Starting phenix.real_space_refine on Tue Mar 3 11:13:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wyj_21966/03_2026/6wyj_21966.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wyj_21966/03_2026/6wyj_21966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wyj_21966/03_2026/6wyj_21966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wyj_21966/03_2026/6wyj_21966.map" model { file = "/net/cci-nas-00/data/ceres_data/6wyj_21966/03_2026/6wyj_21966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wyj_21966/03_2026/6wyj_21966.cif" } resolution = 3.7 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= 0.007 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 18 5.16 5 C 1942 2.51 5 N 465 2.21 5 O 524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2949 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2949 Classifications: {'peptide': 398} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 381} Chain breaks: 2 Time building chain proxies: 0.85, per 1000 atoms: 0.29 Number of scatterers: 2949 At special positions: 0 Unit cell: (69.02, 70.006, 78.88, 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 18 16.00 O 524 8.00 N 465 7.00 C 1942 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: 0.24 Conformation dependent library (CDL) restraints added in 112.6 milliseconds 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 88.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 11 through 33 removed outlier: 3.735A pdb=" N LYS A 15 " --> pdb=" O PRO A 11 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 44 through 73 removed outlier: 4.195A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N MET A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 3.565A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 108 removed outlier: 3.549A pdb=" N GLY A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 92 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.816A pdb=" N LEU A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 151 through 170 removed outlier: 3.573A pdb=" N THR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 218 removed outlier: 3.560A pdb=" N ARG A 177 " --> pdb=" O ASN A 173 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 225 through 255 removed outlier: 3.585A pdb=" N PHE A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.590A pdb=" N LYS A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.729A pdb=" N LYS A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.507A pdb=" N PHE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Proline residue: A 304 - end of helix removed outlier: 4.087A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 330 removed outlier: 3.639A pdb=" N ALA A 315 " --> pdb=" O MET A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.814A pdb=" N ILE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N MET A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 416 removed outlier: 3.714A pdb=" N ALA A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 389 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N MET A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 398 " --> pdb=" O ASP A 394 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET A 399 " --> pdb=" O MET A 395 " (cutoff:3.500A) 230 hydrogen bonds defined for protein. 690 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: 0.41 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 907 1.34 - 1.46: 524 1.46 - 1.57: 1532 1.57 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 2997 Sorted by residual: bond pdb=" N GLU A 174 " pdb=" CA GLU A 174 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.35e-02 5.49e+03 8.99e+00 bond pdb=" CA MET A 311 " pdb=" CB MET A 311 " ideal model delta sigma weight residual 1.531 1.467 0.064 3.28e-02 9.30e+02 3.77e+00 bond pdb=" CB THR A 154 " pdb=" CG2 THR A 154 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.42e+00 bond pdb=" CB THR A 275 " pdb=" CG2 THR A 275 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.54e+00 bond pdb=" CG LEU A 190 " pdb=" CD1 LEU A 190 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.37e+00 ... (remaining 2992 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 3723 0.99 - 1.99: 281 1.99 - 2.98: 45 2.98 - 3.97: 19 3.97 - 4.97: 10 Bond angle restraints: 4078 Sorted by residual: angle pdb=" C ASN A 173 " pdb=" N GLU A 174 " pdb=" CA GLU A 174 " ideal model delta sigma weight residual 120.99 125.55 -4.56 1.86e+00 2.89e-01 6.00e+00 angle pdb=" N PRO A 356 " pdb=" CA PRO A 356 " pdb=" C PRO A 356 " ideal model delta sigma weight residual 112.47 117.44 -4.97 2.06e+00 2.36e-01 5.81e+00 angle pdb=" CA TYR A 299 " pdb=" CB TYR A 299 " pdb=" CG TYR A 299 " ideal model delta sigma weight residual 113.90 118.19 -4.29 1.80e+00 3.09e-01 5.68e+00 angle pdb=" C ALA A 205 " pdb=" CA ALA A 205 " pdb=" CB ALA A 205 " ideal model delta sigma weight residual 113.49 109.32 4.17 1.82e+00 3.02e-01 5.26e+00 angle pdb=" CA ALA A 205 " pdb=" C ALA A 205 " pdb=" N PRO A 206 " ideal model delta sigma weight residual 120.52 118.83 1.69 8.30e-01 1.45e+00 4.13e+00 ... (remaining 4073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 1653 17.19 - 34.37: 107 34.37 - 51.56: 15 51.56 - 68.74: 3 68.74 - 85.93: 3 Dihedral angle restraints: 1781 sinusoidal: 649 harmonic: 1132 Sorted by residual: dihedral pdb=" CA VAL A 355 " pdb=" C VAL A 355 " pdb=" N PRO A 356 " pdb=" CA PRO A 356 " ideal model delta harmonic sigma weight residual 180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA THR A 352 " pdb=" C THR A 352 " pdb=" N ALA A 353 " pdb=" CA ALA A 353 " ideal model delta harmonic sigma weight residual 180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP A 37 " pdb=" CB ASP A 37 " pdb=" CG ASP A 37 " pdb=" OD1 ASP A 37 " ideal model delta sinusoidal sigma weight residual -30.00 -89.49 59.49 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 1778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 271 0.035 - 0.069: 173 0.069 - 0.104: 64 0.104 - 0.139: 8 0.139 - 0.173: 4 Chirality restraints: 520 Sorted by residual: chirality pdb=" CA PRO A 356 " pdb=" N PRO A 356 " pdb=" C PRO A 356 " pdb=" CB PRO A 356 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" CA PRO A 60 " pdb=" N PRO A 60 " pdb=" C PRO A 60 " pdb=" CB PRO A 60 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CB ILE A 411 " pdb=" CA ILE A 411 " pdb=" CG1 ILE A 411 " pdb=" CG2 ILE A 411 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 517 not shown) Planarity restraints: 496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 205 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO A 206 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 299 " 0.010 2.00e-02 2.50e+03 6.87e-03 9.43e-01 pdb=" CG TYR A 299 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR A 299 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 299 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 299 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 299 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 299 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 299 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 59 " -0.016 5.00e-02 4.00e+02 2.42e-02 9.33e-01 pdb=" N PRO A 60 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 60 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 60 " -0.013 5.00e-02 4.00e+02 ... (remaining 493 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 840 2.79 - 3.32: 3220 3.32 - 3.85: 4503 3.85 - 4.37: 5358 4.37 - 4.90: 8867 Nonbonded interactions: 22788 Sorted by model distance: nonbonded pdb=" O SER A 179 " pdb=" OG1 THR A 182 " model vdw 2.268 3.040 nonbonded pdb=" O GLU A 172 " pdb=" NH2 ARG A 177 " model vdw 2.322 3.120 nonbonded pdb=" O LEU A 282 " pdb=" OG1 THR A 285 " model vdw 2.328 3.040 nonbonded pdb=" O THR A 271 " pdb=" OG1 THR A 275 " model vdw 2.377 3.040 nonbonded pdb=" O ILE A 187 " pdb=" N LEU A 190 " model vdw 2.422 3.120 ... (remaining 22783 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: 1.060 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.910 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 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 : 0.010 0.064 2997 Z= 0.358 Angle : 0.644 4.965 4078 Z= 0.351 Chirality : 0.049 0.173 520 Planarity : 0.003 0.030 496 Dihedral : 12.333 85.929 1061 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % 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: -4.80 (0.30), residues: 393 helix: -2.79 (0.21), residues: 301 sheet: None (None), residues: 0 loop : -3.77 (0.47), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 276 TYR 0.016 0.002 TYR A 299 PHE 0.010 0.001 PHE A 50 HIS 0.001 0.000 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00957 ( 2997) covalent geometry : angle 0.64404 ( 4078) hydrogen bonds : bond 0.27428 ( 230) hydrogen bonds : angle 9.19128 ( 690) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.103 Fit side-chains REVERT: A 215 TYR cc_start: 0.7777 (t80) cc_final: 0.7532 (t80) REVERT: A 310 ASN cc_start: 0.9176 (t0) cc_final: 0.8693 (t0) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0616 time to fit residues: 2.4735 Evaluate side-chains 29 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.159095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3452 r_free = 0.3452 target = 0.142026 restraints weight = 3350.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.142026 restraints weight = 5129.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.142026 restraints weight = 5129.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.142026 restraints weight = 5129.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.142026 restraints weight = 5129.241| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2997 Z= 0.191 Angle : 0.602 5.528 4078 Z= 0.325 Chirality : 0.043 0.180 520 Planarity : 0.005 0.036 496 Dihedral : 4.522 26.769 421 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.96 % Allowed : 7.03 % Favored : 92.01 % 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: -0.30 (0.39), residues: 393 helix: 0.33 (0.27), residues: 322 sheet: None (None), residues: 0 loop : -2.31 (0.66), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 397 TYR 0.022 0.002 TYR A 299 PHE 0.013 0.002 PHE A 273 HIS 0.001 0.000 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 2997) covalent geometry : angle 0.60159 ( 4078) hydrogen bonds : bond 0.07399 ( 230) hydrogen bonds : angle 4.90138 ( 690) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.103 Fit side-chains REVERT: A 169 MET cc_start: 0.7316 (mtm) cc_final: 0.6983 (mtm) outliers start: 3 outliers final: 0 residues processed: 36 average time/residue: 0.0507 time to fit residues: 2.3953 Evaluate side-chains 33 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.157261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.138474 restraints weight = 3420.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 85)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.131449 restraints weight = 5233.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.130663 restraints weight = 5975.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.131246 restraints weight = 5141.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.131043 restraints weight = 4125.245| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2997 Z= 0.169 Angle : 0.546 5.371 4078 Z= 0.292 Chirality : 0.042 0.182 520 Planarity : 0.004 0.035 496 Dihedral : 4.180 23.696 421 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.60 % Allowed : 10.22 % Favored : 88.18 % 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: 1.01 (0.41), residues: 393 helix: 1.25 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -1.83 (0.64), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 287 TYR 0.018 0.002 TYR A 299 PHE 0.012 0.001 PHE A 210 HIS 0.001 0.000 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 2997) covalent geometry : angle 0.54566 ( 4078) hydrogen bonds : bond 0.06796 ( 230) hydrogen bonds : angle 4.42249 ( 690) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.103 Fit side-chains REVERT: A 90 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8378 (mp) outliers start: 5 outliers final: 3 residues processed: 46 average time/residue: 0.0422 time to fit residues: 2.5919 Evaluate side-chains 44 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.160306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.142083 restraints weight = 3446.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.138494 restraints weight = 4963.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 84)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.137615 restraints weight = 5344.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.131418 restraints weight = 4895.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.131957 restraints weight = 4285.598| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2997 Z= 0.189 Angle : 0.573 5.366 4078 Z= 0.303 Chirality : 0.042 0.168 520 Planarity : 0.004 0.036 496 Dihedral : 4.193 19.187 421 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.92 % Allowed : 12.46 % Favored : 85.62 % 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: 1.11 (0.41), residues: 393 helix: 1.35 (0.28), residues: 315 sheet: None (None), residues: 0 loop : -1.75 (0.64), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 397 TYR 0.018 0.002 TYR A 299 PHE 0.015 0.001 PHE A 273 HIS 0.001 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 2997) covalent geometry : angle 0.57339 ( 4078) hydrogen bonds : bond 0.07095 ( 230) hydrogen bonds : angle 4.43450 ( 690) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.100 Fit side-chains REVERT: A 90 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8347 (mp) REVERT: A 367 LEU cc_start: 0.7568 (mt) cc_final: 0.7346 (mt) outliers start: 6 outliers final: 4 residues processed: 49 average time/residue: 0.0449 time to fit residues: 2.9333 Evaluate side-chains 43 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 389 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 25 optimal weight: 0.0040 chunk 14 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.155120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.141801 restraints weight = 3361.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.138132 restraints weight = 5283.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.136735 restraints weight = 5254.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 80)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.134276 restraints weight = 5682.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 77)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.132813 restraints weight = 6499.435| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2997 Z= 0.154 Angle : 0.519 5.369 4078 Z= 0.274 Chirality : 0.041 0.177 520 Planarity : 0.004 0.035 496 Dihedral : 4.017 18.989 421 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.56 % Allowed : 14.06 % Favored : 83.39 % 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: 1.45 (0.42), residues: 393 helix: 1.55 (0.28), residues: 318 sheet: None (None), residues: 0 loop : -1.57 (0.66), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 397 TYR 0.016 0.002 TYR A 299 PHE 0.012 0.001 PHE A 273 HIS 0.001 0.000 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 2997) covalent geometry : angle 0.51904 ( 4078) hydrogen bonds : bond 0.06219 ( 230) hydrogen bonds : angle 4.20438 ( 690) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.102 Fit side-chains REVERT: A 90 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8421 (mp) REVERT: A 367 LEU cc_start: 0.8103 (mt) cc_final: 0.7828 (mt) outliers start: 8 outliers final: 5 residues processed: 47 average time/residue: 0.0629 time to fit residues: 3.7152 Evaluate side-chains 44 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 389 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.164337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 127)---------------| | r_work = 0.3432 r_free = 0.3432 target = 0.138925 restraints weight = 3330.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.137716 restraints weight = 3724.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.138153 restraints weight = 3358.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.138524 restraints weight = 3118.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.138524 restraints weight = 2976.666| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2997 Z= 0.141 Angle : 0.515 6.888 4078 Z= 0.264 Chirality : 0.040 0.187 520 Planarity : 0.004 0.034 496 Dihedral : 3.913 18.999 421 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.88 % Allowed : 14.70 % Favored : 82.43 % 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: 1.64 (0.42), residues: 393 helix: 1.67 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.42 (0.67), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 397 TYR 0.014 0.001 TYR A 299 PHE 0.013 0.001 PHE A 273 HIS 0.001 0.000 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 2997) covalent geometry : angle 0.51487 ( 4078) hydrogen bonds : bond 0.05693 ( 230) hydrogen bonds : angle 4.05695 ( 690) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.104 Fit side-chains REVERT: A 56 MET cc_start: 0.8582 (ttt) cc_final: 0.8325 (ttt) REVERT: A 90 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8410 (mp) REVERT: A 367 LEU cc_start: 0.7866 (mt) cc_final: 0.7614 (mt) outliers start: 9 outliers final: 6 residues processed: 47 average time/residue: 0.0597 time to fit residues: 3.5161 Evaluate side-chains 45 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 389 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.156003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.141519 restraints weight = 3396.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.138860 restraints weight = 4931.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.137769 restraints weight = 5243.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.136290 restraints weight = 5449.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.135906 restraints weight = 5712.022| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2997 Z= 0.153 Angle : 0.529 5.365 4078 Z= 0.273 Chirality : 0.041 0.181 520 Planarity : 0.004 0.033 496 Dihedral : 3.894 16.985 421 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.56 % Allowed : 15.65 % Favored : 81.79 % 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: 1.62 (0.42), residues: 393 helix: 1.61 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -1.28 (0.67), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 397 TYR 0.015 0.001 TYR A 299 PHE 0.013 0.001 PHE A 273 HIS 0.001 0.000 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 2997) covalent geometry : angle 0.52934 ( 4078) hydrogen bonds : bond 0.06057 ( 230) hydrogen bonds : angle 4.11017 ( 690) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.101 Fit side-chains REVERT: A 56 MET cc_start: 0.8588 (ttt) cc_final: 0.8336 (ttt) REVERT: A 90 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8423 (mp) REVERT: A 367 LEU cc_start: 0.8250 (mt) cc_final: 0.7970 (mt) outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 0.0582 time to fit residues: 3.4022 Evaluate side-chains 45 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 389 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 33 optimal weight: 0.1980 chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 36 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.158400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.143515 restraints weight = 3417.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 80)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.139385 restraints weight = 6439.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.139447 restraints weight = 5641.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.139261 restraints weight = 5957.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.138874 restraints weight = 5468.743| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2997 Z= 0.136 Angle : 0.503 5.348 4078 Z= 0.259 Chirality : 0.040 0.200 520 Planarity : 0.004 0.032 496 Dihedral : 3.799 17.039 421 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.88 % Allowed : 15.65 % Favored : 81.47 % 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: 1.79 (0.42), residues: 393 helix: 1.76 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.38 (0.65), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 397 TYR 0.013 0.001 TYR A 299 PHE 0.013 0.001 PHE A 273 HIS 0.001 0.000 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 2997) covalent geometry : angle 0.50324 ( 4078) hydrogen bonds : bond 0.05512 ( 230) hydrogen bonds : angle 3.97503 ( 690) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.096 Fit side-chains REVERT: A 56 MET cc_start: 0.8570 (ttt) cc_final: 0.8348 (ttt) REVERT: A 90 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8367 (mp) REVERT: A 367 LEU cc_start: 0.8275 (mt) cc_final: 0.7996 (mt) outliers start: 9 outliers final: 5 residues processed: 49 average time/residue: 0.0546 time to fit residues: 3.3742 Evaluate side-chains 44 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 389 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 18 optimal weight: 0.0270 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.159202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.142762 restraints weight = 3409.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.139967 restraints weight = 5066.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.138783 restraints weight = 5205.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.136291 restraints weight = 6614.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.136057 restraints weight = 6504.522| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2997 Z= 0.141 Angle : 0.514 5.356 4078 Z= 0.265 Chirality : 0.040 0.193 520 Planarity : 0.004 0.031 496 Dihedral : 3.799 16.111 421 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.88 % Allowed : 15.97 % Favored : 81.15 % 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: 1.78 (0.42), residues: 393 helix: 1.77 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.46 (0.63), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 397 TYR 0.014 0.001 TYR A 215 PHE 0.041 0.002 PHE A 273 HIS 0.001 0.000 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 2997) covalent geometry : angle 0.51351 ( 4078) hydrogen bonds : bond 0.05579 ( 230) hydrogen bonds : angle 3.98390 ( 690) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.092 Fit side-chains REVERT: A 56 MET cc_start: 0.8568 (ttt) cc_final: 0.8339 (ttt) REVERT: A 90 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8373 (mp) REVERT: A 367 LEU cc_start: 0.8188 (mt) cc_final: 0.7860 (mt) outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 0.0534 time to fit residues: 3.2384 Evaluate side-chains 46 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 389 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.155446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.138586 restraints weight = 3415.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.134973 restraints weight = 5447.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.134164 restraints weight = 6372.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 84)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.125467 restraints weight = 5771.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.127201 restraints weight = 4559.353| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2997 Z= 0.179 Angle : 0.577 7.206 4078 Z= 0.300 Chirality : 0.042 0.177 520 Planarity : 0.004 0.033 496 Dihedral : 3.930 15.646 421 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.24 % Allowed : 16.61 % Favored : 81.15 % 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: 1.54 (0.41), residues: 393 helix: 1.59 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -1.52 (0.60), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 287 TYR 0.015 0.001 TYR A 299 PHE 0.041 0.002 PHE A 273 HIS 0.001 0.000 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 2997) covalent geometry : angle 0.57727 ( 4078) hydrogen bonds : bond 0.06421 ( 230) hydrogen bonds : angle 4.18561 ( 690) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.098 Fit side-chains REVERT: A 56 MET cc_start: 0.8605 (ttt) cc_final: 0.8369 (ttt) REVERT: A 90 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8376 (mp) outliers start: 7 outliers final: 6 residues processed: 45 average time/residue: 0.0554 time to fit residues: 3.1145 Evaluate side-chains 43 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 389 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.157652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.143373 restraints weight = 3412.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.143373 restraints weight = 5955.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.143373 restraints weight = 5933.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.143373 restraints weight = 5933.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.143373 restraints weight = 5933.346| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2997 Z= 0.156 Angle : 0.547 7.056 4078 Z= 0.283 Chirality : 0.041 0.193 520 Planarity : 0.004 0.035 496 Dihedral : 3.862 15.124 421 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.56 % Allowed : 16.29 % Favored : 81.15 % 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: 1.61 (0.41), residues: 393 helix: 1.66 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -1.60 (0.59), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 397 TYR 0.014 0.001 TYR A 215 PHE 0.040 0.002 PHE A 273 HIS 0.001 0.000 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 2997) covalent geometry : angle 0.54685 ( 4078) hydrogen bonds : bond 0.05957 ( 230) hydrogen bonds : angle 4.08760 ( 690) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 671.05 seconds wall clock time: 12 minutes 7.10 seconds (727.10 seconds total)