Starting phenix.real_space_refine on Wed Mar 5 15:49:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yv1_10940/03_2025/6yv1_10940.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yv1_10940/03_2025/6yv1_10940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6yv1_10940/03_2025/6yv1_10940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yv1_10940/03_2025/6yv1_10940.map" model { file = "/net/cci-nas-00/data/ceres_data/6yv1_10940/03_2025/6yv1_10940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yv1_10940/03_2025/6yv1_10940.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 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 14 5.16 5 C 1697 2.51 5 N 363 2.21 5 O 422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2496 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2496 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 18, 'TRANS': 309} Chain breaks: 7 Time building chain proxies: 2.45, per 1000 atoms: 0.98 Number of scatterers: 2496 At special positions: 0 Unit cell: (56.079, 61.938, 73.656, 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 14 16.00 O 422 8.00 N 363 7.00 C 1697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 300.7 milliseconds 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 612 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 76.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 31 through 42 Processing helix chain 'A' and resid 50 through 60 removed outlier: 4.267A pdb=" N SER A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 87 removed outlier: 3.567A pdb=" N GLU A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 116 Processing helix chain 'A' and resid 120 through 137 removed outlier: 3.564A pdb=" N CYS A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 167 Processing helix chain 'A' and resid 179 through 197 removed outlier: 3.715A pdb=" N ILE A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.918A pdb=" N ALA A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.805A pdb=" N THR A 242 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.638A pdb=" N ILE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 276 removed outlier: 3.727A pdb=" N SER A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR A 274 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.711A pdb=" N LEU A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 285' Processing helix chain 'A' and resid 288 through 297 removed outlier: 3.736A pdb=" N THR A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 297 " --> pdb=" O PHE A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 317 removed outlier: 3.694A pdb=" N ALA A 310 " --> pdb=" O PRO A 306 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 361 removed outlier: 3.645A pdb=" N ILE A 361 " --> pdb=" O PHE A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.519A pdb=" N ILE A 366 " --> pdb=" O THR A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 395 removed outlier: 3.962A pdb=" N VAL A 375 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN A 376 " --> pdb=" O ASN A 372 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA A 381 " --> pdb=" O TYR A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 427 removed outlier: 3.678A pdb=" N LEU A 419 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 445 142 hydrogen bonds defined for protein. 420 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: 0.57 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 520 1.33 - 1.45: 554 1.45 - 1.57: 1464 1.57 - 1.69: 0 1.69 - 1.81: 19 Bond restraints: 2557 Sorted by residual: bond pdb=" C CYS A 144 " pdb=" O CYS A 144 " ideal model delta sigma weight residual 1.234 1.215 0.019 1.26e-02 6.30e+03 2.18e+00 bond pdb=" C LYS A 145 " pdb=" N PRO A 146 " ideal model delta sigma weight residual 1.329 1.343 -0.014 1.18e-02 7.18e+03 1.47e+00 bond pdb=" CA PRO A 146 " pdb=" C PRO A 146 " ideal model delta sigma weight residual 1.517 1.527 -0.010 9.30e-03 1.16e+04 1.12e+00 bond pdb=" C PRO A 146 " pdb=" O PRO A 146 " ideal model delta sigma weight residual 1.240 1.229 0.011 1.12e-02 7.97e+03 1.00e+00 bond pdb=" C ILE A 444 " pdb=" O ILE A 444 " ideal model delta sigma weight residual 1.241 1.230 0.010 1.03e-02 9.43e+03 9.86e-01 ... (remaining 2552 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 3376 1.20 - 2.40: 87 2.40 - 3.60: 19 3.60 - 4.79: 5 4.79 - 5.99: 13 Bond angle restraints: 3500 Sorted by residual: angle pdb=" C ILE A 107 " pdb=" CA ILE A 107 " pdb=" CB ILE A 107 " ideal model delta sigma weight residual 114.35 108.36 5.99 1.06e+00 8.90e-01 3.20e+01 angle pdb=" N VAL A 50 " pdb=" CA VAL A 50 " pdb=" C VAL A 50 " ideal model delta sigma weight residual 113.53 108.73 4.80 9.80e-01 1.04e+00 2.40e+01 angle pdb=" C LYS A 145 " pdb=" N PRO A 146 " pdb=" CA PRO A 146 " ideal model delta sigma weight residual 120.38 125.03 -4.65 1.03e+00 9.43e-01 2.04e+01 angle pdb=" CA ILE A 107 " pdb=" C ILE A 107 " pdb=" N PRO A 108 " ideal model delta sigma weight residual 121.00 117.26 3.74 8.30e-01 1.45e+00 2.03e+01 angle pdb=" N GLY A 143 " pdb=" CA GLY A 143 " pdb=" C GLY A 143 " ideal model delta sigma weight residual 112.73 118.02 -5.29 1.20e+00 6.94e-01 1.94e+01 ... (remaining 3495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 1341 15.93 - 31.87: 88 31.87 - 47.80: 27 47.80 - 63.73: 7 63.73 - 79.67: 2 Dihedral angle restraints: 1465 sinusoidal: 515 harmonic: 950 Sorted by residual: dihedral pdb=" CA LEU A 262 " pdb=" CB LEU A 262 " pdb=" CG LEU A 262 " pdb=" CD1 LEU A 262 " ideal model delta sinusoidal sigma weight residual 180.00 120.91 59.09 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LEU A 298 " pdb=" CA LEU A 298 " pdb=" CB LEU A 298 " pdb=" CG LEU A 298 " ideal model delta sinusoidal sigma weight residual -60.00 -9.24 -50.76 3 1.50e+01 4.44e-03 8.94e+00 dihedral pdb=" CB GLU A 85 " pdb=" CG GLU A 85 " pdb=" CD GLU A 85 " pdb=" OE1 GLU A 85 " ideal model delta sinusoidal sigma weight residual 0.00 -79.67 79.67 1 3.00e+01 1.11e-03 8.75e+00 ... (remaining 1462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 224 0.022 - 0.043: 128 0.043 - 0.065: 60 0.065 - 0.087: 18 0.087 - 0.109: 13 Chirality restraints: 443 Sorted by residual: chirality pdb=" CA VAL A 142 " pdb=" N VAL A 142 " pdb=" C VAL A 142 " pdb=" CB VAL A 142 " both_signs ideal model delta sigma weight residual False 2.44 2.33 0.11 2.00e-01 2.50e+01 2.95e-01 chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.83e-01 chirality pdb=" CA ILE A 90 " pdb=" N ILE A 90 " pdb=" C ILE A 90 " pdb=" CB ILE A 90 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.73e-01 ... (remaining 440 not shown) Planarity restraints: 409 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 146 " 0.027 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO A 147 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 147 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 147 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 63 " 0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO A 64 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 144 " 0.006 2.00e-02 2.50e+03 1.28e-02 1.64e+00 pdb=" C CYS A 144 " -0.022 2.00e-02 2.50e+03 pdb=" O CYS A 144 " 0.008 2.00e-02 2.50e+03 pdb=" N LYS A 145 " 0.007 2.00e-02 2.50e+03 ... (remaining 406 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 730 2.80 - 3.32: 2290 3.32 - 3.85: 4012 3.85 - 4.37: 4630 4.37 - 4.90: 7978 Nonbonded interactions: 19640 Sorted by model distance: nonbonded pdb=" O PHE A 49 " pdb=" OH TYR A 135 " model vdw 2.272 3.040 nonbonded pdb=" O LEU A 238 " pdb=" OG1 THR A 242 " model vdw 2.273 3.040 nonbonded pdb=" O VAL A 309 " pdb=" OG1 THR A 313 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR A 226 " pdb=" O LEU A 424 " model vdw 2.308 3.040 nonbonded pdb=" OE1 GLU A 282 " pdb=" NH1 ARG A 296 " model vdw 2.417 3.120 ... (remaining 19635 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.300 Find NCS groups from input model: 0.020 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 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 0.022 2557 Z= 0.144 Angle : 0.580 5.992 3500 Z= 0.369 Chirality : 0.036 0.109 443 Planarity : 0.004 0.042 409 Dihedral : 12.662 79.667 853 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.85 % Allowed : 8.89 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.37), residues: 312 helix: -2.71 (0.26), residues: 228 sheet: None (None), residues: 0 loop : -3.02 (0.62), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 383 PHE 0.006 0.001 PHE A 311 TYR 0.006 0.001 TYR A 110 ARG 0.001 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.269 Fit side-chains REVERT: A 101 MET cc_start: 0.8537 (mmt) cc_final: 0.8178 (mmt) outliers start: 5 outliers final: 2 residues processed: 26 average time/residue: 0.1373 time to fit residues: 4.4657 Evaluate side-chains 14 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 298 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.063264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.054560 restraints weight = 11781.872| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.38 r_work: 0.3043 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2557 Z= 0.188 Angle : 0.581 6.587 3500 Z= 0.289 Chirality : 0.039 0.109 443 Planarity : 0.004 0.044 409 Dihedral : 4.091 41.286 344 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.22 % Allowed : 11.48 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.46), residues: 312 helix: -0.70 (0.33), residues: 234 sheet: None (None), residues: 0 loop : -2.72 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 383 PHE 0.009 0.001 PHE A 385 TYR 0.013 0.001 TYR A 110 ARG 0.000 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.255 Fit side-chains REVERT: A 101 MET cc_start: 0.9151 (mmt) cc_final: 0.8672 (mmm) REVERT: A 285 GLN cc_start: 0.9077 (pm20) cc_final: 0.8797 (pm20) REVERT: A 439 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.7221 (t80) outliers start: 6 outliers final: 2 residues processed: 20 average time/residue: 0.1254 time to fit residues: 3.3541 Evaluate side-chains 16 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 13 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 439 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.062946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.054044 restraints weight = 11812.655| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.42 r_work: 0.3028 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2557 Z= 0.179 Angle : 0.555 7.585 3500 Z= 0.271 Chirality : 0.038 0.111 443 Planarity : 0.004 0.047 409 Dihedral : 3.494 29.094 343 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.11 % Allowed : 11.85 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.50), residues: 312 helix: 0.02 (0.35), residues: 244 sheet: None (None), residues: 0 loop : -2.72 (0.78), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 383 PHE 0.010 0.001 PHE A 385 TYR 0.006 0.001 TYR A 110 ARG 0.000 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 439 TYR cc_start: 0.8352 (OUTLIER) cc_final: 0.7219 (t80) outliers start: 3 outliers final: 2 residues processed: 18 average time/residue: 0.1605 time to fit residues: 3.6987 Evaluate side-chains 16 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 13 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 439 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 3 optimal weight: 0.0970 chunk 31 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3387 r_free = 0.3387 target = 0.062520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.053550 restraints weight = 11927.709| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.48 r_work: 0.3011 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2557 Z= 0.170 Angle : 0.551 7.414 3500 Z= 0.264 Chirality : 0.038 0.112 443 Planarity : 0.004 0.047 409 Dihedral : 3.064 12.933 341 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.85 % Allowed : 12.59 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.50), residues: 312 helix: 0.45 (0.35), residues: 244 sheet: None (None), residues: 0 loop : -2.47 (0.78), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 383 PHE 0.016 0.001 PHE A 450 TYR 0.006 0.001 TYR A 135 ARG 0.000 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.291 Fit side-chains REVERT: A 60 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7953 (pm20) REVERT: A 439 TYR cc_start: 0.8330 (OUTLIER) cc_final: 0.7230 (t80) outliers start: 5 outliers final: 3 residues processed: 17 average time/residue: 0.1476 time to fit residues: 3.3236 Evaluate side-chains 18 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 439 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 29 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3355 r_free = 0.3355 target = 0.061587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.052778 restraints weight = 11936.699| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.38 r_work: 0.2986 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2557 Z= 0.220 Angle : 0.582 7.988 3500 Z= 0.281 Chirality : 0.039 0.111 443 Planarity : 0.004 0.048 409 Dihedral : 3.220 13.787 341 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.59 % Allowed : 13.70 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.50), residues: 312 helix: 0.64 (0.35), residues: 247 sheet: None (None), residues: 0 loop : -1.93 (0.82), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 383 PHE 0.012 0.001 PHE A 385 TYR 0.007 0.001 TYR A 135 ARG 0.000 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 13 time to evaluate : 0.281 Fit side-chains REVERT: A 60 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7934 (pm20) REVERT: A 439 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7255 (t80) outliers start: 7 outliers final: 3 residues processed: 19 average time/residue: 0.1324 time to fit residues: 3.3203 Evaluate side-chains 18 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 452 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3360 r_free = 0.3360 target = 0.061860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.052865 restraints weight = 12150.979| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.51 r_work: 0.2985 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2557 Z= 0.190 Angle : 0.565 8.503 3500 Z= 0.270 Chirality : 0.039 0.121 443 Planarity : 0.004 0.049 409 Dihedral : 3.173 13.693 341 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.22 % Allowed : 14.81 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.51), residues: 312 helix: 0.86 (0.35), residues: 247 sheet: None (None), residues: 0 loop : -1.87 (0.82), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 383 PHE 0.018 0.001 PHE A 450 TYR 0.005 0.001 TYR A 135 ARG 0.000 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.250 Fit side-chains REVERT: A 60 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7933 (pm20) REVERT: A 278 MET cc_start: 0.9086 (ptp) cc_final: 0.7987 (ptp) REVERT: A 439 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.7245 (t80) outliers start: 6 outliers final: 2 residues processed: 18 average time/residue: 0.1293 time to fit residues: 3.0817 Evaluate side-chains 17 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 439 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3370 r_free = 0.3370 target = 0.062405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.053381 restraints weight = 12318.564| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.47 r_work: 0.3004 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2557 Z= 0.192 Angle : 0.582 9.627 3500 Z= 0.278 Chirality : 0.039 0.110 443 Planarity : 0.004 0.049 409 Dihedral : 3.185 13.836 341 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.85 % Allowed : 17.04 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.51), residues: 312 helix: 1.00 (0.35), residues: 245 sheet: None (None), residues: 0 loop : -1.74 (0.85), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 383 PHE 0.011 0.001 PHE A 385 TYR 0.006 0.001 TYR A 135 ARG 0.000 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.281 Fit side-chains REVERT: A 60 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7950 (pm20) REVERT: A 278 MET cc_start: 0.8775 (ptp) cc_final: 0.8419 (ptp) REVERT: A 439 TYR cc_start: 0.8359 (OUTLIER) cc_final: 0.7352 (t80) outliers start: 5 outliers final: 3 residues processed: 18 average time/residue: 0.1306 time to fit residues: 3.1111 Evaluate side-chains 18 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 452 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 23 optimal weight: 0.0050 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 = 0.3373 r_free = 0.3373 target = 0.062218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.053396 restraints weight = 11943.550| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.41 r_work: 0.3007 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2557 Z= 0.162 Angle : 0.577 9.089 3500 Z= 0.276 Chirality : 0.039 0.123 443 Planarity : 0.004 0.049 409 Dihedral : 3.103 13.704 341 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.85 % Allowed : 17.04 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.51), residues: 312 helix: 1.10 (0.35), residues: 245 sheet: None (None), residues: 0 loop : -1.76 (0.83), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 383 PHE 0.010 0.001 PHE A 385 TYR 0.005 0.000 TYR A 135 ARG 0.000 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.250 Fit side-chains REVERT: A 60 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7912 (pm20) REVERT: A 278 MET cc_start: 0.8778 (ptp) cc_final: 0.8460 (ptp) REVERT: A 439 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.7248 (t80) outliers start: 5 outliers final: 3 residues processed: 18 average time/residue: 0.1345 time to fit residues: 3.1925 Evaluate side-chains 18 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 452 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 0.0980 chunk 16 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3356 r_free = 0.3356 target = 0.061556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.052724 restraints weight = 11871.688| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.40 r_work: 0.2988 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2557 Z= 0.186 Angle : 0.591 9.400 3500 Z= 0.280 Chirality : 0.039 0.110 443 Planarity : 0.003 0.049 409 Dihedral : 3.153 13.589 341 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.85 % Allowed : 16.67 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.51), residues: 312 helix: 1.20 (0.35), residues: 245 sheet: None (None), residues: 0 loop : -1.63 (0.85), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 383 PHE 0.011 0.001 PHE A 385 TYR 0.006 0.001 TYR A 135 ARG 0.001 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.268 Fit side-chains REVERT: A 60 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7921 (pm20) REVERT: A 278 MET cc_start: 0.8899 (ptp) cc_final: 0.8581 (ptp) REVERT: A 439 TYR cc_start: 0.8338 (OUTLIER) cc_final: 0.7321 (t80) outliers start: 5 outliers final: 3 residues processed: 18 average time/residue: 0.1335 time to fit residues: 3.2018 Evaluate side-chains 18 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 452 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 1 optimal weight: 0.2980 chunk 31 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.0870 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 0.0070 chunk 24 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 overall best weight: 0.3176 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.063086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.054221 restraints weight = 11753.736| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.44 r_work: 0.3033 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2557 Z= 0.154 Angle : 0.562 9.619 3500 Z= 0.267 Chirality : 0.038 0.116 443 Planarity : 0.004 0.048 409 Dihedral : 3.040 13.712 341 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.48 % Allowed : 17.04 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.52), residues: 312 helix: 1.31 (0.35), residues: 245 sheet: None (None), residues: 0 loop : -1.37 (0.87), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 230 PHE 0.010 0.001 PHE A 385 TYR 0.005 0.000 TYR A 135 ARG 0.001 0.000 ARG A 296 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.274 Fit side-chains REVERT: A 53 LYS cc_start: 0.9536 (tmtt) cc_final: 0.9268 (tmtt) REVERT: A 60 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7914 (pm20) REVERT: A 278 MET cc_start: 0.8828 (ptp) cc_final: 0.8601 (ptp) REVERT: A 439 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.7317 (t80) outliers start: 4 outliers final: 2 residues processed: 17 average time/residue: 0.1381 time to fit residues: 3.1685 Evaluate side-chains 16 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 12 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 452 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 1 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.062171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.053332 restraints weight = 11775.042| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.41 r_work: 0.3011 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2557 Z= 0.173 Angle : 0.571 9.893 3500 Z= 0.271 Chirality : 0.039 0.111 443 Planarity : 0.003 0.048 409 Dihedral : 3.078 13.556 341 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.48 % Allowed : 17.41 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.52), residues: 312 helix: 1.34 (0.35), residues: 245 sheet: None (None), residues: 0 loop : -1.28 (0.88), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 383 PHE 0.011 0.001 PHE A 385 TYR 0.006 0.000 TYR A 135 ARG 0.001 0.000 ARG A 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1424.12 seconds wall clock time: 25 minutes 13.73 seconds (1513.73 seconds total)