Starting phenix.real_space_refine on Tue Aug 4 14:44:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nen_49328/08_2026/9nen_49328.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nen_49328/08_2026/9nen_49328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nen_49328/08_2026/9nen_49328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nen_49328/08_2026/9nen_49328.map" model { file = "/net/cci-nas-00/data/ceres_data/9nen_49328/08_2026/9nen_49328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nen_49328/08_2026/9nen_49328.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 30 5.16 5 C 2521 2.51 5 N 675 2.21 5 O 721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3947 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3947 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain breaks: 3 Time building chain proxies: 1.53, per 1000 atoms: 0.39 Number of scatterers: 3947 At special positions: 0 Unit cell: (56.826, 79.695, 100.485, 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 30 16.00 O 721 8.00 N 675 7.00 C 2521 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: 0.48 Conformation dependent library (CDL) restraints added in 178.9 milliseconds 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 944 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 1 sheets defined 60.3% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 28 through 40 removed outlier: 3.598A pdb=" N LEU A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 40 " --> pdb=" O PHE A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 59 through 66 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 89 through 101 Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.752A pdb=" N ALA A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 121 through 135 Processing helix chain 'A' and resid 145 through 159 removed outlier: 3.516A pdb=" N ILE A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS A 159 " --> pdb=" O TRP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 169 removed outlier: 3.558A pdb=" N LEU A 166 " --> pdb=" O MET A 162 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 186 removed outlier: 3.885A pdb=" N LEU A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 205 removed outlier: 3.569A pdb=" N ILE A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 removed outlier: 4.030A pdb=" N GLU A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 237 removed outlier: 3.540A pdb=" N LEU A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 245 removed outlier: 4.185A pdb=" N VAL A 244 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 240 through 245' Processing helix chain 'A' and resid 261 through 264 Processing helix chain 'A' and resid 265 through 275 removed outlier: 3.655A pdb=" N ALA A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 298 through 309 removed outlier: 3.737A pdb=" N SER A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 317 Processing helix chain 'A' and resid 322 through 334 removed outlier: 4.209A pdb=" N GLY A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 360 removed outlier: 3.505A pdb=" N LYS A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 391 through 407 removed outlier: 3.651A pdb=" N MET A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR A 404 " --> pdb=" O CYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 440 removed outlier: 4.099A pdb=" N ILE A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 456 Processing helix chain 'A' and resid 478 through 491 removed outlier: 3.514A pdb=" N TYR A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET A 490 " --> pdb=" O TYR A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 535 removed outlier: 3.544A pdb=" N VAL A 529 " --> pdb=" O GLY A 525 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 47 removed outlier: 6.093A pdb=" N PHE A 464 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N CYS A 499 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL A 466 " --> pdb=" O CYS A 499 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU A 372 " --> pdb=" O ILE A 465 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE A 467 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA A 374 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE A 371 " --> pdb=" O TYR A 411 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL A 413 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU A 373 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N PHE A 415 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL A 375 " --> pdb=" O PHE A 415 " (cutoff:3.500A) 165 hydrogen bonds defined for protein. 480 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: 0.53 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1271 1.34 - 1.46: 822 1.46 - 1.58: 1876 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 4017 Sorted by residual: bond pdb=" CB LYS A 49 " pdb=" CG LYS A 49 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.74e-01 bond pdb=" CB GLU A 267 " pdb=" CG GLU A 267 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.10e-01 bond pdb=" CB ASP A 427 " pdb=" CG ASP A 427 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.06e-01 bond pdb=" N GLY A 476 " pdb=" CA GLY A 476 " ideal model delta sigma weight residual 1.449 1.461 -0.012 1.45e-02 4.76e+03 7.00e-01 bond pdb=" CA ILE A 48 " pdb=" C ILE A 48 " ideal model delta sigma weight residual 1.518 1.527 -0.008 1.13e-02 7.83e+03 5.33e-01 ... (remaining 4012 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 5276 1.30 - 2.59: 101 2.59 - 3.89: 24 3.89 - 5.18: 9 5.18 - 6.48: 4 Bond angle restraints: 5414 Sorted by residual: angle pdb=" CB LYS A 49 " pdb=" CG LYS A 49 " pdb=" CD LYS A 49 " ideal model delta sigma weight residual 111.30 117.78 -6.48 2.30e+00 1.89e-01 7.93e+00 angle pdb=" CA LYS A 49 " pdb=" CB LYS A 49 " pdb=" CG LYS A 49 " ideal model delta sigma weight residual 114.10 119.15 -5.05 2.00e+00 2.50e-01 6.38e+00 angle pdb=" N ALA A 474 " pdb=" CA ALA A 474 " pdb=" C ALA A 474 " ideal model delta sigma weight residual 108.19 111.40 -3.21 1.29e+00 6.01e-01 6.18e+00 angle pdb=" C PHE A 506 " pdb=" N THR A 507 " pdb=" CA THR A 507 " ideal model delta sigma weight residual 122.46 125.95 -3.49 1.41e+00 5.03e-01 6.13e+00 angle pdb=" CA ILE A 48 " pdb=" CB ILE A 48 " pdb=" CG1 ILE A 48 " ideal model delta sigma weight residual 110.40 113.81 -3.41 1.70e+00 3.46e-01 4.02e+00 ... (remaining 5409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 2019 17.52 - 35.04: 289 35.04 - 52.57: 114 52.57 - 70.09: 24 70.09 - 87.61: 5 Dihedral angle restraints: 2451 sinusoidal: 1000 harmonic: 1451 Sorted by residual: dihedral pdb=" CA LEU A 282 " pdb=" C LEU A 282 " pdb=" N ARG A 283 " pdb=" CA ARG A 283 " ideal model delta harmonic sigma weight residual 180.00 162.41 17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ASN A 310 " pdb=" CB ASN A 310 " pdb=" CG ASN A 310 " pdb=" OD1 ASN A 310 " ideal model delta sinusoidal sigma weight residual -90.00 -153.83 63.83 2 2.00e+01 2.50e-03 9.67e+00 dihedral pdb=" CA GLU A 42 " pdb=" CB GLU A 42 " pdb=" CG GLU A 42 " pdb=" CD GLU A 42 " ideal model delta sinusoidal sigma weight residual -60.00 -118.09 58.09 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 2448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 383 0.029 - 0.057: 170 0.057 - 0.086: 45 0.086 - 0.114: 22 0.114 - 0.143: 6 Chirality restraints: 626 Sorted by residual: chirality pdb=" CG LEU A 341 " pdb=" CB LEU A 341 " pdb=" CD1 LEU A 341 " pdb=" CD2 LEU A 341 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA VAL A 424 " pdb=" N VAL A 424 " pdb=" C VAL A 424 " pdb=" CB VAL A 424 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA ILE A 492 " pdb=" N ILE A 492 " pdb=" C ILE A 492 " pdb=" CB ILE A 492 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 ... (remaining 623 not shown) Planarity restraints: 675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 320 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO A 321 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 27 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C VAL A 27 " 0.022 2.00e-02 2.50e+03 pdb=" O VAL A 27 " -0.008 2.00e-02 2.50e+03 pdb=" N THR A 28 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 510 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO A 511 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 511 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 511 " -0.017 5.00e-02 4.00e+02 ... (remaining 672 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 137 2.72 - 3.26: 3892 3.26 - 3.81: 6221 3.81 - 4.35: 7893 4.35 - 4.90: 12757 Nonbonded interactions: 30900 Sorted by model distance: nonbonded pdb=" O ASP A 469 " pdb=" OG1 THR A 472 " model vdw 2.172 3.040 nonbonded pdb=" OG SER A 380 " pdb=" OD1 ASN A 470 " model vdw 2.283 3.040 nonbonded pdb=" O SER A 416 " pdb=" OG SER A 416 " model vdw 2.291 3.040 nonbonded pdb=" O LEU A 273 " pdb=" NZ LYS A 307 " model vdw 2.297 3.120 nonbonded pdb=" O THR A 459 " pdb=" OH TYR A 486 " model vdw 2.298 3.040 ... (remaining 30895 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.380 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.760 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 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 : 0.002 0.030 4017 Z= 0.098 Angle : 0.526 6.479 5414 Z= 0.267 Chirality : 0.038 0.143 626 Planarity : 0.003 0.040 675 Dihedral : 19.478 87.609 1507 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.62 % Allowed : 40.60 % Favored : 57.77 % 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: -1.69 (0.37), residues: 493 helix: -0.90 (0.30), residues: 276 sheet: 0.69 (0.81), residues: 34 loop : -1.64 (0.47), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 69 TYR 0.008 0.001 TYR A 486 PHE 0.006 0.001 PHE A 522 TRP 0.017 0.001 TRP A 206 HIS 0.002 0.000 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 ( 4017) covalent geometry : angle 0.52594 / 0.27 ( 5414) hydrogen bonds : bond 0.28006 / 18.17 ( 165) hydrogen bonds : angle 8.76754 / 6.14 ( 480) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.139 Fit side-chains REVERT: A 42 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6288 (mm-30) REVERT: A 74 ILE cc_start: 0.7381 (mm) cc_final: 0.7169 (mt) REVERT: A 233 GLU cc_start: 0.6073 (pt0) cc_final: 0.5342 (pm20) REVERT: A 267 GLU cc_start: 0.7281 (tp30) cc_final: 0.7073 (tp30) REVERT: A 275 GLU cc_start: 0.6815 (mp0) cc_final: 0.6558 (mp0) REVERT: A 311 GLU cc_start: 0.6467 (tp30) cc_final: 0.6055 (tp30) REVERT: A 315 LYS cc_start: 0.6430 (mtpt) cc_final: 0.6063 (mtpt) REVERT: A 519 MET cc_start: 0.7618 (mtp) cc_final: 0.7336 (mtt) outliers start: 7 outliers final: 5 residues processed: 91 average time/residue: 0.1052 time to fit residues: 11.1276 Evaluate side-chains 91 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 472 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.0670 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.139618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.127821 restraints weight = 5453.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.131393 restraints weight = 2848.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.133629 restraints weight = 1667.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.135139 restraints weight = 1058.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.136048 restraints weight = 707.887| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4017 Z= 0.200 Angle : 0.592 7.374 5414 Z= 0.307 Chirality : 0.042 0.138 626 Planarity : 0.005 0.046 675 Dihedral : 5.424 44.364 537 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 7.42 % Allowed : 33.64 % Favored : 58.93 % 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: -1.28 (0.38), residues: 493 helix: -0.47 (0.30), residues: 285 sheet: 0.61 (0.89), residues: 33 loop : -1.60 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 32 TYR 0.021 0.002 TYR A 486 PHE 0.013 0.002 PHE A 39 TRP 0.012 0.002 TRP A 206 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 ( 4017) covalent geometry : angle 0.59176 / 0.31 ( 5414) hydrogen bonds : bond 0.04221 / 2.76 ( 165) hydrogen bonds : angle 5.42091 / 3.68 ( 480) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.084 Fit side-chains REVERT: A 42 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6648 (mm-30) REVERT: A 66 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.5747 (mt-10) REVERT: A 74 ILE cc_start: 0.7534 (mm) cc_final: 0.7195 (mt) REVERT: A 93 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7385 (mm) REVERT: A 233 GLU cc_start: 0.6339 (pt0) cc_final: 0.5466 (pm20) REVERT: A 288 MET cc_start: 0.7193 (mtm) cc_final: 0.6953 (mtt) REVERT: A 311 GLU cc_start: 0.6593 (tp30) cc_final: 0.6036 (tp30) REVERT: A 315 LYS cc_start: 0.6544 (mtpt) cc_final: 0.5884 (mtpt) REVERT: A 384 ARG cc_start: 0.7872 (tpp-160) cc_final: 0.7586 (mtp180) REVERT: A 451 MET cc_start: 0.7531 (mtm) cc_final: 0.7179 (mtm) REVERT: A 452 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6544 (mt) REVERT: A 519 MET cc_start: 0.7849 (mtp) cc_final: 0.7484 (mtt) outliers start: 32 outliers final: 14 residues processed: 123 average time/residue: 0.0909 time to fit residues: 13.0659 Evaluate side-chains 124 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 452 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 19 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 69.5568 > 50:) chunk 5 optimal weight: 0.2980 chunk 40 optimal weight: 0.8980 chunk 49 optimal weight: 0.1980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.139915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.128109 restraints weight = 5396.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.131612 restraints weight = 2837.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.133968 restraints weight = 1672.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.135425 restraints weight = 1049.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.136426 restraints weight = 711.529| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4017 Z= 0.146 Angle : 0.557 9.805 5414 Z= 0.282 Chirality : 0.041 0.150 626 Planarity : 0.004 0.048 675 Dihedral : 4.633 19.180 531 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 5.57 % Allowed : 34.80 % Favored : 59.63 % 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: -1.08 (0.38), residues: 493 helix: -0.25 (0.31), residues: 286 sheet: 0.59 (0.91), residues: 33 loop : -1.62 (0.49), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 405 TYR 0.019 0.002 TYR A 486 PHE 0.011 0.001 PHE A 415 TRP 0.009 0.001 TRP A 206 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 4017) covalent geometry : angle 0.55739 / 0.28 ( 5414) hydrogen bonds : bond 0.03522 / 2.25 ( 165) hydrogen bonds : angle 4.88685 / 3.31 ( 480) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.088 Fit side-chains REVERT: A 32 ARG cc_start: 0.7549 (mtt90) cc_final: 0.7223 (mtt90) REVERT: A 42 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6565 (mm-30) REVERT: A 66 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.5777 (mt-10) REVERT: A 288 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6864 (mtt) REVERT: A 311 GLU cc_start: 0.6577 (tp30) cc_final: 0.5986 (tp30) REVERT: A 315 LYS cc_start: 0.6493 (mtpt) cc_final: 0.5675 (mtpt) REVERT: A 384 ARG cc_start: 0.7853 (tpp-160) cc_final: 0.7602 (mtp180) REVERT: A 452 ILE cc_start: 0.6874 (mp) cc_final: 0.6479 (mt) outliers start: 24 outliers final: 13 residues processed: 120 average time/residue: 0.0759 time to fit residues: 10.7158 Evaluate side-chains 120 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 410 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.0020 chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 26 optimal weight: 0.0980 chunk 38 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 2 optimal weight: 0.0980 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 overall best weight: 0.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.140955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.129272 restraints weight = 5240.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.132822 restraints weight = 2737.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.135101 restraints weight = 1600.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.136577 restraints weight = 1010.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.137547 restraints weight = 678.485| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4017 Z= 0.118 Angle : 0.540 9.685 5414 Z= 0.272 Chirality : 0.040 0.160 626 Planarity : 0.004 0.048 675 Dihedral : 4.514 19.139 531 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.64 % Allowed : 36.19 % Favored : 59.16 % 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: -1.02 (0.39), residues: 493 helix: -0.13 (0.31), residues: 290 sheet: 0.55 (0.95), residues: 33 loop : -1.76 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.016 0.001 TYR A 486 PHE 0.010 0.001 PHE A 415 TRP 0.005 0.001 TRP A 343 HIS 0.002 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 4017) covalent geometry : angle 0.53954 / 0.27 ( 5414) hydrogen bonds : bond 0.03037 / 1.93 ( 165) hydrogen bonds : angle 4.55817 / 3.08 ( 480) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.134 Fit side-chains REVERT: A 32 ARG cc_start: 0.7515 (mtt90) cc_final: 0.7222 (mtt90) REVERT: A 42 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6408 (mm-30) REVERT: A 66 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.5701 (mt-10) REVERT: A 74 ILE cc_start: 0.7527 (mm) cc_final: 0.7325 (mt) REVERT: A 267 GLU cc_start: 0.7211 (tp30) cc_final: 0.6912 (tp30) REVERT: A 288 MET cc_start: 0.7172 (mtm) cc_final: 0.6880 (mtt) REVERT: A 311 GLU cc_start: 0.6570 (tp30) cc_final: 0.5932 (tp30) REVERT: A 315 LYS cc_start: 0.6438 (mtpt) cc_final: 0.5617 (mtpt) REVERT: A 384 ARG cc_start: 0.7836 (tpp-160) cc_final: 0.7576 (mtp180) outliers start: 20 outliers final: 12 residues processed: 116 average time/residue: 0.0885 time to fit residues: 12.0451 Evaluate side-chains 120 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 538 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 0.9990 chunk 39 optimal weight: 0.0970 chunk 4 optimal weight: 0.0060 chunk 48 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 0.0370 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 overall best weight: 0.2872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.140513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.128671 restraints weight = 5393.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.132290 restraints weight = 2808.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.134569 restraints weight = 1639.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.135955 restraints weight = 1035.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.137016 restraints weight = 706.619| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4017 Z= 0.126 Angle : 0.559 10.610 5414 Z= 0.277 Chirality : 0.041 0.160 626 Planarity : 0.004 0.048 675 Dihedral : 4.497 19.162 531 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.10 % Allowed : 35.96 % Favored : 58.93 % 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: -0.94 (0.39), residues: 493 helix: -0.08 (0.31), residues: 293 sheet: 0.41 (0.97), residues: 33 loop : -1.69 (0.49), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 405 TYR 0.015 0.001 TYR A 486 PHE 0.012 0.001 PHE A 415 TRP 0.010 0.001 TRP A 206 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 4017) covalent geometry : angle 0.55879 / 0.28 ( 5414) hydrogen bonds : bond 0.03019 / 1.94 ( 165) hydrogen bonds : angle 4.44649 / 2.99 ( 480) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.085 Fit side-chains REVERT: A 32 ARG cc_start: 0.7543 (mtt90) cc_final: 0.7297 (mtt90) REVERT: A 42 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6483 (mm-30) REVERT: A 66 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.5713 (mt-10) REVERT: A 74 ILE cc_start: 0.7545 (mm) cc_final: 0.7285 (mt) REVERT: A 117 GLU cc_start: 0.6155 (OUTLIER) cc_final: 0.5944 (pm20) REVERT: A 233 GLU cc_start: 0.6433 (pt0) cc_final: 0.6185 (pt0) REVERT: A 267 GLU cc_start: 0.7218 (tp30) cc_final: 0.6877 (tp30) REVERT: A 311 GLU cc_start: 0.6555 (tp30) cc_final: 0.6060 (tp30) REVERT: A 384 ARG cc_start: 0.7824 (tpp-160) cc_final: 0.7574 (mtp180) outliers start: 22 outliers final: 14 residues processed: 116 average time/residue: 0.0746 time to fit residues: 10.1221 Evaluate side-chains 119 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 538 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 43 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 44 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.139118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.127126 restraints weight = 5461.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.130746 restraints weight = 2852.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.133051 restraints weight = 1667.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.134547 restraints weight = 1050.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.135543 restraints weight = 705.163| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4017 Z= 0.166 Angle : 0.588 11.690 5414 Z= 0.293 Chirality : 0.042 0.149 626 Planarity : 0.004 0.048 675 Dihedral : 4.643 19.420 531 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 6.03 % Allowed : 34.34 % Favored : 59.63 % 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: -1.00 (0.39), residues: 493 helix: -0.10 (0.31), residues: 288 sheet: 0.17 (0.96), residues: 33 loop : -1.67 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.019 0.002 TYR A 486 PHE 0.013 0.002 PHE A 415 TRP 0.010 0.001 TRP A 206 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 4017) covalent geometry : angle 0.58788 / 0.29 ( 5414) hydrogen bonds : bond 0.03190 / 2.05 ( 165) hydrogen bonds : angle 4.55096 / 3.08 ( 480) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.119 Fit side-chains REVERT: A 42 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6273 (mm-30) REVERT: A 66 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.5852 (mt-10) REVERT: A 74 ILE cc_start: 0.7600 (mm) cc_final: 0.7266 (mt) REVERT: A 117 GLU cc_start: 0.6165 (OUTLIER) cc_final: 0.5916 (pm20) REVERT: A 267 GLU cc_start: 0.7214 (tp30) cc_final: 0.6896 (tp30) REVERT: A 288 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6681 (mtm) REVERT: A 311 GLU cc_start: 0.6569 (tp30) cc_final: 0.6087 (tp30) REVERT: A 384 ARG cc_start: 0.7819 (tpp-160) cc_final: 0.7514 (mtp85) REVERT: A 385 VAL cc_start: 0.7709 (t) cc_final: 0.7373 (m) outliers start: 26 outliers final: 15 residues processed: 123 average time/residue: 0.0726 time to fit residues: 10.5624 Evaluate side-chains 126 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 538 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 40 optimal weight: 0.0000 chunk 16 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.139189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.127124 restraints weight = 5463.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.130654 restraints weight = 2852.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.133026 restraints weight = 1693.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.134532 restraints weight = 1080.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.135499 restraints weight = 730.548| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4017 Z= 0.156 Angle : 0.594 12.501 5414 Z= 0.294 Chirality : 0.042 0.166 626 Planarity : 0.004 0.049 675 Dihedral : 4.706 19.500 531 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 5.57 % Allowed : 34.34 % Favored : 60.09 % 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 (0.39), residues: 493 helix: -0.02 (0.32), residues: 285 sheet: 0.10 (0.96), residues: 33 loop : -1.49 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 32 TYR 0.018 0.002 TYR A 486 PHE 0.013 0.002 PHE A 415 TRP 0.008 0.001 TRP A 206 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 4017) covalent geometry : angle 0.59430 / 0.29 ( 5414) hydrogen bonds : bond 0.03064 / 1.98 ( 165) hydrogen bonds : angle 4.50829 / 3.04 ( 480) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.145 Fit side-chains REVERT: A 66 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.5771 (mt-10) REVERT: A 74 ILE cc_start: 0.7583 (mm) cc_final: 0.7213 (mt) REVERT: A 117 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5939 (pm20) REVERT: A 233 GLU cc_start: 0.6265 (mt-10) cc_final: 0.5990 (pm20) REVERT: A 267 GLU cc_start: 0.7219 (tp30) cc_final: 0.6873 (tp30) REVERT: A 288 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6685 (mtm) REVERT: A 311 GLU cc_start: 0.6583 (tp30) cc_final: 0.6076 (tp30) REVERT: A 384 ARG cc_start: 0.7816 (tpp-160) cc_final: 0.7513 (mtp85) REVERT: A 385 VAL cc_start: 0.7692 (t) cc_final: 0.7363 (m) REVERT: A 452 ILE cc_start: 0.6828 (OUTLIER) cc_final: 0.6472 (mt) REVERT: A 519 MET cc_start: 0.7862 (mtp) cc_final: 0.7528 (mtt) outliers start: 24 outliers final: 14 residues processed: 123 average time/residue: 0.0787 time to fit residues: 11.4660 Evaluate side-chains 127 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 481 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 16 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 0.0970 chunk 34 optimal weight: 0.7980 chunk 41 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 chunk 12 optimal weight: 0.3980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.139414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.127523 restraints weight = 5389.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.131027 restraints weight = 2813.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.133378 restraints weight = 1665.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.134877 restraints weight = 1056.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.135874 restraints weight = 711.836| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4017 Z= 0.135 Angle : 0.581 13.250 5414 Z= 0.284 Chirality : 0.041 0.156 626 Planarity : 0.004 0.049 675 Dihedral : 4.636 18.931 531 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.18 % Allowed : 36.19 % Favored : 59.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.39), residues: 493 helix: 0.01 (0.32), residues: 290 sheet: -0.00 (0.95), residues: 33 loop : -1.53 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 32 TYR 0.018 0.001 TYR A 486 PHE 0.013 0.001 PHE A 415 TRP 0.007 0.001 TRP A 206 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 4017) covalent geometry : angle 0.58096 / 0.28 ( 5414) hydrogen bonds : bond 0.02892 / 1.86 ( 165) hydrogen bonds : angle 4.42005 / 2.97 ( 480) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.132 Fit side-chains REVERT: A 42 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6402 (mm-30) REVERT: A 66 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.5821 (mt-10) REVERT: A 74 ILE cc_start: 0.7584 (mm) cc_final: 0.7209 (mt) REVERT: A 117 GLU cc_start: 0.6172 (OUTLIER) cc_final: 0.5920 (pm20) REVERT: A 267 GLU cc_start: 0.7172 (tp30) cc_final: 0.6848 (tp30) REVERT: A 311 GLU cc_start: 0.6561 (tp30) cc_final: 0.6078 (tp30) REVERT: A 384 ARG cc_start: 0.7813 (tpp-160) cc_final: 0.7523 (mtp85) REVERT: A 519 MET cc_start: 0.7878 (mtp) cc_final: 0.7516 (mtt) outliers start: 18 outliers final: 12 residues processed: 119 average time/residue: 0.0699 time to fit residues: 9.8892 Evaluate side-chains 122 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 481 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 43 optimal weight: 0.4980 chunk 10 optimal weight: 0.2980 chunk 32 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.139059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.127093 restraints weight = 5480.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.130609 restraints weight = 2848.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.132981 restraints weight = 1684.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.134451 restraints weight = 1065.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.135420 restraints weight = 722.863| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4017 Z= 0.146 Angle : 0.590 13.857 5414 Z= 0.289 Chirality : 0.042 0.152 626 Planarity : 0.004 0.049 675 Dihedral : 4.644 18.908 531 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.94 % Allowed : 36.19 % Favored : 59.86 % 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: -0.93 (0.39), residues: 493 helix: -0.04 (0.31), residues: 290 sheet: -0.20 (0.90), residues: 34 loop : -1.58 (0.51), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 32 TYR 0.019 0.001 TYR A 486 PHE 0.013 0.001 PHE A 415 TRP 0.008 0.001 TRP A 206 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 4017) covalent geometry : angle 0.58995 / 0.29 ( 5414) hydrogen bonds : bond 0.02940 / 1.90 ( 165) hydrogen bonds : angle 4.45120 / 3.00 ( 480) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.134 Fit side-chains REVERT: A 42 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6436 (mm-30) REVERT: A 66 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.5798 (mt-10) REVERT: A 117 GLU cc_start: 0.6174 (OUTLIER) cc_final: 0.5915 (pm20) REVERT: A 233 GLU cc_start: 0.6258 (mt-10) cc_final: 0.6058 (pt0) REVERT: A 267 GLU cc_start: 0.7200 (tp30) cc_final: 0.6857 (tp30) REVERT: A 311 GLU cc_start: 0.6567 (tp30) cc_final: 0.6073 (tp30) REVERT: A 384 ARG cc_start: 0.7809 (tpp-160) cc_final: 0.7518 (mtp85) outliers start: 17 outliers final: 11 residues processed: 115 average time/residue: 0.0949 time to fit residues: 12.8348 Evaluate side-chains 120 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 481 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 0.2980 chunk 44 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.137537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.125753 restraints weight = 5408.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.129249 restraints weight = 2821.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.131490 restraints weight = 1653.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132974 restraints weight = 1053.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.133923 restraints weight = 712.592| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4017 Z= 0.186 Angle : 0.631 13.676 5414 Z= 0.312 Chirality : 0.043 0.149 626 Planarity : 0.004 0.049 675 Dihedral : 4.842 19.343 531 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.48 % Allowed : 36.89 % Favored : 59.63 % 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: -1.00 (0.39), residues: 493 helix: -0.12 (0.31), residues: 285 sheet: -0.46 (0.89), residues: 34 loop : -1.48 (0.51), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 32 TYR 0.020 0.002 TYR A 486 PHE 0.014 0.002 PHE A 415 TRP 0.011 0.001 TRP A 343 HIS 0.005 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 ( 4017) covalent geometry : angle 0.63098 / 0.31 ( 5414) hydrogen bonds : bond 0.03165 / 2.05 ( 165) hydrogen bonds : angle 4.58453 / 3.11 ( 480) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.090 Fit side-chains REVERT: A 42 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6067 (mm-30) REVERT: A 63 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7563 (mtm-85) REVERT: A 66 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.5769 (mt-10) REVERT: A 117 GLU cc_start: 0.6194 (OUTLIER) cc_final: 0.5947 (pm20) REVERT: A 267 GLU cc_start: 0.7221 (tp30) cc_final: 0.6868 (tp30) REVERT: A 311 GLU cc_start: 0.6592 (tp30) cc_final: 0.6089 (tp30) REVERT: A 384 ARG cc_start: 0.7805 (tpp-160) cc_final: 0.7511 (mtp85) REVERT: A 385 VAL cc_start: 0.7731 (t) cc_final: 0.7445 (m) REVERT: A 419 MET cc_start: 0.6834 (mmm) cc_final: 0.6238 (mmm) REVERT: A 519 MET cc_start: 0.7918 (mtp) cc_final: 0.7595 (mtt) outliers start: 15 outliers final: 12 residues processed: 121 average time/residue: 0.0739 time to fit residues: 10.5617 Evaluate side-chains 126 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 481 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.0980 chunk 44 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 0.0020 chunk 10 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 0.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.138532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.126760 restraints weight = 5426.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.130268 restraints weight = 2807.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.132506 restraints weight = 1642.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.133972 restraints weight = 1038.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.134902 restraints weight = 700.144| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4017 Z= 0.129 Angle : 0.597 14.119 5414 Z= 0.296 Chirality : 0.042 0.172 626 Planarity : 0.004 0.049 675 Dihedral : 4.659 19.091 531 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.71 % Allowed : 36.43 % Favored : 59.86 % 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: -0.94 (0.39), residues: 493 helix: -0.03 (0.31), residues: 289 sheet: -0.39 (0.91), residues: 33 loop : -1.57 (0.51), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 32 TYR 0.018 0.001 TYR A 486 PHE 0.011 0.001 PHE A 415 TRP 0.008 0.001 TRP A 206 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 4017) covalent geometry : angle 0.59678 / 0.30 ( 5414) hydrogen bonds : bond 0.02889 / 1.88 ( 165) hydrogen bonds : angle 4.46178 / 3.02 ( 480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 835.95 seconds wall clock time: 15 minutes 4.15 seconds (904.15 seconds total)