Starting phenix.real_space_refine on Tue Feb 11 04:25:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j9e_6240/02_2025/3j9e_6240.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j9e_6240/02_2025/3j9e_6240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3j9e_6240/02_2025/3j9e_6240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j9e_6240/02_2025/3j9e_6240.map" model { file = "/net/cci-nas-00/data/ceres_data/3j9e_6240/02_2025/3j9e_6240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j9e_6240/02_2025/3j9e_6240.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 ------------------------------------------------------------------------------- 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= 0.008 sd= 0.212 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: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2584 2.51 5 N 722 2.21 5 O 777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4098 Number of models: 1 Model: "" Number of chains: 1 Chain: "D" Number of atoms: 4098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4098 Classifications: {'peptide': 520} Link IDs: {'CIS': 9, 'PTRANS': 15, 'TRANS': 495} Chain breaks: 1 Time building chain proxies: 2.94, per 1000 atoms: 0.72 Number of scatterers: 4098 At special positions: 0 Unit cell: (63.63, 87.87, 99.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 777 8.00 N 722 7.00 C 2584 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: 0.91 Conformation dependent library (CDL) restraints added in 515.2 milliseconds 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 60.0% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'D' and resid 22 through 39 Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.544A pdb=" N SER D 45 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ALA D 46 " --> pdb=" O ILE D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 66 removed outlier: 3.896A pdb=" N LEU D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY D 66 " --> pdb=" O GLY D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 115 removed outlier: 3.717A pdb=" N LYS D 98 " --> pdb=" O GLY D 94 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU D 110 " --> pdb=" O GLN D 106 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 123 removed outlier: 3.610A pdb=" N LYS D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 134 removed outlier: 4.063A pdb=" N GLU D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 179 removed outlier: 4.285A pdb=" N GLU D 179 " --> pdb=" O ALA D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 210 Processing helix chain 'D' and resid 224 through 231 removed outlier: 3.689A pdb=" N ALA D 230 " --> pdb=" O ASP D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 256 removed outlier: 3.526A pdb=" N TYR D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 266 Processing helix chain 'D' and resid 279 through 289 Processing helix chain 'D' and resid 295 through 324 removed outlier: 3.893A pdb=" N ALA D 309 " --> pdb=" O SER D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 340 Processing helix chain 'D' and resid 347 through 354 removed outlier: 3.507A pdb=" N MET D 351 " --> pdb=" O HIS D 347 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE D 354 " --> pdb=" O VAL D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 384 through 388 removed outlier: 3.642A pdb=" N ASN D 388 " --> pdb=" O HIS D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 439 Processing helix chain 'D' and resid 449 through 453 removed outlier: 3.895A pdb=" N SER D 453 " --> pdb=" O LEU D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 483 Processing helix chain 'D' and resid 483 through 491 Processing helix chain 'D' and resid 494 through 508 Processing sheet with id=A, first strand: chain 'D' and resid 217 through 219 removed outlier: 3.694A pdb=" N GLN D 218 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'D' and resid 401 through 406 removed outlier: 6.313A pdb=" N ILE D 364 " --> pdb=" O SER D 463 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER D 463 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL D 366 " --> pdb=" O LEU D 461 " (cutoff:3.500A) 231 hydrogen bonds defined for protein. 669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.74 - 1.10: 2 1.10 - 1.47: 2183 1.47 - 1.83: 1978 1.83 - 2.19: 2 2.19 - 2.55: 1 Bond restraints: 4166 Sorted by residual: bond pdb=" C LYS D 454 " pdb=" N THR D 455 " ideal model delta sigma weight residual 1.332 2.549 -1.217 1.40e-02 5.10e+03 7.55e+03 bond pdb=" C GLY D 442 " pdb=" N THR D 443 " ideal model delta sigma weight residual 1.331 2.157 -0.826 1.29e-02 6.01e+03 4.10e+03 bond pdb=" C GLU D 67 " pdb=" N SER D 68 " ideal model delta sigma weight residual 1.332 0.743 0.589 1.40e-02 5.10e+03 1.77e+03 bond pdb=" C LYS D 13 " pdb=" N LYS D 14 " ideal model delta sigma weight residual 1.332 0.842 0.491 1.38e-02 5.25e+03 1.26e+03 bond pdb=" C LEU D 513 " pdb=" N GLY D 514 " ideal model delta sigma weight residual 1.328 1.521 -0.193 1.24e-02 6.50e+03 2.42e+02 ... (remaining 4161 not shown) Histogram of bond angle deviations from ideal: 0.00 - 20.40: 5602 20.40 - 40.81: 3 40.81 - 61.21: 2 61.21 - 81.61: 2 81.61 - 102.02: 2 Bond angle restraints: 5611 Sorted by residual: angle pdb=" O GLY D 442 " pdb=" C GLY D 442 " pdb=" N THR D 443 " ideal model delta sigma weight residual 122.70 20.68 102.02 1.30e+00 5.92e-01 6.16e+03 angle pdb=" O ALA D 138 " pdb=" C ALA D 138 " pdb=" N ASN D 139 " ideal model delta sigma weight residual 122.96 38.51 84.45 1.13e+00 7.83e-01 5.59e+03 angle pdb=" O LEU D 513 " pdb=" C LEU D 513 " pdb=" N GLY D 514 " ideal model delta sigma weight residual 123.10 42.69 80.41 1.29e+00 6.01e-01 3.88e+03 angle pdb=" O LYS D 13 " pdb=" C LYS D 13 " pdb=" N LYS D 14 " ideal model delta sigma weight residual 122.92 70.70 52.22 1.17e+00 7.31e-01 1.99e+03 angle pdb=" C LYS D 454 " pdb=" N THR D 455 " pdb=" CA THR D 455 " ideal model delta sigma weight residual 121.54 44.01 77.53 1.91e+00 2.74e-01 1.65e+03 ... (remaining 5606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 2081 17.93 - 35.87: 290 35.87 - 53.80: 128 53.80 - 71.73: 44 71.73 - 89.67: 8 Dihedral angle restraints: 2551 sinusoidal: 1047 harmonic: 1504 Sorted by residual: dihedral pdb=" CA PHE D 123 " pdb=" C PHE D 123 " pdb=" N GLY D 124 " pdb=" CA GLY D 124 " ideal model delta harmonic sigma weight residual -180.00 -132.64 -47.36 0 5.00e+00 4.00e-02 8.97e+01 dihedral pdb=" CA LYS D 454 " pdb=" C LYS D 454 " pdb=" N THR D 455 " pdb=" CA THR D 455 " ideal model delta harmonic sigma weight residual -180.00 -138.13 -41.87 0 5.00e+00 4.00e-02 7.01e+01 dihedral pdb=" CA ALA D 138 " pdb=" C ALA D 138 " pdb=" N ASN D 139 " pdb=" CA ASN D 139 " ideal model delta harmonic sigma weight residual 0.00 40.93 -40.93 0 5.00e+00 4.00e-02 6.70e+01 ... (remaining 2548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 447 0.087 - 0.173: 153 0.173 - 0.260: 23 0.260 - 0.347: 5 0.347 - 0.434: 1 Chirality restraints: 629 Sorted by residual: chirality pdb=" CA ARG D 492 " pdb=" N ARG D 492 " pdb=" C ARG D 492 " pdb=" CB ARG D 492 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.70e+00 chirality pdb=" CA GLU D 83 " pdb=" N GLU D 83 " pdb=" C GLU D 83 " pdb=" CB GLU D 83 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA LEU D 401 " pdb=" N LEU D 401 " pdb=" C LEU D 401 " pdb=" CB LEU D 401 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 626 not shown) Planarity restraints: 730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 13 " 0.145 2.00e-02 2.50e+03 2.70e-01 7.28e+02 pdb=" C LYS D 13 " -0.467 2.00e-02 2.50e+03 pdb=" O LYS D 13 " 0.183 2.00e-02 2.50e+03 pdb=" N LYS D 14 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 513 " -0.142 2.00e-02 2.50e+03 2.36e-01 5.57e+02 pdb=" C LEU D 513 " 0.308 2.00e-02 2.50e+03 pdb=" O LEU D 513 " -0.300 2.00e-02 2.50e+03 pdb=" N GLY D 514 " 0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 138 " -0.117 2.00e-02 2.50e+03 1.71e-01 2.92e+02 pdb=" C ALA D 138 " 0.249 2.00e-02 2.50e+03 pdb=" O ALA D 138 " 0.062 2.00e-02 2.50e+03 pdb=" N ASN D 139 " -0.193 2.00e-02 2.50e+03 ... (remaining 727 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.96: 12 1.96 - 2.69: 371 2.69 - 3.43: 5801 3.43 - 4.16: 9728 4.16 - 4.90: 16842 Nonbonded interactions: 32754 Sorted by model distance: nonbonded pdb=" N LYS D 454 " pdb=" OG1 THR D 455 " model vdw 1.223 3.120 nonbonded pdb=" CA LYS D 454 " pdb=" OG1 THR D 455 " model vdw 1.275 3.470 nonbonded pdb=" O LYS D 13 " pdb=" CA LYS D 14 " model vdw 1.312 2.776 nonbonded pdb=" O LYS D 13 " pdb=" CB LYS D 14 " model vdw 1.397 3.440 nonbonded pdb=" O LEU D 513 " pdb=" CA GLY D 514 " model vdw 1.510 2.752 ... (remaining 32749 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.100 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.770 Find NCS groups from input model: 0.080 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 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 : 0.032 1.217 4166 Z= 1.737 Angle : 3.283 102.017 5611 Z= 2.334 Chirality : 0.085 0.434 629 Planarity : 0.018 0.270 730 Dihedral : 21.306 89.665 1579 Min Nonbonded Distance : 1.223 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 2.93 % Allowed : 9.77 % Favored : 87.30 % Rotamer: Outliers : 24.26 % Allowed : 14.42 % Favored : 61.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.60 % Twisted Proline : 0.00 % Twisted General : 1.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.31), residues: 512 helix: -2.02 (0.24), residues: 273 sheet: -3.20 (0.71), residues: 40 loop : -2.15 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.006 TRP D 371 HIS 0.014 0.004 HIS D 365 PHE 0.024 0.005 PHE D 133 TYR 0.032 0.005 TYR D 256 ARG 0.009 0.001 ARG D 430 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 85 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: D 67 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6733 (tp30) REVERT: D 92 GLU cc_start: 0.8303 (tp30) cc_final: 0.7936 (tt0) REVERT: D 98 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7468 (mptt) REVERT: D 100 LYS cc_start: 0.9065 (tttt) cc_final: 0.8766 (tptm) REVERT: D 169 MET cc_start: 0.9458 (OUTLIER) cc_final: 0.9176 (mmm) REVERT: D 172 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9244 (tp) REVERT: D 177 GLN cc_start: 0.9444 (OUTLIER) cc_final: 0.8363 (mp10) REVERT: D 178 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8792 (mtmt) REVERT: D 195 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8862 (mtp85) REVERT: D 250 ARG cc_start: 0.9323 (OUTLIER) cc_final: 0.9078 (ptp-110) REVERT: D 259 LYS cc_start: 0.9556 (OUTLIER) cc_final: 0.9349 (mtmt) REVERT: D 260 LYS cc_start: 0.9473 (tttt) cc_final: 0.9186 (ttmm) REVERT: D 275 THR cc_start: 0.9483 (OUTLIER) cc_final: 0.9258 (p) REVERT: D 284 SER cc_start: 0.9568 (OUTLIER) cc_final: 0.9333 (t) REVERT: D 292 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.9163 (ptpp) REVERT: D 293 GLU cc_start: 0.9227 (pp20) cc_final: 0.8956 (pp20) REVERT: D 308 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8593 (mtm110) REVERT: D 311 GLN cc_start: 0.9463 (OUTLIER) cc_final: 0.9109 (mt0) REVERT: D 312 GLU cc_start: 0.9353 (mm-30) cc_final: 0.9137 (mm-30) REVERT: D 315 LYS cc_start: 0.9498 (OUTLIER) cc_final: 0.9217 (mtmm) REVERT: D 325 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9172 (mt) REVERT: D 335 GLU cc_start: 0.9243 (tp30) cc_final: 0.8989 (tp30) REVERT: D 338 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8593 (mt) REVERT: D 345 VAL cc_start: 0.9361 (t) cc_final: 0.9160 (m) REVERT: D 423 ARG cc_start: 0.9530 (OUTLIER) cc_final: 0.9148 (mtm180) REVERT: D 435 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9096 (tp) REVERT: D 478 GLN cc_start: 0.9571 (OUTLIER) cc_final: 0.9322 (mm-40) REVERT: D 488 MET cc_start: 0.9548 (mtt) cc_final: 0.9322 (mtp) outliers start: 106 outliers final: 49 residues processed: 167 average time/residue: 0.2406 time to fit residues: 46.7112 Evaluate side-chains 140 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 71 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 292 LYS Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 338 ILE Chi-restraints excluded: chain D residue 348 PRO Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 403 HIS Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 423 ARG Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 444 GLN Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 448 ARG Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 454 LYS Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 478 GLN Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 517 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 0.0370 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 HIS D 465 HIS D 496 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.133553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.092878 restraints weight = 4791.471| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.06 r_work: 0.2748 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4166 Z= 0.216 Angle : 0.857 15.336 5611 Z= 0.460 Chirality : 0.045 0.158 629 Planarity : 0.005 0.043 730 Dihedral : 15.496 77.921 718 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 1.16 % Allowed : 8.91 % Favored : 89.92 % Rotamer: Outliers : 9.61 % Allowed : 21.28 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.59 % Twisted Proline : 0.00 % Twisted General : 0.80 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.36), residues: 516 helix: 0.61 (0.30), residues: 275 sheet: -2.62 (0.69), residues: 40 loop : -2.39 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 411 HIS 0.007 0.001 HIS D 457 PHE 0.023 0.002 PHE D 378 TYR 0.027 0.002 TYR D 429 ARG 0.004 0.001 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 86 time to evaluate : 0.471 Fit side-chains REVERT: D 103 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7273 (tt0) REVERT: D 135 ASN cc_start: 0.8912 (p0) cc_final: 0.8424 (p0) REVERT: D 177 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.8596 (mt0) REVERT: D 198 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8736 (mp) REVERT: D 260 LYS cc_start: 0.9247 (tttt) cc_final: 0.8961 (ttmm) REVERT: D 275 THR cc_start: 0.9350 (OUTLIER) cc_final: 0.9150 (p) REVERT: D 293 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8115 (pp20) REVERT: D 294 ILE cc_start: 0.9085 (pt) cc_final: 0.8807 (pt) REVERT: D 302 SER cc_start: 0.9090 (p) cc_final: 0.8842 (m) REVERT: D 305 SER cc_start: 0.9569 (t) cc_final: 0.9302 (t) REVERT: D 308 ARG cc_start: 0.8312 (ptp90) cc_final: 0.8045 (mtm110) REVERT: D 310 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8738 (mt) REVERT: D 312 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8251 (mm-30) REVERT: D 325 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8863 (mt) REVERT: D 338 ILE cc_start: 0.8642 (mt) cc_final: 0.8430 (mm) REVERT: D 398 SER cc_start: 0.9238 (t) cc_final: 0.9022 (p) REVERT: D 430 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7752 (tpp-160) REVERT: D 435 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8993 (tp) REVERT: D 443 THR cc_start: 0.5772 (OUTLIER) cc_final: 0.5543 (m) REVERT: D 474 ARG cc_start: 0.8938 (ttp80) cc_final: 0.8715 (ttp-170) REVERT: D 478 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8846 (mm-40) outliers start: 42 outliers final: 15 residues processed: 118 average time/residue: 0.2023 time to fit residues: 28.3960 Evaluate side-chains 91 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 448 ARG Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 478 GLN Chi-restraints excluded: chain D residue 486 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 2 optimal weight: 50.0000 chunk 46 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 36 optimal weight: 0.0570 chunk 6 optimal weight: 0.0170 chunk 4 optimal weight: 30.0000 chunk 48 optimal weight: 0.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 GLN ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 403 HIS D 496 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.150877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.112694 restraints weight = 4638.095| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.48 r_work: 0.2835 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4166 Z= 0.193 Angle : 0.734 15.346 5611 Z= 0.395 Chirality : 0.043 0.151 629 Planarity : 0.004 0.044 730 Dihedral : 10.383 57.926 611 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.97 % Allowed : 8.14 % Favored : 90.89 % Rotamer: Outliers : 6.41 % Allowed : 23.57 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.38), residues: 516 helix: 1.54 (0.31), residues: 276 sheet: -1.80 (0.67), residues: 50 loop : -2.25 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 411 HIS 0.005 0.001 HIS D 496 PHE 0.023 0.002 PHE D 378 TYR 0.024 0.001 TYR D 429 ARG 0.004 0.000 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.470 Fit side-chains REVERT: D 103 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7268 (tt0) REVERT: D 135 ASN cc_start: 0.8916 (p0) cc_final: 0.8304 (p0) REVERT: D 198 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8802 (mp) REVERT: D 226 ASP cc_start: 0.8502 (p0) cc_final: 0.8238 (p0) REVERT: D 260 LYS cc_start: 0.9332 (tttt) cc_final: 0.9066 (ttmm) REVERT: D 293 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7975 (pp20) REVERT: D 294 ILE cc_start: 0.9061 (pt) cc_final: 0.8773 (pt) REVERT: D 312 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8349 (mm-30) REVERT: D 325 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8922 (mt) REVERT: D 418 GLN cc_start: 0.8557 (mm110) cc_final: 0.8268 (mp10) REVERT: D 478 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8907 (mm-40) outliers start: 28 outliers final: 8 residues processed: 99 average time/residue: 0.1858 time to fit residues: 22.4038 Evaluate side-chains 74 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 448 ARG Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 478 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 5 optimal weight: 50.0000 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 363 GLN D 478 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.153749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.116124 restraints weight = 4618.696| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.61 r_work: 0.2921 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4166 Z= 0.178 Angle : 0.700 14.768 5611 Z= 0.371 Chirality : 0.041 0.135 629 Planarity : 0.004 0.043 730 Dihedral : 7.953 57.083 579 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 1.16 % Allowed : 6.40 % Favored : 92.44 % Rotamer: Outliers : 4.35 % Allowed : 23.57 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.39), residues: 516 helix: 2.02 (0.32), residues: 277 sheet: -1.35 (0.74), residues: 45 loop : -2.25 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 411 HIS 0.005 0.001 HIS D 380 PHE 0.022 0.002 PHE D 378 TYR 0.024 0.001 TYR D 429 ARG 0.003 0.000 ARG D 430 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.487 Fit side-chains REVERT: D 67 GLU cc_start: 0.4731 (OUTLIER) cc_final: 0.4277 (tt0) REVERT: D 103 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7372 (tt0) REVERT: D 135 ASN cc_start: 0.8903 (p0) cc_final: 0.8460 (p0) REVERT: D 198 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8777 (mp) REVERT: D 260 LYS cc_start: 0.9384 (tttt) cc_final: 0.9116 (ttmm) REVERT: D 312 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8340 (mm-30) REVERT: D 418 GLN cc_start: 0.8403 (mm110) cc_final: 0.8188 (mp10) REVERT: D 478 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.7254 (mp10) outliers start: 19 outliers final: 10 residues processed: 83 average time/residue: 0.1754 time to fit residues: 18.0707 Evaluate side-chains 74 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 478 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 13 optimal weight: 0.0670 chunk 16 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 50.0000 chunk 24 optimal weight: 0.6980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.153531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.116054 restraints weight = 4717.843| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.43 r_work: 0.2810 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4166 Z= 0.189 Angle : 0.694 14.690 5611 Z= 0.367 Chirality : 0.041 0.137 629 Planarity : 0.004 0.043 730 Dihedral : 7.058 56.591 573 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 1.16 % Allowed : 7.17 % Favored : 91.67 % Rotamer: Outliers : 3.89 % Allowed : 24.94 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.39), residues: 516 helix: 2.22 (0.32), residues: 277 sheet: -1.24 (0.75), residues: 45 loop : -2.13 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 411 HIS 0.004 0.001 HIS D 380 PHE 0.022 0.002 PHE D 378 TYR 0.022 0.001 TYR D 429 ARG 0.003 0.000 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.485 Fit side-chains REVERT: D 103 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7354 (tt0) REVERT: D 135 ASN cc_start: 0.8960 (p0) cc_final: 0.8438 (p0) REVERT: D 198 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8759 (mp) REVERT: D 208 GLU cc_start: 0.8166 (tp30) cc_final: 0.7815 (mm-30) REVERT: D 212 MET cc_start: 0.9114 (mtm) cc_final: 0.8887 (mtp) REVERT: D 260 LYS cc_start: 0.9344 (tttt) cc_final: 0.9069 (ttmm) REVERT: D 312 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8337 (mm-30) REVERT: D 418 GLN cc_start: 0.8509 (mm110) cc_final: 0.8267 (mp10) outliers start: 17 outliers final: 9 residues processed: 80 average time/residue: 0.2118 time to fit residues: 21.1491 Evaluate side-chains 73 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 438 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 272 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 = 0.3494 r_free = 0.3494 target = 0.138268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.098843 restraints weight = 4764.536| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.07 r_work: 0.2837 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4166 Z= 0.185 Angle : 0.679 14.589 5611 Z= 0.360 Chirality : 0.041 0.140 629 Planarity : 0.004 0.043 730 Dihedral : 6.307 58.169 570 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.97 % Allowed : 6.98 % Favored : 92.05 % Rotamer: Outliers : 2.75 % Allowed : 25.63 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.39), residues: 516 helix: 2.36 (0.32), residues: 276 sheet: -1.22 (0.75), residues: 45 loop : -2.02 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 411 HIS 0.004 0.001 HIS D 380 PHE 0.021 0.002 PHE D 378 TYR 0.022 0.001 TYR D 429 ARG 0.004 0.000 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.484 Fit side-chains REVERT: D 103 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7283 (tt0) REVERT: D 135 ASN cc_start: 0.8970 (p0) cc_final: 0.8461 (p0) REVERT: D 149 ASP cc_start: 0.8628 (m-30) cc_final: 0.8415 (m-30) REVERT: D 198 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8737 (mp) REVERT: D 208 GLU cc_start: 0.8113 (tp30) cc_final: 0.7776 (mm-30) REVERT: D 229 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7868 (mt-10) REVERT: D 260 LYS cc_start: 0.9323 (tttt) cc_final: 0.8991 (ttmm) REVERT: D 312 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8333 (mm-30) REVERT: D 418 GLN cc_start: 0.8457 (mm110) cc_final: 0.8165 (mp10) outliers start: 12 outliers final: 10 residues processed: 76 average time/residue: 0.1749 time to fit residues: 16.6819 Evaluate side-chains 72 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 438 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 0.0070 chunk 2 optimal weight: 50.0000 chunk 22 optimal weight: 0.0870 chunk 38 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 272 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 = 0.3569 r_free = 0.3569 target = 0.144369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.104781 restraints weight = 4667.059| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.09 r_work: 0.2860 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4166 Z= 0.168 Angle : 0.654 14.402 5611 Z= 0.347 Chirality : 0.040 0.135 629 Planarity : 0.004 0.042 730 Dihedral : 6.166 59.233 570 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.97 % Allowed : 7.75 % Favored : 91.28 % Rotamer: Outliers : 2.29 % Allowed : 25.86 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.39), residues: 516 helix: 2.44 (0.32), residues: 276 sheet: -1.06 (0.76), residues: 44 loop : -1.99 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 411 HIS 0.003 0.001 HIS D 380 PHE 0.020 0.002 PHE D 378 TYR 0.021 0.001 TYR D 429 ARG 0.006 0.000 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.469 Fit side-chains REVERT: D 135 ASN cc_start: 0.8970 (p0) cc_final: 0.8424 (p0) REVERT: D 149 ASP cc_start: 0.8618 (m-30) cc_final: 0.8385 (m-30) REVERT: D 182 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8230 (mt-10) REVERT: D 198 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8698 (mp) REVERT: D 212 MET cc_start: 0.9098 (mtp) cc_final: 0.8893 (mtp) REVERT: D 260 LYS cc_start: 0.9355 (tttt) cc_final: 0.9015 (ttmm) REVERT: D 312 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8344 (mm-30) REVERT: D 418 GLN cc_start: 0.8438 (mm110) cc_final: 0.8165 (mp10) outliers start: 10 outliers final: 9 residues processed: 73 average time/residue: 0.1642 time to fit residues: 15.2373 Evaluate side-chains 71 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 438 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 30.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 272 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 = 0.3419 r_free = 0.3419 target = 0.132481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.093863 restraints weight = 4759.407| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.43 r_work: 0.2729 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 4166 Z= 0.362 Angle : 0.753 14.207 5611 Z= 0.394 Chirality : 0.045 0.160 629 Planarity : 0.004 0.046 730 Dihedral : 6.404 59.476 568 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.97 % Allowed : 8.33 % Favored : 90.70 % Rotamer: Outliers : 3.43 % Allowed : 24.49 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.39), residues: 516 helix: 2.10 (0.31), residues: 283 sheet: -1.90 (0.82), residues: 35 loop : -1.99 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 371 HIS 0.005 0.001 HIS D 412 PHE 0.023 0.003 PHE D 392 TYR 0.023 0.002 TYR D 429 ARG 0.004 0.000 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: D 149 ASP cc_start: 0.8713 (m-30) cc_final: 0.8497 (m-30) REVERT: D 198 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8721 (mp) REVERT: D 208 GLU cc_start: 0.8271 (tp30) cc_final: 0.7820 (mm-30) REVERT: D 260 LYS cc_start: 0.9357 (tttt) cc_final: 0.9004 (ttmm) REVERT: D 312 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8373 (mm-30) REVERT: D 418 GLN cc_start: 0.8539 (mm110) cc_final: 0.8172 (mp10) outliers start: 15 outliers final: 13 residues processed: 73 average time/residue: 0.1799 time to fit residues: 16.7138 Evaluate side-chains 74 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 490 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.153333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.116415 restraints weight = 4608.041| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.37 r_work: 0.2835 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4166 Z= 0.183 Angle : 0.671 13.996 5611 Z= 0.353 Chirality : 0.041 0.132 629 Planarity : 0.004 0.044 730 Dihedral : 6.060 59.728 568 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.97 % Allowed : 8.14 % Favored : 90.89 % Rotamer: Outliers : 3.43 % Allowed : 24.94 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.40), residues: 516 helix: 2.38 (0.32), residues: 276 sheet: -1.31 (0.76), residues: 45 loop : -1.98 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 411 HIS 0.003 0.001 HIS D 380 PHE 0.021 0.002 PHE D 378 TYR 0.022 0.001 TYR D 429 ARG 0.006 0.000 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: D 135 ASN cc_start: 0.9027 (p0) cc_final: 0.8495 (p0) REVERT: D 149 ASP cc_start: 0.8593 (m-30) cc_final: 0.8384 (m-30) REVERT: D 182 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8286 (mt-10) REVERT: D 198 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8709 (mp) REVERT: D 208 GLU cc_start: 0.8099 (tp30) cc_final: 0.7721 (mm-30) REVERT: D 260 LYS cc_start: 0.9351 (tttt) cc_final: 0.9007 (ttmm) REVERT: D 312 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8327 (mm-30) REVERT: D 418 GLN cc_start: 0.8421 (mm110) cc_final: 0.8119 (mp10) outliers start: 15 outliers final: 10 residues processed: 74 average time/residue: 0.1578 time to fit residues: 15.2509 Evaluate side-chains 70 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 438 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 1 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 30.0000 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.134435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.096135 restraints weight = 4766.105| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.47 r_work: 0.2779 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4166 Z= 0.246 Angle : 0.693 13.793 5611 Z= 0.363 Chirality : 0.042 0.142 629 Planarity : 0.004 0.044 730 Dihedral : 6.111 59.520 568 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.97 % Allowed : 7.56 % Favored : 91.47 % Rotamer: Outliers : 2.52 % Allowed : 26.09 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.40), residues: 516 helix: 2.35 (0.32), residues: 276 sheet: -1.35 (0.75), residues: 45 loop : -1.98 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 411 HIS 0.004 0.001 HIS D 412 PHE 0.021 0.002 PHE D 378 TYR 0.022 0.001 TYR D 429 ARG 0.006 0.000 ARG D 308 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: D 135 ASN cc_start: 0.9050 (p0) cc_final: 0.8499 (p0) REVERT: D 149 ASP cc_start: 0.8666 (m-30) cc_final: 0.8461 (m-30) REVERT: D 182 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8295 (mt-10) REVERT: D 198 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8705 (mp) REVERT: D 208 GLU cc_start: 0.8177 (tp30) cc_final: 0.7775 (mm-30) REVERT: D 260 LYS cc_start: 0.9362 (tttt) cc_final: 0.9011 (ttmm) REVERT: D 312 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8365 (mm-30) REVERT: D 418 GLN cc_start: 0.8501 (mm110) cc_final: 0.8223 (mp10) outliers start: 11 outliers final: 10 residues processed: 69 average time/residue: 0.1558 time to fit residues: 13.8540 Evaluate side-chains 70 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 438 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 2 optimal weight: 50.0000 chunk 18 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.152960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.115525 restraints weight = 4582.265| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.94 r_work: 0.2860 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4166 Z= 0.201 Angle : 0.672 13.584 5611 Z= 0.352 Chirality : 0.041 0.135 629 Planarity : 0.004 0.042 730 Dihedral : 5.986 59.335 568 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.97 % Allowed : 7.95 % Favored : 91.09 % Rotamer: Outliers : 3.20 % Allowed : 25.17 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.40), residues: 516 helix: 2.40 (0.32), residues: 276 sheet: -1.30 (0.77), residues: 45 loop : -1.96 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 411 HIS 0.003 0.001 HIS D 380 PHE 0.021 0.002 PHE D 378 TYR 0.022 0.001 TYR D 429 ARG 0.006 0.000 ARG D 308 =============================================================================== Job complete usr+sys time: 2487.13 seconds wall clock time: 44 minutes 48.21 seconds (2688.21 seconds total)