Starting phenix.real_space_refine on Tue Feb 3 20:46:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ny5_49922/02_2026/9ny5_49922.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ny5_49922/02_2026/9ny5_49922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ny5_49922/02_2026/9ny5_49922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ny5_49922/02_2026/9ny5_49922.map" model { file = "/net/cci-nas-00/data/ceres_data/9ny5_49922/02_2026/9ny5_49922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ny5_49922/02_2026/9ny5_49922.cif" } resolution = 3.21 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 21 5.16 5 C 4269 2.51 5 N 1167 2.21 5 O 1289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6746 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1367 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 9, 'TRANS': 161} Chain: "A" Number of atoms: 2715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2715 Classifications: {'peptide': 333} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 325} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1621 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain breaks: 1 Chain: "B" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1043 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Time building chain proxies: 1.62, per 1000 atoms: 0.24 Number of scatterers: 6746 At special positions: 0 Unit cell: (73.95, 86.275, 144.275, 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 21 16.00 O 1289 8.00 N 1167 7.00 C 4269 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: 0.58 Conformation dependent library (CDL) restraints added in 252.7 milliseconds 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1612 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 2 sheets defined 71.2% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'C' and resid 14 through 22 removed outlier: 3.597A pdb=" N GLU C 19 " --> pdb=" O ASN C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 45 removed outlier: 3.640A pdb=" N TRP C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 54 No H-bonds generated for 'chain 'C' and resid 52 through 54' Processing helix chain 'C' and resid 55 through 61 removed outlier: 4.005A pdb=" N PHE C 59 " --> pdb=" O CYS C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 70 removed outlier: 3.661A pdb=" N LEU C 70 " --> pdb=" O ARG C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 85 removed outlier: 3.667A pdb=" N LEU C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 82 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE C 83 " --> pdb=" O TYR C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 97 removed outlier: 3.623A pdb=" N ILE C 97 " --> pdb=" O PRO C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 104 removed outlier: 4.019A pdb=" N ASP C 102 " --> pdb=" O HIS C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 117 removed outlier: 4.443A pdb=" N ASP C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 162 removed outlier: 3.660A pdb=" N GLU C 150 " --> pdb=" O ASP C 146 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR C 153 " --> pdb=" O LYS C 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 28 removed outlier: 3.855A pdb=" N LEU A 22 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 80 removed outlier: 4.131A pdb=" N TRP A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 86 Processing helix chain 'A' and resid 107 through 114 Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 136 through 147 removed outlier: 5.020A pdb=" N TYR A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASN A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 159 Processing helix chain 'A' and resid 168 through 181 Processing helix chain 'A' and resid 189 through 210 removed outlier: 3.803A pdb=" N LYS A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 235 removed outlier: 3.713A pdb=" N LYS A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 259 through 269 removed outlier: 3.795A pdb=" N ILE A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 295 Processing helix chain 'A' and resid 301 through 326 removed outlier: 3.856A pdb=" N TYR A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU A 309 " --> pdb=" O TYR A 305 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 325 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A 326 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 343 Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.623A pdb=" N LYS A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 241 Processing helix chain 'D' and resid 257 through 271 removed outlier: 4.199A pdb=" N ASN D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL D 264 " --> pdb=" O ARG D 260 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU D 265 " --> pdb=" O LEU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 317 removed outlier: 3.697A pdb=" N TYR D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU D 287 " --> pdb=" O LYS D 283 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS D 305 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN D 311 " --> pdb=" O LYS D 307 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN D 312 " --> pdb=" O SER D 308 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN D 317 " --> pdb=" O ILE D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 345 removed outlier: 3.614A pdb=" N LEU D 341 " --> pdb=" O SER D 337 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR D 342 " --> pdb=" O LYS D 338 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN D 343 " --> pdb=" O TRP D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 361 through 376 removed outlier: 4.010A pdb=" N LEU D 372 " --> pdb=" O ALA D 368 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 374 " --> pdb=" O SER D 370 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU D 376 " --> pdb=" O LEU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 416 removed outlier: 3.649A pdb=" N LYS D 390 " --> pdb=" O LEU D 386 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER D 402 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR D 409 " --> pdb=" O LYS D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 439 removed outlier: 3.662A pdb=" N VAL D 428 " --> pdb=" O ASP D 424 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY D 433 " --> pdb=" O GLY D 429 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU D 434 " --> pdb=" O LYS D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 442 No H-bonds generated for 'chain 'D' and resid 440 through 442' Processing helix chain 'B' and resid 287 through 335 removed outlier: 4.419A pdb=" N ASN B 321 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 347 Processing helix chain 'B' and resid 356 through 375 removed outlier: 5.440A pdb=" N GLU B 363 " --> pdb=" O SER B 359 " (cutoff:3.500A) Proline residue: B 364 - end of helix removed outlier: 3.688A pdb=" N ALA B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 415 Processing sheet with id=AA1, first strand: chain 'C' and resid 121 through 123 Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 163 removed outlier: 7.129A pdb=" N PHE A 96 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE A 163 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU A 98 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU A 97 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 216 " --> pdb=" O CYS A 34 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1379 1.33 - 1.45: 1519 1.45 - 1.57: 3924 1.57 - 1.70: 0 1.70 - 1.82: 34 Bond restraints: 6856 Sorted by residual: bond pdb=" N LEU D 376 " pdb=" CA LEU D 376 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.16e-02 7.43e+03 8.40e+00 bond pdb=" C GLU B 353 " pdb=" N PRO B 354 " ideal model delta sigma weight residual 1.332 1.363 -0.031 1.12e-02 7.97e+03 7.76e+00 bond pdb=" C PRO C 26 " pdb=" O PRO C 26 " ideal model delta sigma weight residual 1.239 1.205 0.033 1.27e-02 6.20e+03 6.89e+00 bond pdb=" N LYS A 210 " pdb=" CA LYS A 210 " ideal model delta sigma weight residual 1.452 1.485 -0.032 1.25e-02 6.40e+03 6.66e+00 bond pdb=" N LEU B 414 " pdb=" CA LEU B 414 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.32e-02 5.74e+03 5.95e+00 ... (remaining 6851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 8813 1.90 - 3.80: 346 3.80 - 5.70: 57 5.70 - 7.60: 21 7.60 - 9.50: 9 Bond angle restraints: 9246 Sorted by residual: angle pdb=" C ILE C 23 " pdb=" N ASN C 24 " pdb=" CA ASN C 24 " ideal model delta sigma weight residual 122.21 115.26 6.95 1.48e+00 4.57e-01 2.21e+01 angle pdb=" N ASN C 24 " pdb=" CA ASN C 24 " pdb=" C ASN C 24 " ideal model delta sigma weight residual 110.70 103.65 7.05 1.55e+00 4.16e-01 2.07e+01 angle pdb=" CA GLN B 410 " pdb=" CB GLN B 410 " pdb=" CG GLN B 410 " ideal model delta sigma weight residual 114.10 122.72 -8.62 2.00e+00 2.50e-01 1.86e+01 angle pdb=" C ASN A 344 " pdb=" N VAL A 345 " pdb=" CA VAL A 345 " ideal model delta sigma weight residual 121.97 129.73 -7.76 1.80e+00 3.09e-01 1.86e+01 angle pdb=" N LEU B 414 " pdb=" CA LEU B 414 " pdb=" C LEU B 414 " ideal model delta sigma weight residual 113.50 108.26 5.24 1.23e+00 6.61e-01 1.82e+01 ... (remaining 9241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 3428 17.23 - 34.46: 531 34.46 - 51.68: 204 51.68 - 68.91: 44 68.91 - 86.14: 11 Dihedral angle restraints: 4218 sinusoidal: 1746 harmonic: 2472 Sorted by residual: dihedral pdb=" CA VAL B 361 " pdb=" C VAL B 361 " pdb=" N LEU B 362 " pdb=" CA LEU B 362 " ideal model delta harmonic sigma weight residual -180.00 -157.48 -22.52 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA GLU B 363 " pdb=" C GLU B 363 " pdb=" N PRO B 364 " pdb=" CA PRO B 364 " ideal model delta harmonic sigma weight residual 180.00 159.39 20.61 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ASP A 300 " pdb=" C ASP A 300 " pdb=" N TYR A 301 " pdb=" CA TYR A 301 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 4215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 866 0.065 - 0.130: 147 0.130 - 0.195: 24 0.195 - 0.260: 9 0.260 - 0.325: 1 Chirality restraints: 1047 Sorted by residual: chirality pdb=" CB THR A 161 " pdb=" CA THR A 161 " pdb=" OG1 THR A 161 " pdb=" CG2 THR A 161 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB VAL B 407 " pdb=" CA VAL B 407 " pdb=" CG1 VAL B 407 " pdb=" CG2 VAL B 407 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA HIS A 188 " pdb=" N HIS A 188 " pdb=" C HIS A 188 " pdb=" CB HIS A 188 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 1044 not shown) Planarity restraints: 1177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 363 " 0.056 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO B 364 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 364 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 364 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 57 " 0.054 5.00e-02 4.00e+02 8.12e-02 1.05e+01 pdb=" N PRO C 58 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 58 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 58 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 298 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" CG ASP B 298 " -0.055 2.00e-02 2.50e+03 pdb=" OD1 ASP B 298 " 0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP B 298 " 0.019 2.00e-02 2.50e+03 ... (remaining 1174 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1785 2.80 - 3.33: 6310 3.33 - 3.85: 11569 3.85 - 4.38: 13156 4.38 - 4.90: 22113 Nonbonded interactions: 54933 Sorted by model distance: nonbonded pdb=" OG SER A 70 " pdb=" OD1 ASP A 72 " model vdw 2.278 3.040 nonbonded pdb=" OG SER D 232 " pdb=" O ASP D 406 " model vdw 2.299 3.040 nonbonded pdb=" OG SER D 337 " pdb=" O ALA D 366 " model vdw 2.305 3.040 nonbonded pdb=" OE2 GLU A 309 " pdb=" CE2 TYR A 348 " model vdw 2.312 3.340 nonbonded pdb=" O GLN A 110 " pdb=" OG1 THR A 114 " model vdw 2.314 3.040 ... (remaining 54928 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.400 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 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 0.047 6856 Z= 0.230 Angle : 0.898 9.495 9246 Z= 0.510 Chirality : 0.054 0.325 1047 Planarity : 0.006 0.084 1177 Dihedral : 19.443 86.140 2606 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.46 % Allowed : 32.67 % Favored : 65.87 % 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: -3.18 (0.24), residues: 822 helix: -2.02 (0.18), residues: 539 sheet: -1.23 (1.46), residues: 10 loop : -1.96 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 155 TYR 0.040 0.003 TYR A 232 PHE 0.020 0.002 PHE D 431 TRP 0.010 0.001 TRP A 74 HIS 0.029 0.002 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 6856) covalent geometry : angle 0.89772 ( 9246) hydrogen bonds : bond 0.21232 ( 391) hydrogen bonds : angle 7.57659 ( 1167) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 112 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7658 (mt) REVERT: D 316 MET cc_start: 0.6040 (mmt) cc_final: 0.5655 (mmt) outliers start: 11 outliers final: 1 residues processed: 112 average time/residue: 0.0800 time to fit residues: 12.2741 Evaluate side-chains 97 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain A residue 112 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 ASN C 167 ASN A 145 ASN D 281 ASN D 312 ASN D 383 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.165814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.138572 restraints weight = 11019.563| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.48 r_work: 0.3765 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6856 Z= 0.144 Angle : 0.578 10.329 9246 Z= 0.303 Chirality : 0.039 0.129 1047 Planarity : 0.005 0.066 1177 Dihedral : 5.299 51.885 911 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 5.05 % Allowed : 28.69 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.28), residues: 822 helix: -0.27 (0.21), residues: 559 sheet: -1.07 (1.46), residues: 10 loop : -1.59 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 419 TYR 0.024 0.002 TYR A 232 PHE 0.009 0.001 PHE A 99 TRP 0.012 0.001 TRP A 74 HIS 0.003 0.001 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6856) covalent geometry : angle 0.57757 ( 9246) hydrogen bonds : bond 0.04517 ( 391) hydrogen bonds : angle 4.43588 ( 1167) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 98 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7945 (mt) REVERT: A 143 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.7013 (mp) REVERT: A 206 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8415 (tt) REVERT: A 235 LYS cc_start: 0.6477 (OUTLIER) cc_final: 0.6092 (pttp) REVERT: B 404 MET cc_start: 0.8749 (mmm) cc_final: 0.8362 (mmt) outliers start: 38 outliers final: 18 residues processed: 124 average time/residue: 0.0756 time to fit residues: 12.9902 Evaluate side-chains 114 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 419 ARG Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 398 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.0050 chunk 77 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 63 optimal weight: 0.0010 overall best weight: 0.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS ** B 410 GLN ** 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 = 0.4323 r_free = 0.4323 target = 0.165506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.136051 restraints weight = 11055.092| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.57 r_work: 0.3769 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6856 Z= 0.122 Angle : 0.540 10.817 9246 Z= 0.276 Chirality : 0.039 0.126 1047 Planarity : 0.004 0.064 1177 Dihedral : 4.859 47.300 909 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 5.31 % Allowed : 27.76 % Favored : 66.93 % 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: -0.32 (0.29), residues: 822 helix: 0.41 (0.21), residues: 562 sheet: -1.10 (1.52), residues: 10 loop : -1.47 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 297 TYR 0.016 0.001 TYR A 348 PHE 0.008 0.001 PHE A 359 TRP 0.012 0.001 TRP A 74 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 6856) covalent geometry : angle 0.53981 ( 9246) hydrogen bonds : bond 0.03935 ( 391) hydrogen bonds : angle 4.06495 ( 1167) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8407 (tt) REVERT: D 291 GLU cc_start: 0.8444 (tp30) cc_final: 0.8230 (mm-30) REVERT: D 419 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6667 (mmp80) outliers start: 40 outliers final: 25 residues processed: 122 average time/residue: 0.0684 time to fit residues: 11.7706 Evaluate side-chains 116 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 419 ARG Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 398 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 65 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN ** B 410 GLN ** 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 = 0.4306 r_free = 0.4306 target = 0.163967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.134358 restraints weight = 11185.521| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.54 r_work: 0.3750 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6856 Z= 0.139 Angle : 0.552 10.712 9246 Z= 0.282 Chirality : 0.040 0.132 1047 Planarity : 0.004 0.062 1177 Dihedral : 4.488 19.185 907 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 6.11 % Allowed : 26.56 % Favored : 67.33 % 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: -0.02 (0.29), residues: 822 helix: 0.73 (0.22), residues: 565 sheet: -1.33 (1.52), residues: 10 loop : -1.61 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 297 TYR 0.021 0.002 TYR A 232 PHE 0.009 0.001 PHE A 359 TRP 0.011 0.001 TRP A 74 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6856) covalent geometry : angle 0.55227 ( 9246) hydrogen bonds : bond 0.03756 ( 391) hydrogen bonds : angle 3.97221 ( 1167) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 93 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.7247 (mt) cc_final: 0.6829 (mp) REVERT: A 81 MET cc_start: 0.7168 (mmt) cc_final: 0.6784 (ptm) REVERT: A 206 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8448 (tt) REVERT: A 235 LYS cc_start: 0.6719 (OUTLIER) cc_final: 0.6356 (pttp) REVERT: A 351 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7070 (tm-30) REVERT: D 419 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6671 (mmp80) outliers start: 46 outliers final: 27 residues processed: 126 average time/residue: 0.0721 time to fit residues: 12.8379 Evaluate side-chains 117 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 419 ARG Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 398 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 68 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.0020 chunk 19 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 0.0010 chunk 8 optimal weight: 0.8980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.165026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.137112 restraints weight = 11003.194| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.39 r_work: 0.3777 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6856 Z= 0.112 Angle : 0.528 11.077 9246 Z= 0.269 Chirality : 0.039 0.138 1047 Planarity : 0.004 0.061 1177 Dihedral : 4.374 20.017 907 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 5.44 % Allowed : 27.09 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.29), residues: 822 helix: 1.00 (0.22), residues: 561 sheet: -1.45 (1.54), residues: 10 loop : -1.58 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 419 TYR 0.014 0.001 TYR A 232 PHE 0.009 0.001 PHE A 359 TRP 0.010 0.001 TRP A 74 HIS 0.006 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 6856) covalent geometry : angle 0.52824 ( 9246) hydrogen bonds : bond 0.03480 ( 391) hydrogen bonds : angle 3.82996 ( 1167) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 93 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8375 (tt) REVERT: A 235 LYS cc_start: 0.6650 (OUTLIER) cc_final: 0.6231 (pttp) REVERT: A 351 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7094 (tm-30) REVERT: D 419 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6711 (mmp80) outliers start: 41 outliers final: 31 residues processed: 121 average time/residue: 0.0751 time to fit residues: 12.4825 Evaluate side-chains 124 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 89 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 419 ARG Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 398 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 67 optimal weight: 2.9990 chunk 64 optimal weight: 0.0670 chunk 52 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.162234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.132757 restraints weight = 11252.212| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.55 r_work: 0.3717 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 6856 Z= 0.153 Angle : 0.565 12.212 9246 Z= 0.287 Chirality : 0.042 0.307 1047 Planarity : 0.004 0.060 1177 Dihedral : 4.439 19.005 907 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 5.84 % Allowed : 27.36 % Favored : 66.80 % 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: 0.26 (0.29), residues: 822 helix: 1.02 (0.22), residues: 562 sheet: -1.33 (1.53), residues: 10 loop : -1.69 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 419 TYR 0.021 0.002 TYR D 392 PHE 0.015 0.001 PHE D 431 TRP 0.011 0.001 TRP A 74 HIS 0.011 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 6856) covalent geometry : angle 0.56520 ( 9246) hydrogen bonds : bond 0.03631 ( 391) hydrogen bonds : angle 3.90725 ( 1167) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 90 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8418 (tt) REVERT: A 235 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6515 (pttp) REVERT: D 419 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6721 (mmp80) outliers start: 44 outliers final: 29 residues processed: 121 average time/residue: 0.0856 time to fit residues: 14.1501 Evaluate side-chains 117 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 419 ARG Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 398 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 12 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.161855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.132949 restraints weight = 10930.742| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.46 r_work: 0.3721 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 6856 Z= 0.157 Angle : 0.590 15.374 9246 Z= 0.295 Chirality : 0.043 0.473 1047 Planarity : 0.004 0.060 1177 Dihedral : 4.461 19.331 907 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 5.98 % Allowed : 27.76 % Favored : 66.27 % 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: 0.26 (0.29), residues: 822 helix: 1.03 (0.22), residues: 561 sheet: -1.12 (1.53), residues: 10 loop : -1.72 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 297 TYR 0.057 0.002 TYR A 232 PHE 0.010 0.001 PHE A 359 TRP 0.009 0.001 TRP A 74 HIS 0.009 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 6856) covalent geometry : angle 0.59014 ( 9246) hydrogen bonds : bond 0.03588 ( 391) hydrogen bonds : angle 3.93696 ( 1167) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 87 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 169 ASP cc_start: 0.7935 (p0) cc_final: 0.7730 (p0) REVERT: A 206 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8424 (tt) REVERT: A 235 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6636 (pttp) REVERT: D 419 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6738 (mmp80) outliers start: 45 outliers final: 33 residues processed: 119 average time/residue: 0.0775 time to fit residues: 12.6963 Evaluate side-chains 120 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 84 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 TYR Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 419 ARG Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 398 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.160384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.130710 restraints weight = 11259.766| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.48 r_work: 0.3692 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 6856 Z= 0.179 Angle : 0.635 15.492 9246 Z= 0.318 Chirality : 0.045 0.503 1047 Planarity : 0.004 0.059 1177 Dihedral : 4.535 19.789 907 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 6.64 % Allowed : 27.22 % Favored : 66.14 % 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: 0.20 (0.29), residues: 822 helix: 0.99 (0.22), residues: 562 sheet: -1.12 (1.50), residues: 10 loop : -1.76 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 297 TYR 0.037 0.002 TYR A 232 PHE 0.011 0.001 PHE A 359 TRP 0.011 0.001 TRP A 74 HIS 0.007 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 6856) covalent geometry : angle 0.63501 ( 9246) hydrogen bonds : bond 0.03672 ( 391) hydrogen bonds : angle 4.04238 ( 1167) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 85 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 MET cc_start: 0.6833 (OUTLIER) cc_final: 0.6632 (ptt) REVERT: A 206 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8477 (tt) REVERT: A 235 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6741 (pttp) REVERT: A 351 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: D 419 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6706 (mmp80) outliers start: 50 outliers final: 36 residues processed: 122 average time/residue: 0.0831 time to fit residues: 13.6739 Evaluate side-chains 121 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 80 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 TYR Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 419 ARG Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 398 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.3980 chunk 8 optimal weight: 0.0370 chunk 75 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 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 = 0.4291 r_free = 0.4291 target = 0.162614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.132534 restraints weight = 11231.990| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.61 r_work: 0.3723 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6856 Z= 0.131 Angle : 0.603 16.584 9246 Z= 0.299 Chirality : 0.044 0.512 1047 Planarity : 0.004 0.060 1177 Dihedral : 4.447 19.952 907 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 5.44 % Allowed : 28.95 % Favored : 65.60 % 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: 0.43 (0.30), residues: 822 helix: 1.17 (0.22), residues: 560 sheet: -0.42 (1.68), residues: 10 loop : -1.70 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 297 TYR 0.039 0.001 TYR A 232 PHE 0.011 0.001 PHE A 359 TRP 0.011 0.001 TRP A 74 HIS 0.008 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6856) covalent geometry : angle 0.60340 ( 9246) hydrogen bonds : bond 0.03467 ( 391) hydrogen bonds : angle 3.92290 ( 1167) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 92 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6679 (pptt) REVERT: A 351 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7271 (tm-30) REVERT: D 392 TYR cc_start: 0.8715 (t80) cc_final: 0.8451 (t80) REVERT: D 419 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6708 (mmp80) REVERT: B 404 MET cc_start: 0.8584 (mmm) cc_final: 0.8118 (mmm) outliers start: 41 outliers final: 34 residues processed: 124 average time/residue: 0.0826 time to fit residues: 14.0418 Evaluate side-chains 124 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 87 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 TYR Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 419 ARG Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 398 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 19 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 49 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.161652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.131528 restraints weight = 11250.710| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.64 r_work: 0.3719 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 6856 Z= 0.150 Angle : 0.639 16.883 9246 Z= 0.317 Chirality : 0.044 0.504 1047 Planarity : 0.004 0.060 1177 Dihedral : 4.450 19.557 907 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.91 % Allowed : 29.75 % Favored : 65.34 % 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: 0.34 (0.30), residues: 822 helix: 1.10 (0.22), residues: 565 sheet: -0.47 (1.66), residues: 10 loop : -1.78 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 297 TYR 0.035 0.002 TYR A 232 PHE 0.011 0.001 PHE A 359 TRP 0.014 0.001 TRP A 80 HIS 0.007 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6856) covalent geometry : angle 0.63867 ( 9246) hydrogen bonds : bond 0.03526 ( 391) hydrogen bonds : angle 3.98160 ( 1167) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.6948 (OUTLIER) cc_final: 0.6666 (pptt) REVERT: A 351 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7327 (tm-30) REVERT: D 392 TYR cc_start: 0.8720 (t80) cc_final: 0.8444 (t80) REVERT: D 419 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6708 (mmp80) REVERT: B 404 MET cc_start: 0.8551 (mmm) cc_final: 0.8045 (mmm) outliers start: 37 outliers final: 33 residues processed: 114 average time/residue: 0.0854 time to fit residues: 13.2252 Evaluate side-chains 121 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 85 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 TYR Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 419 ARG Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 398 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 76 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.0980 chunk 66 optimal weight: 0.9980 chunk 1 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.162955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.131518 restraints weight = 11111.987| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.66 r_work: 0.3722 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6856 Z= 0.130 Angle : 0.619 16.895 9246 Z= 0.310 Chirality : 0.044 0.500 1047 Planarity : 0.004 0.060 1177 Dihedral : 4.403 19.861 907 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.91 % Allowed : 29.75 % Favored : 65.34 % 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: 0.47 (0.30), residues: 822 helix: 1.20 (0.22), residues: 564 sheet: -0.31 (1.75), residues: 10 loop : -1.74 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 297 TYR 0.035 0.001 TYR A 232 PHE 0.010 0.001 PHE A 359 TRP 0.013 0.001 TRP A 80 HIS 0.007 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6856) covalent geometry : angle 0.61888 ( 9246) hydrogen bonds : bond 0.03393 ( 391) hydrogen bonds : angle 3.90271 ( 1167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1945.44 seconds wall clock time: 34 minutes 14.44 seconds (2054.44 seconds total)