.59 - 3.89: 78 3.89 - 5.18: 9 5.18 - 6.48: 3 Bond angle restraints: 19955 Sorted by residual: angle pdb=" N THR B 555 " pdb=" CA THR B 555 " pdb=" CB THR B 555 " ideal model delta sigma weight residual 110.88 114.46 -3.58 1.38e+00 5.25e-01 6.75e+00 angle pdb=" CA TYR B 155 " pdb=" CB TYR B 155 " pdb=" CG TYR B 155 " ideal model delta sigma weight residual 113.90 109.45 4.45 1.80e+00 3.09e-01 6.11e+00 angle pdb=" C VAL B 992 " pdb=" N VAL B 993 " pdb=" CA VAL B 993 " ideal model delta sigma weight residual 120.56 117.71 2.85 1.28e+00 6.10e-01 4.96e+00 angle pdb=" C ASP B 10 " pdb=" CA ASP B 10 " pdb=" CB ASP B 10 " ideal model delta sigma weight residual 111.17 107.94 3.23 1.54e+00 4.22e-01 4.39e+00 angle pdb=" CA GLY B1011 " pdb=" C GLY B1011 " pdb=" N ASP B1012 " ideal model delta sigma weight residual 115.62 117.20 -1.58 7.60e-01 1.73e+00 4.32e+00 ... (remaining 19950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 7690 17.92 - 35.84: 581 35.84 - 53.76: 274 53.76 - 71.68: 157 71.68 - 89.60: 24 Dihedral angle restraints: 8726 sinusoidal: 4792 harmonic: 3934 Sorted by residual: dihedral pdb=" CA ARG B1333 " pdb=" C ARG B1333 " pdb=" N LYS B1334 " pdb=" CA LYS B1334 " ideal model delta harmonic sigma weight residual 180.00 159.28 20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ASN B 497 " pdb=" C ASN B 497 " pdb=" N PHE B 498 " pdb=" CA PHE B 498 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA PHE B 86 " pdb=" C PHE B 86 " pdb=" N SER B 87 " pdb=" CA SER B 87 " ideal model delta harmonic sigma weight residual -180.00 -162.44 -17.56 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 8723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1809 0.046 - 0.093: 399 0.093 - 0.139: 71 0.139 - 0.185: 3 0.185 - 0.232: 1 Chirality restraints: 2283 Sorted by residual: chirality pdb=" CA ASP B 10 " pdb=" N ASP B 10 " pdb=" C ASP B 10 " pdb=" CB ASP B 10 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB VAL B 743 " pdb=" CA VAL B 743 " pdb=" CG1 VAL B 743 " pdb=" CG2 VAL B 743 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.32e-01 chirality pdb=" C1' A A 51 " pdb=" O4' A A 51 " pdb=" C2' A A 51 " pdb=" N9 A A 51 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.62e-01 ... (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: 8.730 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: 0.560 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.510 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:9.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 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 : 0.005 0.074 14352 Z= 0.247 Angle : 0.527 6.476 19955 Z= 0.291 Chirality : 0.039 0.232 2283 Planarity : 0.004 0.031 2055 Dihedral : 17.437 89.597 6180 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 covalent geometry : bond 0.00541 (14352) covalent geometry : angle 0.52697 (19955) hydrogen bonds : bond 0.11888 ( 642) hydrogen bonds : angle 5.47487 ( 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 : 0.486 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: 0.7686 time to fit residues: 141.3849 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 : 0.490 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 14 ASN B 113 HIS B 116 HIS B 129 HIS B 228 GLN B 459 ASN B 805 GLN B 807 GLN ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 885 GLN B 920 GLN B1041 ASN ** B1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.132982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.081981 restraints weight = 23125.831| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.08 r_work: 0.3044 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 14352 Z= 0.247 Angle : 0.570 9.226 19955 Z= 0.303 Chirality : 0.040 0.160 2283 Planarity : 0.004 0.041 2055 Dihedral : 18.949 91.897 3356 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.99 % Allowed : 11.39 % Favored : 85.62 % 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: 0.60 (0.23), residues: 1329 helix: 1.16 (0.20), residues: 675 sheet: -0.73 (0.43), residues: 129 loop : -0.17 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 557 TYR 0.028 0.002 TYR B1001 PHE 0.021 0.002 PHE B1038 TRP 0.010 0.001 TRP B 476 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00556 (14352) covalent geometry : angle 0.57038 (19955) hydrogen bonds : bond 0.04357 ( 642) hydrogen bonds : angle 4.50391 ( 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 114 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 78 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: B 4 LYS cc_start: 0.8737 (mttt) cc_final: 0.8438 (mtmt) REVERT: B 228 GLN cc_start: 0.6042 (OUTLIER) cc_final: 0.5823 (mt0) REVERT: B 312 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7798 (pp) REVERT: B 629 ARG cc_start: 0.7479 (mmt90) cc_final: 0.6943 (ttp80) REVERT: B 655 ARG cc_start: 0.6628 (mtm-85) cc_final: 0.5830 (tpt170) REVERT: B 682 PHE cc_start: 0.8095 (m-80) cc_final: 0.7620 (m-80) REVERT: B 694 MET cc_start: 0.8555 (mmt) cc_final: 0.8246 (mmm) REVERT: B 704 PHE cc_start: 0.6543 (m-80) cc_final: 0.6258 (m-10) REVERT: B 706 GLU cc_start: 0.8012 (tp30) cc_final: 0.7768 (pp20) REVERT: B 710 LYS cc_start: 0.8562 (mttt) cc_final: 0.8155 (tptp) REVERT: B 809 GLU cc_start: 0.7866 (tt0) cc_final: 0.7177 (mp0) REVERT: B 855 LYS cc_start: 0.4932 (mttt) cc_final: 0.4243 (mtpp) REVERT: B 881 ASN cc_start: 0.8042 (m-40) cc_final: 0.7700 (p0) REVERT: B 948 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7718 (mtmt) REVERT: B 1124 LYS cc_start: 0.8895 (mttp) cc_final: 0.8431 (mptm) REVERT: B 1219 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8327 (tt0) REVERT: B 1242 TYR cc_start: 0.5202 (OUTLIER) cc_final: 0.4023 (t80) REVERT: B 1256 GLN cc_start: 0.7504 (tp40) cc_final: 0.6974 (mm-40) REVERT: B 1296 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8009 (mptp) outliers start: 36 outliers final: 12 residues processed: 107 average time/residue: 0.7880 time to fit residues: 90.6786 Evaluate side-chains 82 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 261 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 762 GLU 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 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: 4.9990 chunk 28 optimal weight: 7.9990 chunk 125 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 129 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 GLN B 807 GLN ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1262 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.134456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.084037 restraints weight = 23242.788| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.06 r_work: 0.3081 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14352 Z= 0.153 Angle : 0.498 8.186 19955 Z= 0.266 Chirality : 0.036 0.144 2283 Planarity : 0.003 0.045 2055 Dihedral : 18.882 91.275 3355 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.58 % Allowed : 12.30 % Favored : 85.12 % 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: 0.78 (0.23), residues: 1329 helix: 1.34 (0.20), residues: 675 sheet: -0.62 (0.44), residues: 124 loop : -0.15 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 535 TYR 0.031 0.001 TYR B1001 PHE 0.026 0.001 PHE B 185 TRP 0.010 0.001 TRP B 476 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00340 (14352) covalent geometry : angle 0.49793 (19955) hydrogen bonds : bond 0.03715 ( 642) hydrogen bonds : angle 4.35876 ( 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 101 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: B 4 LYS cc_start: 0.8749 (mttt) cc_final: 0.8457 (mtmt) REVERT: B 629 ARG cc_start: 0.7507 (mmt90) cc_final: 0.6943 (ttp80) REVERT: B 655 ARG cc_start: 0.6633 (mtm-85) cc_final: 0.5864 (tpt170) REVERT: B 664 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.7048 (ttp-110) REVERT: B 682 PHE cc_start: 0.8076 (m-80) cc_final: 0.7584 (m-80) REVERT: B 694 MET cc_start: 0.8542 (mmt) cc_final: 0.8240 (mmm) REVERT: B 706 GLU cc_start: 0.8011 (tp30) cc_final: 0.7778 (pp20) REVERT: B 710 LYS cc_start: 0.8559 (mttt) cc_final: 0.8173 (tptp) REVERT: B 809 GLU cc_start: 0.7844 (tt0) cc_final: 0.7160 (mp0) REVERT: B 855 LYS cc_start: 0.4971 (mttt) cc_final: 0.4225 (mtpt) REVERT: B 881 ASN cc_start: 0.8085 (m-40) cc_final: 0.7746 (p0) REVERT: B 1049 GLU cc_start: 0.6702 (pp20) cc_final: 0.6405 (OUTLIER) REVERT: B 1069 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7836 (p) REVERT: B 1124 LYS cc_start: 0.8880 (mttp) cc_final: 0.8431 (mptm) REVERT: B 1242 TYR cc_start: 0.5080 (OUTLIER) cc_final: 0.3867 (t80) REVERT: B 1256 GLN cc_start: 0.7518 (tp40) cc_final: 0.6960 (mm-40) REVERT: B 1296 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8035 (mptp) outliers start: 31 outliers final: 13 residues processed: 97 average time/residue: 0.7285 time to fit residues: 76.4520 Evaluate side-chains 77 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN 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 740 THR Chi-restraints excluded: chain B residue 870 VAL 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 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: 7.9990 chunk 112 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 140 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3963 r_free = 0.3963 target = 0.131516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.080633 restraints weight = 23113.238| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.09 r_work: 0.2996 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 14352 Z= 0.335 Angle : 0.602 8.130 19955 Z= 0.317 Chirality : 0.043 0.194 2283 Planarity : 0.004 0.049 2055 Dihedral : 18.954 93.116 3349 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.82 % Allowed : 12.05 % Favored : 84.12 % 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 (0.23), residues: 1329 helix: 1.07 (0.20), residues: 675 sheet: -1.00 (0.49), residues: 104 loop : -0.19 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 403 TYR 0.030 0.002 TYR B1001 PHE 0.017 0.002 PHE B1038 TRP 0.010 0.002 TRP B 476 HIS 0.007 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00756 (14352) covalent geometry : angle 0.60229 (19955) hydrogen bonds : bond 0.04583 ( 642) hydrogen bonds : angle 4.47383 ( 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 116 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 70 time to evaluate : 0.482 Fit side-chains REVERT: B 4 LYS cc_start: 0.8770 (mttt) cc_final: 0.8451 (mtmm) REVERT: B 629 ARG cc_start: 0.7467 (mmt90) cc_final: 0.6845 (ttp80) REVERT: B 637 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8772 (mtpt) REVERT: B 655 ARG cc_start: 0.6625 (mtm-85) cc_final: 0.5907 (tpt170) REVERT: B 664 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.7126 (ttp-170) REVERT: B 682 PHE cc_start: 0.8149 (m-80) cc_final: 0.7690 (m-80) REVERT: B 694 MET cc_start: 0.8540 (mmt) cc_final: 0.8233 (mmm) REVERT: B 704 PHE cc_start: 0.6475 (m-80) cc_final: 0.6163 (m-10) REVERT: B 706 GLU cc_start: 0.8010 (tp30) cc_final: 0.7766 (pp20) REVERT: B 710 LYS cc_start: 0.8565 (mttt) cc_final: 0.8173 (tptp) REVERT: B 809 GLU cc_start: 0.7844 (tt0) cc_final: 0.7113 (mp0) REVERT: B 855 LYS cc_start: 0.5003 (mttt) cc_final: 0.4229 (mtpp) REVERT: B 881 ASN cc_start: 0.8099 (m-40) cc_final: 0.7763 (p0) REVERT: B 948 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7762 (mtmt) REVERT: B 1049 GLU cc_start: 0.6689 (pp20) cc_final: 0.6354 (OUTLIER) REVERT: B 1124 LYS cc_start: 0.8860 (mttp) cc_final: 0.8383 (mptm) REVERT: B 1219 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8380 (tt0) REVERT: B 1242 TYR cc_start: 0.5157 (OUTLIER) cc_final: 0.3933 (t80) REVERT: B 1256 GLN cc_start: 0.7505 (tp40) cc_final: 0.7052 (mm-40) REVERT: B 1296 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8030 (mptp) outliers start: 46 outliers final: 18 residues processed: 109 average time/residue: 0.7080 time to fit residues: 83.9936 Evaluate side-chains 89 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 480 GLU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 637 LYS 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 1129 LYS Chi-restraints excluded: chain B residue 1149 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: 2.9990 chunk 89 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 23 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 119 optimal weight: 0.0020 chunk 88 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 HIS 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 = 0.135075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.085235 restraints weight = 23293.901| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.06 r_work: 0.3082 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14352 Z= 0.123 Angle : 0.487 8.366 19955 Z= 0.257 Chirality : 0.035 0.143 2283 Planarity : 0.003 0.049 2055 Dihedral : 18.823 91.511 3349 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.49 % Allowed : 13.72 % 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: 0.85 (0.23), residues: 1329 helix: 1.42 (0.20), residues: 675 sheet: -0.65 (0.44), residues: 124 loop : -0.14 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 395 TYR 0.026 0.001 TYR B1001 PHE 0.026 0.001 PHE B 185 TRP 0.010 0.001 TRP B 476 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00269 (14352) covalent geometry : angle 0.48690 (19955) hydrogen bonds : bond 0.03429 ( 642) hydrogen bonds : angle 4.23080 ( 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 96 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.455 Fit side-chains REVERT: B 4 LYS cc_start: 0.8734 (mttt) cc_final: 0.8420 (mtmm) REVERT: B 534 MET cc_start: 0.2462 (ptt) cc_final: 0.1550 (mtm) REVERT: B 631 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6692 (mtm) REVERT: B 637 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8726 (mtpt) REVERT: B 655 ARG cc_start: 0.6569 (mtm-85) cc_final: 0.5985 (tpt170) REVERT: B 661 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7202 (mmm160) REVERT: B 664 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.7020 (ttp-110) REVERT: B 682 PHE cc_start: 0.8123 (m-80) cc_final: 0.7651 (m-80) REVERT: B 694 MET cc_start: 0.8535 (mmt) cc_final: 0.8219 (mmp) REVERT: B 706 GLU cc_start: 0.7980 (tp30) cc_final: 0.7765 (pp20) REVERT: B 710 LYS cc_start: 0.8562 (mttt) cc_final: 0.8184 (tptp) REVERT: B 796 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.5922 (pt) REVERT: B 809 GLU cc_start: 0.7846 (tt0) cc_final: 0.7085 (mp0) REVERT: B 855 LYS cc_start: 0.5028 (mttt) cc_final: 0.4257 (mtpp) REVERT: B 881 ASN cc_start: 0.8136 (m-40) cc_final: 0.7840 (p0) REVERT: B 948 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7754 (mtmt) REVERT: B 1049 GLU cc_start: 0.6632 (pp20) cc_final: 0.6296 (OUTLIER) REVERT: B 1069 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7684 (p) REVERT: B 1078 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7598 (ptt90) REVERT: B 1124 LYS cc_start: 0.8857 (mttp) cc_final: 0.8373 (mptm) REVERT: B 1242 TYR cc_start: 0.4950 (OUTLIER) cc_final: 0.3650 (t80) REVERT: B 1256 GLN cc_start: 0.7477 (tp40) cc_final: 0.6927 (mm-40) REVERT: B 1296 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8019 (mptp) outliers start: 30 outliers final: 14 residues processed: 93 average time/residue: 0.7494 time to fit residues: 75.3984 Evaluate side-chains 84 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 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 631 MET Chi-restraints excluded: chain B residue 637 LYS 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 796 LEU 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 1149 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: 5.9990 chunk 127 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 0.0010 overall best weight: 3.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3972 r_free = 0.3972 target = 0.132085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.081483 restraints weight = 22975.133| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.07 r_work: 0.3014 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 14352 Z= 0.288 Angle : 0.576 8.795 19955 Z= 0.300 Chirality : 0.041 0.265 2283 Planarity : 0.004 0.050 2055 Dihedral : 18.837 92.163 3349 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.66 % Allowed : 13.47 % Favored : 82.88 % 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: 1.29 (0.20), residues: 675 sheet: -0.93 (0.48), residues: 104 loop : -0.16 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 395 TYR 0.025 0.002 TYR B1001 PHE 0.018 0.002 PHE B1038 TRP 0.010 0.002 TRP B 476 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00648 (14352) covalent geometry : angle 0.57583 (19955) hydrogen bonds : bond 0.04216 ( 642) hydrogen bonds : angle 4.33428 ( 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 111 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 67 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: B 4 LYS cc_start: 0.8766 (mttt) cc_final: 0.8452 (mtmm) REVERT: B 631 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.6825 (mtm) REVERT: B 637 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8737 (mtpt) REVERT: B 655 ARG cc_start: 0.6669 (mtm-85) cc_final: 0.6059 (tpt170) REVERT: B 661 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7353 (mmm160) REVERT: B 664 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.7139 (ttp-170) REVERT: B 694 MET cc_start: 0.8542 (mmt) cc_final: 0.8283 (mmp) REVERT: B 706 GLU cc_start: 0.7994 (tp30) cc_final: 0.7616 (tm-30) REVERT: B 796 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.5918 (pt) REVERT: B 881 ASN cc_start: 0.8147 (m-40) cc_final: 0.7869 (p0) REVERT: B 948 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7776 (mtmt) REVERT: B 1049 GLU cc_start: 0.6681 (pp20) cc_final: 0.6343 (OUTLIER) REVERT: B 1078 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7654 (ptt90) REVERT: B 1124 LYS cc_start: 0.8851 (mttp) cc_final: 0.8379 (mptm) REVERT: B 1242 TYR cc_start: 0.5061 (OUTLIER) cc_final: 0.3759 (t80) REVERT: B 1256 GLN cc_start: 0.7509 (tp40) cc_final: 0.7040 (mm-40) REVERT: B 1296 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8077 (mptp) outliers start: 44 outliers final: 14 residues processed: 105 average time/residue: 0.7420 time to fit residues: 84.3737 Evaluate side-chains 85 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 637 LYS 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 796 LEU 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 1078 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 76 optimal weight: 0.0970 chunk 55 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4006 r_free = 0.4006 target = 0.134677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.084661 restraints weight = 23213.626| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.05 r_work: 0.3074 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2135 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= 0.135 Angle : 0.507 9.162 19955 Z= 0.266 Chirality : 0.036 0.249 2283 Planarity : 0.003 0.049 2055 Dihedral : 18.795 91.476 3347 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.33 % Allowed : 15.21 % 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: 0.92 (0.23), residues: 1329 helix: 1.46 (0.20), residues: 675 sheet: -0.58 (0.44), residues: 124 loop : -0.10 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1303 TYR 0.027 0.001 TYR B1001 PHE 0.017 0.001 PHE B 185 TRP 0.010 0.001 TRP B 476 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00299 (14352) covalent geometry : angle 0.50722 (19955) hydrogen bonds : bond 0.03475 ( 642) hydrogen bonds : angle 4.20403 ( 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 90 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 0.529 Fit side-chains REVERT: B 4 LYS cc_start: 0.8729 (mttt) cc_final: 0.8411 (mtpt) REVERT: B 631 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.6732 (mtm) REVERT: B 637 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8683 (mtpt) REVERT: B 655 ARG cc_start: 0.6618 (mtm-85) cc_final: 0.6028 (tpt170) REVERT: B 661 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7255 (mmm160) REVERT: B 664 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.7045 (ttp-110) REVERT: B 694 MET cc_start: 0.8531 (mmt) cc_final: 0.8207 (mmm) REVERT: B 796 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.5921 (pt) REVERT: B 855 LYS cc_start: 0.4935 (mttt) cc_final: 0.4501 (mtpt) REVERT: B 881 ASN cc_start: 0.8215 (m-40) cc_final: 0.7910 (p0) REVERT: B 900 LEU cc_start: 0.5533 (OUTLIER) cc_final: 0.5204 (mp) REVERT: B 948 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7749 (mtmt) REVERT: B 1049 GLU cc_start: 0.6639 (pp20) cc_final: 0.6301 (OUTLIER) REVERT: B 1124 LYS cc_start: 0.8849 (mttp) cc_final: 0.8357 (mptm) REVERT: B 1242 TYR cc_start: 0.4917 (OUTLIER) cc_final: 0.3566 (t80) REVERT: B 1256 GLN cc_start: 0.7471 (tp40) cc_final: 0.6926 (mm-40) REVERT: B 1296 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8026 (mptp) outliers start: 28 outliers final: 10 residues processed: 84 average time/residue: 0.7814 time to fit residues: 71.0247 Evaluate side-chains 77 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 637 LYS 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 796 LEU Chi-restraints excluded: chain B residue 900 LEU 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: 4.9990 chunk 26 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 888 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.133737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.083439 restraints weight = 23033.394| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.04 r_work: 0.3050 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2162 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= 0.181 Angle : 0.533 10.726 19955 Z= 0.277 Chirality : 0.037 0.304 2283 Planarity : 0.003 0.050 2055 Dihedral : 18.734 91.112 3347 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.49 % Allowed : 15.38 % Favored : 82.13 % 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: 0.89 (0.23), residues: 1329 helix: 1.45 (0.20), residues: 675 sheet: -0.81 (0.46), residues: 118 loop : -0.08 (0.26), residues: 536 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 B1038 TRP 0.010 0.001 TRP B 476 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00406 (14352) covalent geometry : angle 0.53267 (19955) hydrogen bonds : bond 0.03736 ( 642) hydrogen bonds : angle 4.20401 ( 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 93 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 63 time to evaluate : 0.432 Fit side-chains REVERT: B 4 LYS cc_start: 0.8733 (mttt) cc_final: 0.8404 (mtpt) REVERT: B 333 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8427 (p) REVERT: B 631 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.6694 (mtm) REVERT: B 637 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8667 (mtpt) REVERT: B 655 ARG cc_start: 0.6641 (mtm-85) cc_final: 0.6009 (tpt170) REVERT: B 661 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7298 (mmm160) REVERT: B 664 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.7047 (ttp-110) REVERT: B 694 MET cc_start: 0.8527 (mmt) cc_final: 0.8251 (mmp) REVERT: B 807 GLN cc_start: 0.6346 (OUTLIER) cc_final: 0.5920 (tp-100) REVERT: B 809 GLU cc_start: 0.7915 (tt0) cc_final: 0.7250 (mp0) REVERT: B 855 LYS cc_start: 0.4985 (mttt) cc_final: 0.4307 (mtpt) REVERT: B 881 ASN cc_start: 0.8262 (m-40) cc_final: 0.7954 (p0) REVERT: B 900 LEU cc_start: 0.5574 (OUTLIER) cc_final: 0.5285 (mp) REVERT: B 948 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7742 (mtmt) REVERT: B 1049 GLU cc_start: 0.6649 (pp20) cc_final: 0.6310 (OUTLIER) REVERT: B 1124 LYS cc_start: 0.8842 (mttp) cc_final: 0.8358 (mptm) REVERT: B 1242 TYR cc_start: 0.4937 (OUTLIER) cc_final: 0.3579 (t80) REVERT: B 1256 GLN cc_start: 0.7476 (tp40) cc_final: 0.7004 (mm-40) REVERT: B 1296 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8041 (mptp) outliers start: 30 outliers final: 13 residues processed: 83 average time/residue: 0.7419 time to fit residues: 66.7768 Evaluate side-chains 81 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 301 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 637 LYS 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 807 GLN Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 900 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 123 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 102 optimal weight: 0.0570 chunk 31 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 695 GLN ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.136466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.087433 restraints weight = 23336.370| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.04 r_work: 0.3127 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14352 Z= 0.109 Angle : 0.497 10.906 19955 Z= 0.258 Chirality : 0.035 0.346 2283 Planarity : 0.003 0.049 2055 Dihedral : 18.638 89.530 3347 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.91 % Allowed : 15.88 % Favored : 82.21 % 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: 1.07 (0.23), residues: 1329 helix: 1.60 (0.20), residues: 676 sheet: -0.41 (0.45), residues: 124 loop : -0.08 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1303 TYR 0.024 0.001 TYR B1001 PHE 0.014 0.001 PHE B 185 TRP 0.010 0.001 TRP B 476 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00237 (14352) covalent geometry : angle 0.49663 (19955) hydrogen bonds : bond 0.03225 ( 642) hydrogen bonds : angle 4.05930 ( 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 99 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: B 4 LYS cc_start: 0.8726 (mttt) cc_final: 0.8416 (mtpt) REVERT: B 563 GLN cc_start: 0.8343 (mt0) cc_final: 0.7860 (tt0) REVERT: B 631 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6630 (mtm) REVERT: B 637 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8612 (mtpt) REVERT: B 655 ARG cc_start: 0.6503 (mtm-85) cc_final: 0.6044 (tpt170) REVERT: B 664 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.7004 (ttp-170) REVERT: B 691 ARG cc_start: 0.6870 (mtm180) cc_final: 0.6600 (ptt180) REVERT: B 694 MET cc_start: 0.8519 (mmt) cc_final: 0.8252 (mmp) REVERT: B 796 LEU cc_start: 0.6386 (OUTLIER) cc_final: 0.5870 (pt) REVERT: B 879 MET cc_start: 0.1084 (OUTLIER) cc_final: 0.0882 (ptt) REVERT: B 881 ASN cc_start: 0.8281 (m-40) cc_final: 0.7991 (p0) REVERT: B 900 LEU cc_start: 0.5421 (OUTLIER) cc_final: 0.5164 (mp) REVERT: B 948 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7771 (mtmt) REVERT: B 1049 GLU cc_start: 0.6666 (pp20) cc_final: 0.6346 (OUTLIER) REVERT: B 1124 LYS cc_start: 0.8817 (mttp) cc_final: 0.8345 (mptm) REVERT: B 1242 TYR cc_start: 0.4803 (OUTLIER) cc_final: 0.3385 (t80) REVERT: B 1256 GLN cc_start: 0.7466 (tp40) cc_final: 0.6920 (mm-40) REVERT: B 1296 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8077 (mptp) outliers start: 23 outliers final: 10 residues processed: 89 average time/residue: 0.7587 time to fit residues: 73.0198 Evaluate side-chains 82 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 637 LYS Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 664 ARG Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 879 MET Chi-restraints excluded: chain B residue 900 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 124 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 114 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 807 GLN ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.131810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.081825 restraints weight = 23191.873| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.05 r_work: 0.3013 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 14352 Z= 0.299 Angle : 0.608 10.313 19955 Z= 0.314 Chirality : 0.042 0.348 2283 Planarity : 0.004 0.052 2055 Dihedral : 18.724 91.950 3342 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.08 % Allowed : 16.46 % Favored : 81.46 % 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: 0.81 (0.23), residues: 1329 helix: 1.35 (0.20), residues: 676 sheet: -0.76 (0.49), residues: 104 loop : -0.10 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 661 TYR 0.027 0.002 TYR B1001 PHE 0.032 0.002 PHE B1038 TRP 0.010 0.002 TRP B1074 HIS 0.006 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00672 (14352) covalent geometry : angle 0.60806 (19955) hydrogen bonds : bond 0.04307 ( 642) hydrogen bonds : angle 4.28228 ( 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 87 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.462 Fit side-chains REVERT: B 4 LYS cc_start: 0.8769 (mttt) cc_final: 0.8448 (mtpt) REVERT: B 333 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8481 (p) REVERT: B 631 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.6815 (mtm) REVERT: B 655 ARG cc_start: 0.6538 (mtm-85) cc_final: 0.6082 (tpt170) REVERT: B 664 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.7131 (ttp-110) REVERT: B 691 ARG cc_start: 0.6965 (mtm180) cc_final: 0.6682 (ptt180) REVERT: B 694 MET cc_start: 0.8528 (mmt) cc_final: 0.8276 (mmp) REVERT: B 796 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.5896 (pt) REVERT: B 855 LYS cc_start: 0.5049 (mttt) cc_final: 0.4507 (mtpt) REVERT: B 881 ASN cc_start: 0.8307 (m-40) cc_final: 0.8019 (p0) REVERT: B 900 LEU cc_start: 0.5712 (OUTLIER) cc_final: 0.5447 (mp) REVERT: B 948 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7744 (mtmt) REVERT: B 1049 GLU cc_start: 0.6720 (pp20) cc_final: 0.6402 (OUTLIER) REVERT: B 1124 LYS cc_start: 0.8840 (mttp) cc_final: 0.8361 (mptm) REVERT: B 1242 TYR cc_start: 0.5019 (OUTLIER) cc_final: 0.3674 (t80) REVERT: B 1256 GLN cc_start: 0.7473 (tp40) cc_final: 0.6972 (mm-40) REVERT: B 1296 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8103 (mptp) REVERT: B 1303 ARG cc_start: 0.7955 (ttt-90) cc_final: 0.7748 (tpt-90) outliers start: 25 outliers final: 12 residues processed: 79 average time/residue: 0.7005 time to fit residues: 60.2978 Evaluate side-chains 79 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 301 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 664 ARG Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 900 LEU Chi-restraints excluded: chain B residue 948 LYS Chi-restraints excluded: chain B residue 950 ILE Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1069 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 139 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 888 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.134500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.084585 restraints weight = 23065.561| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.05 r_work: 0.3071 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14352 Z= 0.145 Angle : 0.527 10.407 19955 Z= 0.272 Chirality : 0.037 0.330 2283 Planarity : 0.003 0.049 2055 Dihedral : 18.690 91.347 3342 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.83 % Allowed : 17.04 % Favored : 81.13 % 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: 0.97 (0.23), residues: 1329 helix: 1.48 (0.20), residues: 676 sheet: -0.45 (0.44), residues: 124 loop : -0.07 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 661 TYR 0.025 0.001 TYR B1001 PHE 0.024 0.001 PHE B 518 TRP 0.011 0.001 TRP B 476 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00325 (14352) covalent geometry : angle 0.52656 (19955) hydrogen bonds : bond 0.03480 ( 642) hydrogen bonds : angle 4.15080 ( 1765) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6486.58 seconds wall clock time: 111 minutes 0.63 seconds (6660.63 seconds total)