Starting phenix.real_space_refine on Sun Apr 5 02:40:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uxk_64585/04_2026/9uxk_64585.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uxk_64585/04_2026/9uxk_64585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uxk_64585/04_2026/9uxk_64585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uxk_64585/04_2026/9uxk_64585.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uxk_64585/04_2026/9uxk_64585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uxk_64585/04_2026/9uxk_64585.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 23 5.16 5 C 4634 2.51 5 N 1282 2.21 5 O 1428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7367 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1709 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain: "D" Number of atoms: 3138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3138 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 379} Chain: "E" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1161 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 3, 'TRANS': 142} Chain: "F" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1359 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 160} Time building chain proxies: 1.84, per 1000 atoms: 0.25 Number of scatterers: 7367 At special positions: 0 Unit cell: (72.16, 89.38, 145.14, 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 23 16.00 O 1428 8.00 N 1282 7.00 C 4634 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: 0.79 Conformation dependent library (CDL) restraints added in 275.6 milliseconds 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 1 sheets defined 74.3% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'C' and resid 230 through 244 removed outlier: 3.509A pdb=" N LEU C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 271 removed outlier: 3.569A pdb=" N LYS C 271 " --> pdb=" O ASN C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 320 removed outlier: 3.624A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 341 Processing helix chain 'C' and resid 357 through 368 removed outlier: 3.908A pdb=" N GLU C 363 " --> pdb=" O SER C 359 " (cutoff:3.500A) Proline residue: C 364 - end of helix Processing helix chain 'C' and resid 376 through 384 removed outlier: 4.595A pdb=" N ILE C 380 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS C 381 " --> pdb=" O GLU C 377 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY C 384 " --> pdb=" O ILE C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 416 Processing helix chain 'C' and resid 424 through 441 Processing helix chain 'D' and resid 2 through 19 removed outlier: 3.558A pdb=" N VAL D 9 " --> pdb=" O SER D 5 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER D 10 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER D 11 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 29 removed outlier: 3.981A pdb=" N ARG D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA D 29 " --> pdb=" O ARG D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 87 removed outlier: 3.556A pdb=" N TRP D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 113 Processing helix chain 'D' and resid 117 through 132 Processing helix chain 'D' and resid 136 through 148 removed outlier: 4.709A pdb=" N ASN D 141 " --> pdb=" O PRO D 137 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N TYR D 142 " --> pdb=" O SER D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 159 Processing helix chain 'D' and resid 168 through 181 removed outlier: 4.164A pdb=" N ASP D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 207 removed outlier: 4.447A pdb=" N ASP D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLU D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL D 203 " --> pdb=" O TRP D 199 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU D 204 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR D 205 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 246 removed outlier: 3.561A pdb=" N SER D 245 " --> pdb=" O PHE D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 255 Processing helix chain 'D' and resid 259 through 269 Processing helix chain 'D' and resid 271 through 296 Processing helix chain 'D' and resid 299 through 325 removed outlier: 3.515A pdb=" N TYR D 303 " --> pdb=" O GLN D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 344 Processing helix chain 'D' and resid 356 through 370 removed outlier: 3.518A pdb=" N ALA D 360 " --> pdb=" O GLY D 356 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS D 370 " --> pdb=" O SER D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 384 Processing helix chain 'E' and resid 278 through 334 removed outlier: 3.519A pdb=" N ILE E 282 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN E 321 " --> pdb=" O ASN E 317 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR E 322 " --> pdb=" O ARG E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 343 removed outlier: 3.816A pdb=" N LYS E 338 " --> pdb=" O LEU E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 346 No H-bonds generated for 'chain 'E' and resid 344 through 346' Processing helix chain 'E' and resid 355 through 376 Proline residue: E 364 - end of helix Processing helix chain 'E' and resid 381 through 422 Processing helix chain 'F' and resid 6 through 16 Processing helix chain 'F' and resid 17 through 37 removed outlier: 4.035A pdb=" N LYS F 35 " --> pdb=" O ALA F 31 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN F 36 " --> pdb=" O TYR F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 47 removed outlier: 3.592A pdb=" N CYS F 47 " --> pdb=" O SER F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 52 Processing helix chain 'F' and resid 54 through 62 removed outlier: 4.706A pdb=" N VAL F 60 " --> pdb=" O ASP F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 77 Processing helix chain 'F' and resid 83 through 88 removed outlier: 4.089A pdb=" N LEU F 87 " --> pdb=" O GLY F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 96 removed outlier: 3.851A pdb=" N ASP F 94 " --> pdb=" O HIS F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 110 Processing helix chain 'F' and resid 137 through 156 removed outlier: 3.922A pdb=" N GLU F 156 " --> pdb=" O ARG F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 166 removed outlier: 3.534A pdb=" N LEU F 166 " --> pdb=" O LEU F 162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 44 through 46 removed outlier: 3.504A pdb=" N LEU D 97 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N PHE D 96 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE D 163 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU D 98 " --> pdb=" O ILE D 163 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1434 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: 0.91 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2285 1.34 - 1.45: 924 1.45 - 1.57: 4241 1.57 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 7487 Sorted by residual: bond pdb=" N VAL C 378 " pdb=" CA VAL C 378 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.23e-02 6.61e+03 9.34e+00 bond pdb=" N ILE C 380 " pdb=" CA ILE C 380 " ideal model delta sigma weight residual 1.463 1.494 -0.031 1.14e-02 7.69e+03 7.30e+00 bond pdb=" N PRO C 379 " pdb=" CA PRO C 379 " ideal model delta sigma weight residual 1.471 1.497 -0.026 1.32e-02 5.74e+03 4.01e+00 bond pdb=" N GLU D 247 " pdb=" CA GLU D 247 " ideal model delta sigma weight residual 1.462 1.487 -0.025 1.31e-02 5.83e+03 3.75e+00 bond pdb=" CA VAL C 378 " pdb=" C VAL C 378 " ideal model delta sigma weight residual 1.524 1.543 -0.019 1.05e-02 9.07e+03 3.15e+00 ... (remaining 7482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 9605 1.52 - 3.04: 378 3.04 - 4.56: 88 4.56 - 6.08: 22 6.08 - 7.60: 10 Bond angle restraints: 10103 Sorted by residual: angle pdb=" CA ASP D 42 " pdb=" C ASP D 42 " pdb=" N LEU D 43 " ideal model delta sigma weight residual 119.52 116.07 3.45 7.90e-01 1.60e+00 1.91e+01 angle pdb=" CA GLU E 394 " pdb=" CB GLU E 394 " pdb=" CG GLU E 394 " ideal model delta sigma weight residual 114.10 120.77 -6.67 2.00e+00 2.50e-01 1.11e+01 angle pdb=" CA ILE C 380 " pdb=" C ILE C 380 " pdb=" O ILE C 380 " ideal model delta sigma weight residual 121.41 117.94 3.47 1.04e+00 9.25e-01 1.11e+01 angle pdb=" C TRP D 314 " pdb=" CA TRP D 314 " pdb=" CB TRP D 314 " ideal model delta sigma weight residual 110.42 103.93 6.49 1.99e+00 2.53e-01 1.06e+01 angle pdb=" CA TYR D 194 " pdb=" CB TYR D 194 " pdb=" CG TYR D 194 " ideal model delta sigma weight residual 113.90 119.53 -5.63 1.80e+00 3.09e-01 9.78e+00 ... (remaining 10098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 4079 17.03 - 34.05: 418 34.05 - 51.08: 92 51.08 - 68.11: 13 68.11 - 85.14: 15 Dihedral angle restraints: 4617 sinusoidal: 1903 harmonic: 2714 Sorted by residual: dihedral pdb=" CA VAL E 378 " pdb=" C VAL E 378 " pdb=" N PRO E 379 " pdb=" CA PRO E 379 " ideal model delta harmonic sigma weight residual -180.00 -152.13 -27.87 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA ILE D 35 " pdb=" C ILE D 35 " pdb=" N GLY D 36 " pdb=" CA GLY D 36 " ideal model delta harmonic sigma weight residual 180.00 -155.30 -24.70 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA SER C 370 " pdb=" C SER C 370 " pdb=" N ASN C 371 " pdb=" CA ASN C 371 " ideal model delta harmonic sigma weight residual 180.00 156.70 23.30 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 4614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 814 0.042 - 0.083: 256 0.083 - 0.125: 66 0.125 - 0.167: 6 0.167 - 0.209: 2 Chirality restraints: 1144 Sorted by residual: chirality pdb=" CA PRO E 379 " pdb=" N PRO E 379 " pdb=" C PRO E 379 " pdb=" CB PRO E 379 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE D 35 " pdb=" N ILE D 35 " pdb=" C ILE D 35 " pdb=" CB ILE D 35 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.39e-01 chirality pdb=" CA GLN E 410 " pdb=" N GLN E 410 " pdb=" C GLN E 410 " pdb=" CB GLN E 410 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 1141 not shown) Planarity restraints: 1295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 314 " 0.044 2.00e-02 2.50e+03 4.29e-02 4.61e+01 pdb=" CG TRP D 314 " -0.114 2.00e-02 2.50e+03 pdb=" CD1 TRP D 314 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 TRP D 314 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 314 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 314 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP D 314 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 314 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 314 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP D 314 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 378 " -0.068 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO E 379 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO E 379 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO E 379 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER D 246 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C SER D 246 " -0.055 2.00e-02 2.50e+03 pdb=" O SER D 246 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU D 247 " 0.018 2.00e-02 2.50e+03 ... (remaining 1292 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 86 2.65 - 3.21: 7554 3.21 - 3.78: 12105 3.78 - 4.34: 15745 4.34 - 4.90: 25363 Nonbonded interactions: 60853 Sorted by model distance: nonbonded pdb=" O ASP E 406 " pdb=" OG1 THR E 409 " model vdw 2.089 3.040 nonbonded pdb=" OH TYR D 15 " pdb=" O SER D 201 " model vdw 2.092 3.040 nonbonded pdb=" OG SER D 70 " pdb=" OD1 ASP D 72 " model vdw 2.122 3.040 nonbonded pdb=" OG1 THR D 100 " pdb=" OH TYR D 162 " model vdw 2.163 3.040 nonbonded pdb=" NH2 ARG D 244 " pdb=" OD1 ASN D 282 " model vdw 2.168 3.120 ... (remaining 60848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.570 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.450 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 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 : 0.004 0.054 7487 Z= 0.196 Angle : 0.759 7.601 10103 Z= 0.409 Chirality : 0.043 0.209 1144 Planarity : 0.006 0.105 1295 Dihedral : 14.979 85.136 2849 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.15 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.29), residues: 911 helix: 1.18 (0.22), residues: 615 sheet: None (None), residues: 0 loop : -1.48 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 244 TYR 0.026 0.002 TYR D 15 PHE 0.014 0.002 PHE C 431 TRP 0.114 0.005 TRP D 314 HIS 0.004 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 7487) covalent geometry : angle 0.75888 (10103) hydrogen bonds : bond 0.12259 ( 482) hydrogen bonds : angle 5.28022 ( 1434) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 TYR cc_start: 0.7522 (t80) cc_final: 0.7109 (t80) REVERT: C 424 ASP cc_start: 0.7893 (p0) cc_final: 0.7558 (p0) REVERT: D 45 GLU cc_start: 0.6971 (tt0) cc_final: 0.6415 (tp30) REVERT: E 303 LEU cc_start: 0.8987 (tp) cc_final: 0.8615 (tp) REVERT: F 54 TYR cc_start: 0.6948 (m-80) cc_final: 0.6681 (m-80) REVERT: F 115 ILE cc_start: 0.4729 (tp) cc_final: 0.4263 (mt) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1093 time to fit residues: 31.8411 Evaluate side-chains 140 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.0980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 ASN D 234 GLN ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.094884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.075194 restraints weight = 35523.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.077258 restraints weight = 24615.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.078797 restraints weight = 18946.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.079694 restraints weight = 15623.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.080522 restraints weight = 13716.551| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7487 Z= 0.159 Angle : 0.738 11.115 10103 Z= 0.386 Chirality : 0.045 0.271 1144 Planarity : 0.005 0.081 1295 Dihedral : 5.361 48.366 999 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.04 % Favored : 93.30 % Rotamer: Outliers : 1.70 % Allowed : 13.35 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.28), residues: 911 helix: 1.15 (0.21), residues: 625 sheet: None (None), residues: 0 loop : -1.46 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 297 TYR 0.029 0.002 TYR D 194 PHE 0.014 0.002 PHE D 146 TRP 0.045 0.002 TRP D 314 HIS 0.005 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7487) covalent geometry : angle 0.73779 (10103) hydrogen bonds : bond 0.04798 ( 482) hydrogen bonds : angle 4.79076 ( 1434) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 255 GLN cc_start: 0.9120 (mp10) cc_final: 0.8827 (pm20) REVERT: C 413 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7815 (tt) REVERT: C 415 ARG cc_start: 0.9263 (tpp80) cc_final: 0.9000 (mtp85) REVERT: C 423 TYR cc_start: 0.8597 (m-80) cc_final: 0.7614 (m-80) REVERT: C 424 ASP cc_start: 0.8943 (p0) cc_final: 0.8618 (p0) REVERT: D 81 MET cc_start: 0.7990 (ptp) cc_final: 0.6856 (ptp) REVERT: E 303 LEU cc_start: 0.9717 (tp) cc_final: 0.9341 (tp) REVERT: E 305 LYS cc_start: 0.9447 (mtmm) cc_final: 0.9054 (mtmm) REVERT: E 331 ARG cc_start: 0.9062 (ttp80) cc_final: 0.8844 (ttp80) REVERT: F 54 TYR cc_start: 0.8997 (m-80) cc_final: 0.8308 (m-80) REVERT: F 92 ARG cc_start: 0.9012 (mtt180) cc_final: 0.8529 (mtp180) REVERT: F 96 GLN cc_start: 0.9155 (mt0) cc_final: 0.8886 (mt0) REVERT: F 157 MET cc_start: 0.8145 (ppp) cc_final: 0.7441 (ppp) REVERT: F 161 ASP cc_start: 0.8665 (t0) cc_final: 0.8414 (t0) outliers start: 14 outliers final: 7 residues processed: 164 average time/residue: 0.1011 time to fit residues: 21.4754 Evaluate side-chains 142 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain D residue 134 HIS Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain E residue 307 LYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 114 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 43 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 20.0000 chunk 82 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 281 ASN ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.092828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.073624 restraints weight = 35059.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.075662 restraints weight = 23912.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.077095 restraints weight = 18273.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.078120 restraints weight = 15089.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.078724 restraints weight = 13091.422| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7487 Z= 0.158 Angle : 0.678 11.873 10103 Z= 0.356 Chirality : 0.042 0.243 1144 Planarity : 0.005 0.074 1295 Dihedral : 5.194 40.947 999 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.82 % Favored : 93.52 % Rotamer: Outliers : 1.82 % Allowed : 17.60 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.28), residues: 911 helix: 1.11 (0.21), residues: 637 sheet: None (None), residues: 0 loop : -1.39 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 297 TYR 0.016 0.002 TYR D 232 PHE 0.021 0.002 PHE C 426 TRP 0.024 0.002 TRP D 314 HIS 0.008 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 7487) covalent geometry : angle 0.67833 (10103) hydrogen bonds : bond 0.04535 ( 482) hydrogen bonds : angle 4.62880 ( 1434) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 255 GLN cc_start: 0.9197 (mp10) cc_final: 0.8915 (pm20) REVERT: C 423 TYR cc_start: 0.8574 (m-80) cc_final: 0.7637 (m-80) REVERT: C 424 ASP cc_start: 0.8923 (p0) cc_final: 0.8610 (p0) REVERT: D 45 GLU cc_start: 0.6681 (tt0) cc_final: 0.5910 (tm-30) REVERT: D 242 CYS cc_start: 0.8091 (m) cc_final: 0.7703 (p) REVERT: E 303 LEU cc_start: 0.9715 (tp) cc_final: 0.9359 (tp) REVERT: E 331 ARG cc_start: 0.9047 (ttp80) cc_final: 0.8807 (ttp80) REVERT: F 7 ASN cc_start: 0.8849 (t0) cc_final: 0.8550 (t0) REVERT: F 54 TYR cc_start: 0.8979 (m-80) cc_final: 0.8433 (m-80) REVERT: F 84 ASP cc_start: 0.9189 (t0) cc_final: 0.8902 (t0) REVERT: F 157 MET cc_start: 0.8258 (ppp) cc_final: 0.7565 (ppp) REVERT: F 161 ASP cc_start: 0.8666 (t0) cc_final: 0.8371 (t0) outliers start: 15 outliers final: 8 residues processed: 153 average time/residue: 0.0930 time to fit residues: 18.7163 Evaluate side-chains 135 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 134 HIS Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 325 PHE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain E residue 307 LYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 15 optimal weight: 5.9990 chunk 50 optimal weight: 0.0370 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 66 optimal weight: 0.0980 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.098020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.077353 restraints weight = 37367.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.079441 restraints weight = 25899.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.081060 restraints weight = 19924.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.082223 restraints weight = 16358.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.082692 restraints weight = 14107.513| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7487 Z= 0.141 Angle : 0.666 12.780 10103 Z= 0.344 Chirality : 0.042 0.298 1144 Planarity : 0.005 0.116 1295 Dihedral : 5.064 34.516 999 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.71 % Favored : 93.63 % Rotamer: Outliers : 2.55 % Allowed : 18.81 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.28), residues: 911 helix: 1.14 (0.21), residues: 635 sheet: None (None), residues: 0 loop : -1.33 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 297 TYR 0.022 0.002 TYR D 194 PHE 0.023 0.002 PHE C 426 TRP 0.035 0.002 TRP D 314 HIS 0.008 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 7487) covalent geometry : angle 0.66630 (10103) hydrogen bonds : bond 0.04288 ( 482) hydrogen bonds : angle 4.55472 ( 1434) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 255 GLN cc_start: 0.9231 (mp10) cc_final: 0.8976 (pm20) REVERT: C 415 ARG cc_start: 0.9430 (tpp80) cc_final: 0.8813 (mmm-85) REVERT: C 423 TYR cc_start: 0.8442 (m-80) cc_final: 0.7654 (m-80) REVERT: C 424 ASP cc_start: 0.8877 (p0) cc_final: 0.8495 (p0) REVERT: D 42 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.7027 (m-30) REVERT: D 45 GLU cc_start: 0.6522 (tt0) cc_final: 0.5764 (tm-30) REVERT: D 242 CYS cc_start: 0.8090 (m) cc_final: 0.7737 (p) REVERT: E 303 LEU cc_start: 0.9705 (tp) cc_final: 0.9334 (tp) REVERT: E 331 ARG cc_start: 0.9058 (ttp80) cc_final: 0.8813 (ttp80) REVERT: E 394 GLU cc_start: 0.9082 (tp30) cc_final: 0.8651 (mm-30) REVERT: F 1 MET cc_start: 0.5942 (tpp) cc_final: 0.5740 (tpp) REVERT: F 7 ASN cc_start: 0.8842 (t0) cc_final: 0.8571 (t0) REVERT: F 54 TYR cc_start: 0.8901 (m-80) cc_final: 0.8215 (m-10) REVERT: F 115 ILE cc_start: 0.5198 (tp) cc_final: 0.4942 (tp) REVERT: F 157 MET cc_start: 0.8285 (ppp) cc_final: 0.7621 (ppp) REVERT: F 161 ASP cc_start: 0.8708 (t0) cc_final: 0.8402 (t0) outliers start: 21 outliers final: 13 residues processed: 154 average time/residue: 0.0907 time to fit residues: 18.4784 Evaluate side-chains 142 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 267 ASN Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 134 HIS Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain E residue 307 LYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 114 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 64 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 417 ASN D 264 GLN D 365 HIS ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.089526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.069883 restraints weight = 37549.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.072047 restraints weight = 25026.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.073639 restraints weight = 18831.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.074666 restraints weight = 15285.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.075440 restraints weight = 13202.145| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7487 Z= 0.189 Angle : 0.691 9.432 10103 Z= 0.361 Chirality : 0.043 0.249 1144 Planarity : 0.005 0.094 1295 Dihedral : 5.044 25.388 999 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.60 % Favored : 93.74 % Rotamer: Outliers : 3.16 % Allowed : 20.27 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.28), residues: 911 helix: 1.23 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -1.40 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 297 TYR 0.027 0.002 TYR D 194 PHE 0.024 0.002 PHE C 426 TRP 0.024 0.002 TRP D 314 HIS 0.006 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 7487) covalent geometry : angle 0.69071 (10103) hydrogen bonds : bond 0.04374 ( 482) hydrogen bonds : angle 4.59047 ( 1434) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 255 GLN cc_start: 0.9328 (mp10) cc_final: 0.9101 (pm20) REVERT: C 415 ARG cc_start: 0.9462 (tpp80) cc_final: 0.8795 (mmm-85) REVERT: C 423 TYR cc_start: 0.8406 (m-80) cc_final: 0.7569 (m-80) REVERT: C 424 ASP cc_start: 0.9000 (p0) cc_final: 0.8696 (p0) REVERT: D 35 ILE cc_start: -0.4013 (OUTLIER) cc_final: -0.4635 (mm) REVERT: D 42 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7317 (m-30) REVERT: D 74 TRP cc_start: 0.9016 (m100) cc_final: 0.8425 (m100) REVERT: D 242 CYS cc_start: 0.8124 (m) cc_final: 0.7796 (p) REVERT: E 303 LEU cc_start: 0.9748 (tp) cc_final: 0.9387 (tp) REVERT: E 394 GLU cc_start: 0.9218 (tp30) cc_final: 0.8750 (mm-30) REVERT: F 54 TYR cc_start: 0.9105 (m-80) cc_final: 0.8041 (m-10) REVERT: F 75 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8223 (t80) REVERT: F 95 ILE cc_start: 0.9495 (tt) cc_final: 0.9019 (tt) REVERT: F 96 GLN cc_start: 0.9361 (mt0) cc_final: 0.8724 (mp10) REVERT: F 115 ILE cc_start: 0.5803 (tp) cc_final: 0.5592 (tp) outliers start: 26 outliers final: 16 residues processed: 151 average time/residue: 0.0909 time to fit residues: 18.1240 Evaluate side-chains 140 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 267 ASN Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 134 HIS Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain E residue 307 LYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 114 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 32 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 78 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 ASN ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 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 = 0.4042 r_free = 0.4042 target = 0.090556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.070920 restraints weight = 37060.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.073158 restraints weight = 24394.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.074752 restraints weight = 18190.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.075714 restraints weight = 14680.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.076114 restraints weight = 12733.659| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7487 Z= 0.144 Angle : 0.663 8.696 10103 Z= 0.347 Chirality : 0.043 0.245 1144 Planarity : 0.005 0.080 1295 Dihedral : 5.031 23.772 999 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.60 % Favored : 93.74 % Rotamer: Outliers : 2.79 % Allowed : 21.24 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.28), residues: 911 helix: 1.30 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -1.28 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 297 TYR 0.029 0.002 TYR D 20 PHE 0.027 0.002 PHE C 426 TRP 0.022 0.001 TRP D 314 HIS 0.008 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7487) covalent geometry : angle 0.66281 (10103) hydrogen bonds : bond 0.04192 ( 482) hydrogen bonds : angle 4.54507 ( 1434) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 255 GLN cc_start: 0.9389 (mp10) cc_final: 0.9156 (pm20) REVERT: C 415 ARG cc_start: 0.9468 (tpp80) cc_final: 0.8774 (mmm-85) REVERT: C 423 TYR cc_start: 0.8395 (m-80) cc_final: 0.7489 (m-80) REVERT: C 424 ASP cc_start: 0.8964 (p0) cc_final: 0.8664 (p0) REVERT: D 42 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.7093 (m-30) REVERT: D 74 TRP cc_start: 0.8970 (m100) cc_final: 0.8386 (m100) REVERT: D 242 CYS cc_start: 0.8076 (m) cc_final: 0.7783 (p) REVERT: E 303 LEU cc_start: 0.9708 (tp) cc_final: 0.9343 (tp) REVERT: E 394 GLU cc_start: 0.9165 (tp30) cc_final: 0.8705 (mm-30) REVERT: F 54 TYR cc_start: 0.9040 (m-80) cc_final: 0.8003 (m-80) REVERT: F 75 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8274 (t80) REVERT: F 95 ILE cc_start: 0.9483 (tt) cc_final: 0.8980 (tt) REVERT: F 96 GLN cc_start: 0.9334 (mt0) cc_final: 0.8698 (mp10) REVERT: F 115 ILE cc_start: 0.5708 (tp) cc_final: 0.5496 (tp) REVERT: F 157 MET cc_start: 0.8238 (ppp) cc_final: 0.7772 (ppp) outliers start: 23 outliers final: 17 residues processed: 143 average time/residue: 0.0833 time to fit residues: 16.0927 Evaluate side-chains 139 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 267 ASN Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 134 HIS Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain E residue 307 LYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 410 GLN Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 114 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 59 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 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 = 0.4048 r_free = 0.4048 target = 0.090565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.071318 restraints weight = 36987.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.073530 restraints weight = 24429.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.075097 restraints weight = 18269.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.076080 restraints weight = 14809.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.076912 restraints weight = 12786.868| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7487 Z= 0.144 Angle : 0.651 8.421 10103 Z= 0.343 Chirality : 0.041 0.199 1144 Planarity : 0.004 0.060 1295 Dihedral : 5.048 36.271 999 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.71 % Favored : 93.74 % Rotamer: Outliers : 2.79 % Allowed : 21.84 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.28), residues: 911 helix: 1.34 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -1.25 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 297 TYR 0.045 0.002 TYR D 20 PHE 0.028 0.002 PHE C 426 TRP 0.020 0.001 TRP D 314 HIS 0.007 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7487) covalent geometry : angle 0.65141 (10103) hydrogen bonds : bond 0.04143 ( 482) hydrogen bonds : angle 4.48744 ( 1434) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 287 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.9051 (pp20) REVERT: C 415 ARG cc_start: 0.9471 (tpp80) cc_final: 0.8890 (mpp80) REVERT: C 423 TYR cc_start: 0.8402 (m-80) cc_final: 0.7538 (m-80) REVERT: C 424 ASP cc_start: 0.8893 (p0) cc_final: 0.8591 (p0) REVERT: D 42 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.7057 (m-30) REVERT: D 74 TRP cc_start: 0.8958 (m100) cc_final: 0.8419 (m100) REVERT: D 242 CYS cc_start: 0.8059 (m) cc_final: 0.7790 (p) REVERT: E 303 LEU cc_start: 0.9736 (tp) cc_final: 0.9361 (tp) REVERT: E 394 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8696 (mm-30) REVERT: F 54 TYR cc_start: 0.9053 (m-80) cc_final: 0.8176 (m-80) REVERT: F 75 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8275 (t80) REVERT: F 95 ILE cc_start: 0.9478 (tt) cc_final: 0.8926 (tt) REVERT: F 96 GLN cc_start: 0.9338 (mt0) cc_final: 0.8787 (mp10) REVERT: F 157 MET cc_start: 0.8222 (ppp) cc_final: 0.7260 (ppp) REVERT: F 161 ASP cc_start: 0.8838 (t0) cc_final: 0.8516 (t0) outliers start: 23 outliers final: 15 residues processed: 144 average time/residue: 0.0907 time to fit residues: 17.4402 Evaluate side-chains 143 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 267 ASN Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 134 HIS Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 394 GLU Chi-restraints excluded: chain E residue 410 GLN Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 114 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 47 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 84 optimal weight: 0.0370 chunk 35 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 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 = 0.4047 r_free = 0.4047 target = 0.090394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.071193 restraints weight = 37406.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.073352 restraints weight = 24686.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.074887 restraints weight = 18434.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.076010 restraints weight = 14933.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.076650 restraints weight = 12789.988| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7487 Z= 0.142 Angle : 0.662 9.763 10103 Z= 0.350 Chirality : 0.041 0.182 1144 Planarity : 0.004 0.073 1295 Dihedral : 4.991 23.103 999 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.60 % Favored : 93.85 % Rotamer: Outliers : 2.79 % Allowed : 23.79 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.28), residues: 911 helix: 1.38 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -1.21 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 297 TYR 0.038 0.002 TYR D 20 PHE 0.028 0.002 PHE C 426 TRP 0.019 0.001 TRP D 314 HIS 0.006 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7487) covalent geometry : angle 0.66226 (10103) hydrogen bonds : bond 0.04075 ( 482) hydrogen bonds : angle 4.51314 ( 1434) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 415 ARG cc_start: 0.9463 (tpp80) cc_final: 0.8802 (mmm-85) REVERT: C 423 TYR cc_start: 0.8398 (m-80) cc_final: 0.7481 (m-80) REVERT: C 424 ASP cc_start: 0.8863 (p0) cc_final: 0.8542 (p0) REVERT: D 35 ILE cc_start: -0.4166 (OUTLIER) cc_final: -0.4784 (mm) REVERT: D 42 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.7023 (m-30) REVERT: D 74 TRP cc_start: 0.8948 (m100) cc_final: 0.8409 (m100) REVERT: D 180 HIS cc_start: 0.8619 (m-70) cc_final: 0.8249 (m-70) REVERT: D 242 CYS cc_start: 0.8086 (m) cc_final: 0.7818 (p) REVERT: D 292 TRP cc_start: 0.9510 (m-10) cc_final: 0.9268 (m-10) REVERT: D 301 TYR cc_start: 0.8698 (m-10) cc_final: 0.8353 (m-10) REVERT: D 342 LEU cc_start: 0.8891 (mt) cc_final: 0.8649 (mt) REVERT: E 303 LEU cc_start: 0.9739 (tp) cc_final: 0.9386 (tp) REVERT: E 307 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9022 (ptmm) REVERT: E 394 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8706 (mm-30) REVERT: F 1 MET cc_start: 0.6200 (tpt) cc_final: 0.5250 (mpp) REVERT: F 14 GLU cc_start: 0.9077 (tt0) cc_final: 0.8786 (tt0) REVERT: F 54 TYR cc_start: 0.9051 (m-80) cc_final: 0.8156 (m-80) REVERT: F 75 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8348 (t80) REVERT: F 91 PHE cc_start: 0.9302 (m-80) cc_final: 0.8976 (m-80) REVERT: F 95 ILE cc_start: 0.9482 (tt) cc_final: 0.8927 (pt) REVERT: F 96 GLN cc_start: 0.9358 (mt0) cc_final: 0.8811 (mp10) REVERT: F 157 MET cc_start: 0.8265 (ppp) cc_final: 0.7300 (ppp) REVERT: F 161 ASP cc_start: 0.8837 (t0) cc_final: 0.8506 (t0) outliers start: 23 outliers final: 14 residues processed: 144 average time/residue: 0.0808 time to fit residues: 15.7294 Evaluate side-chains 147 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 267 ASN Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 134 HIS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain E residue 307 LYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 394 GLU Chi-restraints excluded: chain E residue 410 GLN Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 114 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 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 = 0.4031 r_free = 0.4031 target = 0.089415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.070207 restraints weight = 36808.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.072354 restraints weight = 24432.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.073850 restraints weight = 18324.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.074933 restraints weight = 14958.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.075675 restraints weight = 12878.743| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7487 Z= 0.162 Angle : 0.696 10.404 10103 Z= 0.371 Chirality : 0.042 0.186 1144 Planarity : 0.005 0.074 1295 Dihedral : 5.001 23.049 999 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.60 % Favored : 93.85 % Rotamer: Outliers : 2.67 % Allowed : 23.91 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.28), residues: 911 helix: 1.39 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -1.34 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 297 TYR 0.036 0.002 TYR D 20 PHE 0.026 0.002 PHE C 426 TRP 0.020 0.002 TRP D 314 HIS 0.006 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 7487) covalent geometry : angle 0.69560 (10103) hydrogen bonds : bond 0.04229 ( 482) hydrogen bonds : angle 4.57287 ( 1434) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 242 MET cc_start: 0.7554 (tpp) cc_final: 0.7160 (tpp) REVERT: C 297 ARG cc_start: 0.8500 (mtt180) cc_final: 0.8288 (mtm-85) REVERT: C 423 TYR cc_start: 0.8384 (m-80) cc_final: 0.7351 (m-80) REVERT: C 424 ASP cc_start: 0.8944 (p0) cc_final: 0.8646 (p0) REVERT: D 35 ILE cc_start: -0.3922 (OUTLIER) cc_final: -0.4561 (mm) REVERT: D 42 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.6971 (m-30) REVERT: D 110 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8444 (mp10) REVERT: D 180 HIS cc_start: 0.8616 (m-70) cc_final: 0.8239 (m-70) REVERT: D 242 CYS cc_start: 0.8062 (m) cc_final: 0.7814 (p) REVERT: D 276 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8186 (mm-30) REVERT: D 342 LEU cc_start: 0.8936 (mt) cc_final: 0.8700 (mt) REVERT: E 303 LEU cc_start: 0.9732 (tp) cc_final: 0.9361 (tp) REVERT: E 307 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.9084 (ptmm) REVERT: E 394 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8724 (mm-30) REVERT: F 1 MET cc_start: 0.6160 (tpt) cc_final: 0.5206 (mpp) REVERT: F 14 GLU cc_start: 0.9030 (tt0) cc_final: 0.8685 (tt0) REVERT: F 54 TYR cc_start: 0.9059 (m-80) cc_final: 0.8008 (m-10) REVERT: F 75 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8354 (t80) REVERT: F 95 ILE cc_start: 0.9649 (tt) cc_final: 0.9304 (tt) REVERT: F 96 GLN cc_start: 0.9340 (mt0) cc_final: 0.8725 (mp10) REVERT: F 157 MET cc_start: 0.8274 (ppp) cc_final: 0.7322 (ppp) REVERT: F 161 ASP cc_start: 0.8818 (t0) cc_final: 0.8480 (t0) outliers start: 22 outliers final: 11 residues processed: 139 average time/residue: 0.0787 time to fit residues: 14.8861 Evaluate side-chains 136 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 267 ASN Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 134 HIS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain E residue 307 LYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 394 GLU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 30.0000 chunk 18 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 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 = 0.4047 r_free = 0.4047 target = 0.089998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.070887 restraints weight = 36633.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.073083 restraints weight = 24072.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.074680 restraints weight = 17935.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.075729 restraints weight = 14492.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.076480 restraints weight = 12447.313| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7487 Z= 0.149 Angle : 0.710 13.901 10103 Z= 0.371 Chirality : 0.043 0.221 1144 Planarity : 0.005 0.074 1295 Dihedral : 4.988 22.385 999 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.49 % Favored : 93.96 % Rotamer: Outliers : 2.18 % Allowed : 24.88 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.29), residues: 911 helix: 1.45 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -1.35 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 297 TYR 0.024 0.001 TYR D 194 PHE 0.029 0.002 PHE C 426 TRP 0.021 0.002 TRP D 314 HIS 0.003 0.001 HIS C 381 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 7487) covalent geometry : angle 0.70969 (10103) hydrogen bonds : bond 0.04154 ( 482) hydrogen bonds : angle 4.62798 ( 1434) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 242 MET cc_start: 0.7413 (tpp) cc_final: 0.7052 (tpp) REVERT: C 297 ARG cc_start: 0.8517 (mtt180) cc_final: 0.8303 (mtm-85) REVERT: C 423 TYR cc_start: 0.8423 (m-80) cc_final: 0.7450 (m-80) REVERT: C 424 ASP cc_start: 0.8930 (p0) cc_final: 0.8634 (p0) REVERT: D 35 ILE cc_start: -0.3990 (OUTLIER) cc_final: -0.4617 (mm) REVERT: D 42 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.6905 (m-30) REVERT: D 108 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8710 (m) REVERT: D 110 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8448 (mp10) REVERT: D 180 HIS cc_start: 0.8567 (m-70) cc_final: 0.8200 (m-70) REVERT: D 242 CYS cc_start: 0.8073 (m) cc_final: 0.7830 (p) REVERT: D 276 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8226 (mm-30) REVERT: D 342 LEU cc_start: 0.8924 (mt) cc_final: 0.8689 (mt) REVERT: E 303 LEU cc_start: 0.9733 (tp) cc_final: 0.9364 (tp) REVERT: E 307 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.9076 (ptmm) REVERT: E 343 GLN cc_start: 0.9435 (mm-40) cc_final: 0.8829 (tm-30) REVERT: E 394 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8679 (mm-30) REVERT: F 1 MET cc_start: 0.6116 (tpt) cc_final: 0.5211 (mpp) REVERT: F 7 ASN cc_start: 0.8844 (t0) cc_final: 0.8523 (t0) REVERT: F 14 GLU cc_start: 0.8973 (tt0) cc_final: 0.8628 (tt0) REVERT: F 54 TYR cc_start: 0.9038 (m-80) cc_final: 0.8048 (m-80) REVERT: F 75 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8345 (t80) REVERT: F 92 ARG cc_start: 0.9007 (mtt180) cc_final: 0.8632 (mtt180) REVERT: F 95 ILE cc_start: 0.9660 (tt) cc_final: 0.9214 (pt) REVERT: F 96 GLN cc_start: 0.9340 (mt0) cc_final: 0.8750 (mp10) REVERT: F 157 MET cc_start: 0.8252 (ppp) cc_final: 0.7275 (ppp) REVERT: F 161 ASP cc_start: 0.8796 (t0) cc_final: 0.8446 (t0) outliers start: 18 outliers final: 10 residues processed: 136 average time/residue: 0.0925 time to fit residues: 16.9619 Evaluate side-chains 139 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 267 ASN Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 134 HIS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain E residue 307 LYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 394 GLU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 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 = 0.4027 r_free = 0.4027 target = 0.089106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.070172 restraints weight = 36201.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.072280 restraints weight = 23879.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.073935 restraints weight = 17826.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.075014 restraints weight = 14357.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.075435 restraints weight = 12310.953| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7487 Z= 0.167 Angle : 0.725 11.572 10103 Z= 0.380 Chirality : 0.043 0.196 1144 Planarity : 0.004 0.073 1295 Dihedral : 4.986 22.633 999 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.71 % Favored : 93.74 % Rotamer: Outliers : 2.31 % Allowed : 24.88 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.29), residues: 911 helix: 1.41 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -1.41 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 174 TYR 0.026 0.002 TYR D 194 PHE 0.027 0.002 PHE C 426 TRP 0.020 0.002 TRP D 314 HIS 0.006 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 7487) covalent geometry : angle 0.72513 (10103) hydrogen bonds : bond 0.04207 ( 482) hydrogen bonds : angle 4.64319 ( 1434) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1531.31 seconds wall clock time: 27 minutes 10.28 seconds (1630.28 seconds total)