Starting phenix.real_space_refine on Fri Aug 22 14:25:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j9e_6240/08_2025/3j9e_6240.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j9e_6240/08_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_6240/08_2025/3j9e_6240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j9e_6240/08_2025/3j9e_6240.map" model { file = "/net/cci-nas-00/data/ceres_data/3j9e_6240/08_2025/3j9e_6240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j9e_6240/08_2025/3j9e_6240.cif" } resolution = 3.3 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 ------------------------------------------------------------------------------- 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.07, per 1000 atoms: 0.26 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: 0.38 Conformation dependent library (CDL) restraints added in 169.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.14 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: 0.76 Time building geometry restraints manager: 0.53 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: 0.150 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.280 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.240 ------------------------------------------------------------------------------- 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= 2.166 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG D 430 TYR 0.032 0.005 TYR D 256 PHE 0.024 0.005 PHE D 133 TRP 0.025 0.006 TRP D 371 HIS 0.014 0.004 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.03159 ( 4166) covalent geometry : angle 3.28300 ( 5611) hydrogen bonds : bond 0.17348 ( 231) hydrogen bonds : angle 8.31461 ( 669) *********************** 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 : 0.108 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: 0.0943 time to fit residues: 18.4829 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 : 0.167 ------------------------------------------------------------------------------- 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 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 50.0000 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.134022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.093344 restraints weight = 4820.938| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.05 r_work: 0.2763 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3184 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= 0.170 Angle : 0.853 15.357 5611 Z= 0.458 Chirality : 0.046 0.158 629 Planarity : 0.005 0.042 730 Dihedral : 15.374 77.148 718 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 1.36 % Allowed : 8.53 % Favored : 90.12 % Rotamer: Outliers : 9.61 % Allowed : 20.82 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.59 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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 aren not related in a simple way. whole: -1.16 (0.36), residues: 516 helix: 0.63 (0.30), residues: 275 sheet: -2.60 (0.69), residues: 40 loop : -2.37 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 290 TYR 0.027 0.002 TYR D 429 PHE 0.023 0.002 PHE D 378 TRP 0.010 0.002 TRP D 411 HIS 0.005 0.001 HIS D 457 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 4166) covalent geometry : angle 0.85294 ( 5611) hydrogen bonds : bond 0.04559 ( 231) hydrogen bonds : angle 4.89873 ( 669) *********************** 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 : 0.139 Fit side-chains REVERT: D 103 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7344 (tt0) REVERT: D 135 ASN cc_start: 0.8904 (p0) cc_final: 0.8441 (p0) REVERT: D 177 GLN cc_start: 0.9314 (OUTLIER) cc_final: 0.8643 (mt0) REVERT: D 195 ARG cc_start: 0.8708 (tpt90) cc_final: 0.8434 (mmm160) REVERT: D 198 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8778 (mp) REVERT: D 260 LYS cc_start: 0.9274 (tttt) cc_final: 0.9013 (ttmm) REVERT: D 275 THR cc_start: 0.9360 (OUTLIER) cc_final: 0.9152 (p) REVERT: D 293 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8111 (pp20) REVERT: D 294 ILE cc_start: 0.9117 (pt) cc_final: 0.8844 (pt) REVERT: D 302 SER cc_start: 0.9145 (p) cc_final: 0.8940 (m) REVERT: D 305 SER cc_start: 0.9554 (t) cc_final: 0.9311 (t) REVERT: D 308 ARG cc_start: 0.8368 (ptp90) cc_final: 0.8073 (mtm110) REVERT: D 310 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8815 (mt) REVERT: D 312 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8289 (mm-30) REVERT: D 325 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8879 (mt) REVERT: D 338 ILE cc_start: 0.8637 (mt) cc_final: 0.8434 (mm) REVERT: D 474 ARG cc_start: 0.8948 (ttp80) cc_final: 0.8741 (ttp-170) REVERT: D 478 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8840 (mm-40) outliers start: 42 outliers final: 14 residues processed: 118 average time/residue: 0.0867 time to fit residues: 12.2960 Evaluate side-chains 88 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.106 ------------------------------------------------------------------------------- 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 448 ARG 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 19 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 41 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 22 optimal weight: 0.3980 chunk 2 optimal weight: 50.0000 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 50.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 496 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.134269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.094310 restraints weight = 4857.437| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.07 r_work: 0.2761 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3820 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= 0.158 Angle : 0.751 15.358 5611 Z= 0.404 Chirality : 0.044 0.163 629 Planarity : 0.004 0.045 730 Dihedral : 10.313 57.092 604 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.97 % Allowed : 8.53 % Favored : 90.50 % Rotamer: Outliers : 5.26 % Allowed : 23.80 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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 aren not related in a simple way. whole: -0.35 (0.37), residues: 516 helix: 1.39 (0.31), residues: 276 sheet: -1.89 (0.66), residues: 50 loop : -2.26 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 290 TYR 0.025 0.002 TYR D 429 PHE 0.024 0.002 PHE D 378 TRP 0.007 0.001 TRP D 371 HIS 0.005 0.001 HIS D 496 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 4166) covalent geometry : angle 0.75071 ( 5611) hydrogen bonds : bond 0.04106 ( 231) hydrogen bonds : angle 4.43522 ( 669) *********************** 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 100 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.137 Fit side-chains REVERT: D 103 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7210 (tt0) REVERT: D 135 ASN cc_start: 0.8945 (p0) cc_final: 0.8347 (p0) REVERT: D 182 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8288 (mt-10) REVERT: D 198 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8757 (mp) REVERT: D 260 LYS cc_start: 0.9309 (tttt) cc_final: 0.9000 (ttmm) REVERT: D 293 GLU cc_start: 0.8181 (pp20) cc_final: 0.7920 (pp20) REVERT: D 294 ILE cc_start: 0.8979 (pt) cc_final: 0.8711 (pt) REVERT: D 308 ARG cc_start: 0.8244 (ptp90) cc_final: 0.8010 (mtm110) REVERT: D 312 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8318 (mm-30) REVERT: D 325 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8976 (mt) outliers start: 23 outliers final: 13 residues processed: 96 average time/residue: 0.0840 time to fit residues: 9.8010 Evaluate side-chains 76 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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 190 MET Chi-restraints excluded: chain D residue 198 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 345 VAL Chi-restraints excluded: chain D residue 398 SER 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 473 LEU 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 35 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 13 optimal weight: 0.0050 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 457 HIS D 478 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.137580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.098612 restraints weight = 4751.109| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.04 r_work: 0.2837 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4258 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= 0.134 Angle : 0.693 14.819 5611 Z= 0.371 Chirality : 0.041 0.132 629 Planarity : 0.004 0.043 730 Dihedral : 8.317 57.065 583 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.97 % Allowed : 7.36 % Favored : 91.67 % Rotamer: Outliers : 5.03 % Allowed : 23.80 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 aren not related in a simple way. whole: 0.18 (0.38), residues: 516 helix: 1.88 (0.32), residues: 277 sheet: -1.49 (0.68), residues: 50 loop : -2.22 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 290 TYR 0.024 0.001 TYR D 429 PHE 0.023 0.002 PHE D 378 TRP 0.009 0.002 TRP D 411 HIS 0.005 0.001 HIS D 380 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 4166) covalent geometry : angle 0.69307 ( 5611) hydrogen bonds : bond 0.03654 ( 231) hydrogen bonds : angle 4.20386 ( 669) *********************** 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 98 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.186 Fit side-chains REVERT: D 67 GLU cc_start: 0.4634 (OUTLIER) cc_final: 0.3763 (tt0) REVERT: D 103 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7305 (tt0) REVERT: D 135 ASN cc_start: 0.8990 (p0) cc_final: 0.8493 (p0) REVERT: D 198 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8744 (mp) REVERT: D 208 GLU cc_start: 0.8198 (tp30) cc_final: 0.7822 (mm-30) REVERT: D 212 MET cc_start: 0.9312 (mtm) cc_final: 0.9075 (mtp) REVERT: D 260 LYS cc_start: 0.9332 (tttt) cc_final: 0.9025 (ttmm) REVERT: D 308 ARG cc_start: 0.8322 (ptp90) cc_final: 0.8017 (mtm110) REVERT: D 312 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8307 (mm-30) REVERT: D 478 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.7103 (mp10) outliers start: 22 outliers final: 9 residues processed: 90 average time/residue: 0.0663 time to fit residues: 7.5400 Evaluate side-chains 78 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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 123 PHE Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 198 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 451 VAL 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 23 optimal weight: 0.0670 chunk 46 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 35 optimal weight: 0.0980 chunk 24 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 363 GLN ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.139493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.100056 restraints weight = 4755.832| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.08 r_work: 0.2836 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4428 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= 0.135 Angle : 0.690 14.719 5611 Z= 0.365 Chirality : 0.041 0.135 629 Planarity : 0.004 0.043 730 Dihedral : 7.025 56.700 573 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.97 % Allowed : 6.98 % Favored : 92.05 % Rotamer: Outliers : 4.12 % Allowed : 24.94 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % 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 aren not related in a simple way. whole: 0.42 (0.39), residues: 516 helix: 2.08 (0.32), residues: 277 sheet: -1.23 (0.75), residues: 45 loop : -2.15 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 290 TYR 0.022 0.001 TYR D 429 PHE 0.021 0.002 PHE D 378 TRP 0.008 0.002 TRP D 411 HIS 0.005 0.001 HIS D 380 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4166) covalent geometry : angle 0.68956 ( 5611) hydrogen bonds : bond 0.03665 ( 231) hydrogen bonds : angle 4.44398 ( 669) *********************** 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 90 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.097 Fit side-chains REVERT: D 103 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7287 (tt0) REVERT: D 135 ASN cc_start: 0.8994 (p0) cc_final: 0.8451 (p0) REVERT: D 198 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8724 (mp) REVERT: D 208 GLU cc_start: 0.8136 (tp30) cc_final: 0.7772 (mm-30) REVERT: D 260 LYS cc_start: 0.9349 (tttt) cc_final: 0.9014 (ttmm) REVERT: D 308 ARG cc_start: 0.8279 (ptp90) cc_final: 0.8071 (mtm110) REVERT: D 312 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8329 (mm-30) outliers start: 18 outliers final: 11 residues processed: 85 average time/residue: 0.0638 time to fit residues: 7.0010 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 : 0.130 ------------------------------------------------------------------------------- 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 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 390 SER Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 450 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 4 optimal weight: 50.0000 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 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 = 0.3449 r_free = 0.3449 target = 0.134892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.095692 restraints weight = 4840.265| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.06 r_work: 0.2786 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4166 Z= 0.170 Angle : 0.698 14.580 5611 Z= 0.370 Chirality : 0.042 0.143 629 Planarity : 0.004 0.045 730 Dihedral : 6.529 59.247 570 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.97 % Allowed : 7.36 % Favored : 91.67 % Rotamer: Outliers : 4.12 % Allowed : 24.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.39), residues: 516 helix: 2.14 (0.32), residues: 276 sheet: -1.28 (0.74), residues: 45 loop : -2.05 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 290 TYR 0.022 0.001 TYR D 429 PHE 0.022 0.002 PHE D 378 TRP 0.007 0.001 TRP D 371 HIS 0.006 0.001 HIS D 410 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 4166) covalent geometry : angle 0.69825 ( 5611) hydrogen bonds : bond 0.03952 ( 231) hydrogen bonds : angle 4.52467 ( 669) *********************** 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 83 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.163 Fit side-chains REVERT: D 103 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7212 (tt0) REVERT: D 135 ASN cc_start: 0.9075 (p0) cc_final: 0.8484 (p0) REVERT: D 198 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8686 (mp) REVERT: D 208 GLU cc_start: 0.8179 (tp30) cc_final: 0.7797 (mm-30) REVERT: D 260 LYS cc_start: 0.9359 (tttt) cc_final: 0.8998 (ttmm) REVERT: D 308 ARG cc_start: 0.8360 (ptp90) cc_final: 0.8075 (mtm110) REVERT: D 312 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8319 (mm-30) REVERT: D 400 ASP cc_start: 0.8067 (m-30) cc_final: 0.7719 (m-30) REVERT: D 410 HIS cc_start: 0.8709 (OUTLIER) cc_final: 0.8489 (t-90) REVERT: D 423 ARG cc_start: 0.8904 (mtm180) cc_final: 0.8065 (mtm180) outliers start: 18 outliers final: 12 residues processed: 81 average time/residue: 0.0711 time to fit residues: 7.2534 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 : 0.094 ------------------------------------------------------------------------------- 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 390 SER Chi-restraints excluded: chain D residue 410 HIS Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 451 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 4 optimal weight: 50.0000 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 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 = 0.3527 r_free = 0.3527 target = 0.140873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.101684 restraints weight = 4762.614| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.05 r_work: 0.2853 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4692 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= 0.133 Angle : 0.656 14.400 5611 Z= 0.351 Chirality : 0.041 0.134 629 Planarity : 0.004 0.043 730 Dihedral : 6.299 59.578 570 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.97 % Allowed : 7.95 % Favored : 91.09 % Rotamer: Outliers : 2.97 % Allowed : 26.32 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % 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 aren not related in a simple way. whole: 0.68 (0.39), residues: 516 helix: 2.28 (0.32), residues: 276 sheet: -1.13 (0.77), residues: 45 loop : -1.99 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 290 TYR 0.021 0.001 TYR D 429 PHE 0.021 0.002 PHE D 378 TRP 0.008 0.001 TRP D 411 HIS 0.004 0.001 HIS D 380 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4166) covalent geometry : angle 0.65608 ( 5611) hydrogen bonds : bond 0.03605 ( 231) hydrogen bonds : angle 4.40607 ( 669) *********************** 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 83 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.157 Fit side-chains REVERT: D 135 ASN cc_start: 0.9058 (p0) cc_final: 0.8514 (p0) REVERT: D 182 GLU cc_start: 0.8560 (mt-10) cc_final: 0.7813 (mp0) REVERT: D 198 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8725 (mp) REVERT: D 208 GLU cc_start: 0.8150 (tp30) cc_final: 0.7791 (mm-30) REVERT: D 260 LYS cc_start: 0.9358 (tttt) cc_final: 0.9036 (ttmm) REVERT: D 308 ARG cc_start: 0.8338 (ptp90) cc_final: 0.8068 (mtm110) REVERT: D 312 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8348 (mm-30) outliers start: 13 outliers final: 11 residues processed: 81 average time/residue: 0.0815 time to fit residues: 8.1870 Evaluate side-chains 77 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.097 ------------------------------------------------------------------------------- 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 336 LYS Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain D residue 425 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 50.0000 chunk 30 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 4 optimal weight: 30.0000 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 50.0000 chunk 31 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.133376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.094252 restraints weight = 4795.151| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.03 r_work: 0.2759 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4166 Z= 0.203 Angle : 0.724 14.164 5611 Z= 0.382 Chirality : 0.043 0.154 629 Planarity : 0.004 0.046 730 Dihedral : 6.500 59.732 570 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.97 % Allowed : 7.75 % Favored : 91.28 % Rotamer: Outliers : 4.35 % Allowed : 25.17 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % 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 aren not related in a simple way. whole: 0.50 (0.39), residues: 516 helix: 2.08 (0.31), residues: 283 sheet: -1.46 (0.73), residues: 45 loop : -2.06 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 290 TYR 0.022 0.002 TYR D 429 PHE 0.022 0.002 PHE D 378 TRP 0.009 0.002 TRP D 371 HIS 0.004 0.001 HIS D 410 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 4166) covalent geometry : angle 0.72363 ( 5611) hydrogen bonds : bond 0.04094 ( 231) hydrogen bonds : angle 4.54444 ( 669) *********************** 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 81 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: D 135 ASN cc_start: 0.9137 (p0) cc_final: 0.8520 (p0) REVERT: D 198 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8714 (mp) REVERT: D 208 GLU cc_start: 0.8262 (tp30) cc_final: 0.7886 (mm-30) REVERT: D 250 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8574 (ptp-170) REVERT: D 260 LYS cc_start: 0.9372 (tttt) cc_final: 0.9028 (ttmm) REVERT: D 308 ARG cc_start: 0.8405 (ptp90) cc_final: 0.8092 (mtm110) REVERT: D 312 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8364 (mm-30) outliers start: 19 outliers final: 16 residues processed: 77 average time/residue: 0.0831 time to fit residues: 7.8996 Evaluate side-chains 76 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 250 ARG Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 517 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 37 optimal weight: 0.0470 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 3 optimal weight: 50.0000 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 380 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 = 0.3680 r_free = 0.3680 target = 0.154375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.117996 restraints weight = 4675.341| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.49 r_work: 0.2865 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4829 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= 0.129 Angle : 0.661 13.938 5611 Z= 0.351 Chirality : 0.040 0.134 629 Planarity : 0.004 0.043 730 Dihedral : 6.164 59.841 570 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.97 % Allowed : 7.56 % Favored : 91.47 % Rotamer: Outliers : 3.66 % Allowed : 24.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.39), residues: 516 helix: 2.36 (0.32), residues: 276 sheet: -1.22 (0.78), residues: 45 loop : -1.96 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 195 TYR 0.021 0.001 TYR D 429 PHE 0.021 0.002 PHE D 378 TRP 0.009 0.001 TRP D 411 HIS 0.004 0.001 HIS D 410 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 4166) covalent geometry : angle 0.66058 ( 5611) hydrogen bonds : bond 0.03534 ( 231) hydrogen bonds : angle 4.40690 ( 669) *********************** 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 80 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: D 135 ASN cc_start: 0.9031 (p0) cc_final: 0.8544 (p0) REVERT: D 182 GLU cc_start: 0.8589 (mt-10) cc_final: 0.7861 (mp0) REVERT: D 198 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8697 (mp) REVERT: D 208 GLU cc_start: 0.8113 (tp30) cc_final: 0.7755 (mm-30) REVERT: D 260 LYS cc_start: 0.9336 (tttt) cc_final: 0.8996 (ttmm) REVERT: D 308 ARG cc_start: 0.8337 (ptp90) cc_final: 0.8034 (mtm110) REVERT: D 312 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8311 (mm-30) outliers start: 16 outliers final: 13 residues processed: 77 average time/residue: 0.0760 time to fit residues: 7.2977 Evaluate side-chains 75 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 390 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 519 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 20 optimal weight: 6.9990 chunk 5 optimal weight: 50.0000 chunk 34 optimal weight: 4.9990 chunk 4 optimal weight: 50.0000 chunk 11 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.132960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.093915 restraints weight = 4797.187| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.02 r_work: 0.2751 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4166 Z= 0.221 Angle : 0.730 13.754 5611 Z= 0.385 Chirality : 0.044 0.150 629 Planarity : 0.004 0.047 730 Dihedral : 6.470 59.291 570 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.97 % Allowed : 7.95 % Favored : 91.09 % Rotamer: Outliers : 3.66 % Allowed : 24.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.39), residues: 516 helix: 2.11 (0.31), residues: 282 sheet: -1.81 (0.84), residues: 35 loop : -2.01 (0.44), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 195 TYR 0.022 0.002 TYR D 429 PHE 0.022 0.003 PHE D 378 TRP 0.009 0.002 TRP D 371 HIS 0.005 0.001 HIS D 386 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 4166) covalent geometry : angle 0.73032 ( 5611) hydrogen bonds : bond 0.04207 ( 231) hydrogen bonds : angle 4.55699 ( 669) ********************** 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 74 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: D 135 ASN cc_start: 0.9105 (p0) cc_final: 0.8561 (p0) REVERT: D 198 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8710 (mp) REVERT: D 208 GLU cc_start: 0.8281 (tp30) cc_final: 0.7858 (mm-30) REVERT: D 260 LYS cc_start: 0.9365 (tttt) cc_final: 0.9015 (ttmm) REVERT: D 308 ARG cc_start: 0.8395 (ptp90) cc_final: 0.8058 (mtm110) REVERT: D 312 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8345 (mm-30) outliers start: 16 outliers final: 14 residues processed: 71 average time/residue: 0.0649 time to fit residues: 5.9932 Evaluate side-chains 73 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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 390 SER Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 519 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.6888 > 50: distance: 82 - 90: 24.790 distance: 90 - 91: 4.548 distance: 90 - 171: 28.048 distance: 91 - 92: 35.625 distance: 91 - 94: 49.195 distance: 92 - 93: 41.921 distance: 92 - 96: 10.542 distance: 93 - 168: 32.083 distance: 94 - 95: 51.750 distance: 96 - 97: 9.113 distance: 97 - 98: 8.461 distance: 98 - 99: 9.766 distance: 98 - 104: 17.270 distance: 100 - 101: 19.124 distance: 101 - 103: 5.174 distance: 104 - 105: 19.486 distance: 105 - 106: 21.032 distance: 105 - 108: 37.348 distance: 106 - 107: 11.273 distance: 106 - 110: 58.515 distance: 108 - 109: 21.593 distance: 110 - 111: 9.818 distance: 111 - 112: 25.208 distance: 111 - 114: 39.384 distance: 112 - 113: 13.805 distance: 112 - 120: 14.410 distance: 113 - 140: 59.841 distance: 114 - 115: 14.230 distance: 115 - 116: 24.365 distance: 115 - 117: 22.458 distance: 116 - 118: 27.276 distance: 117 - 119: 15.480 distance: 118 - 119: 11.240 distance: 120 - 121: 33.616 distance: 121 - 122: 13.865 distance: 121 - 124: 13.603 distance: 122 - 123: 8.182 distance: 122 - 130: 52.149 distance: 124 - 125: 11.678 distance: 125 - 126: 27.598 distance: 125 - 127: 20.182 distance: 126 - 128: 18.188 distance: 127 - 129: 13.956 distance: 128 - 129: 37.373 distance: 130 - 131: 14.139 distance: 131 - 132: 40.929 distance: 131 - 134: 16.474 distance: 132 - 133: 37.757 distance: 132 - 140: 50.023 distance: 134 - 135: 20.149 distance: 135 - 136: 5.957 distance: 135 - 137: 14.367 distance: 136 - 138: 11.282 distance: 137 - 139: 12.627 distance: 138 - 139: 6.531 distance: 140 - 141: 39.447 distance: 141 - 142: 26.493 distance: 141 - 144: 44.551 distance: 142 - 143: 49.965 distance: 142 - 145: 35.897 distance: 145 - 146: 22.658 distance: 146 - 147: 19.524 distance: 146 - 149: 3.181 distance: 147 - 148: 46.006 distance: 147 - 153: 27.249 distance: 149 - 150: 26.849 distance: 150 - 152: 36.319 distance: 154 - 155: 12.730 distance: 154 - 157: 20.957 distance: 155 - 156: 46.769 distance: 155 - 162: 20.805 distance: 157 - 158: 9.552 distance: 158 - 159: 25.823 distance: 159 - 160: 14.116 distance: 162 - 163: 38.499 distance: 163 - 166: 40.075 distance: 164 - 168: 35.068 distance: 166 - 167: 13.415