Starting phenix.real_space_refine on Mon Sep 23 12:34:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yv1_10940/09_2024/6yv1_10940.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yv1_10940/09_2024/6yv1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yv1_10940/09_2024/6yv1_10940.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yv1_10940/09_2024/6yv1_10940.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yv1_10940/09_2024/6yv1_10940.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yv1_10940/09_2024/6yv1_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-5461/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: 2.81, per 1000 atoms: 1.13 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 299.3 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: 0.28 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: 0.62 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: 1.520 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: 0.030 Set scattering table: 0.030 Process input model: 12.140 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: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.400 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.310 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: 0.1487 time to fit residues: 4.8307 Evaluate side-chains 14 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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: 0.7980 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1906 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= 0.189 Angle : 0.578 6.393 3500 Z= 0.288 Chirality : 0.039 0.111 443 Planarity : 0.005 0.044 409 Dihedral : 4.098 41.608 344 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.22 % Allowed : 11.11 % Favored : 86.67 % 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: -0.72 (0.32), residues: 240 sheet: None (None), residues: 0 loop : -2.74 (0.74), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 383 PHE 0.009 0.001 PHE A 385 TYR 0.014 0.001 TYR A 110 ARG 0.000 0.000 ARG A 250 *********************** 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 fitting. rotamer outliers: 6 poor density : 14 time to evaluate : 0.258 Fit side-chains REVERT: A 439 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7298 (t80) outliers start: 6 outliers final: 2 residues processed: 20 average time/residue: 0.1316 time to fit residues: 3.4957 Evaluate side-chains 16 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 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 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 16 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2557 Z= 0.225 Angle : 0.585 6.679 3500 Z= 0.289 Chirality : 0.039 0.110 443 Planarity : 0.004 0.046 409 Dihedral : 3.643 30.517 343 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.85 % Allowed : 12.96 % Favored : 85.19 % 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: -0.96 (0.49), residues: 312 helix: 0.03 (0.35), residues: 244 sheet: None (None), residues: 0 loop : -2.80 (0.76), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 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 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 fitting. rotamer outliers: 5 poor density : 14 time to evaluate : 0.310 Fit side-chains REVERT: A 439 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.7412 (t80) outliers start: 5 outliers final: 3 residues processed: 18 average time/residue: 0.1346 time to fit residues: 3.2538 Evaluate side-chains 17 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 13 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 360 ILE 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 15 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.0870 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2557 Z= 0.191 Angle : 0.555 7.811 3500 Z= 0.270 Chirality : 0.039 0.112 443 Planarity : 0.004 0.047 409 Dihedral : 3.159 12.943 341 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.22 % Allowed : 14.44 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.23 (0.50), residues: 312 helix: 0.46 (0.35), residues: 246 sheet: None (None), residues: 0 loop : -2.25 (0.81), residues: 66 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 0.008 0.001 TYR A 135 ARG 0.001 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 21 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 15 time to evaluate : 0.283 Fit side-chains REVERT: A 439 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7393 (t80) outliers start: 6 outliers final: 3 residues processed: 20 average time/residue: 0.1723 time to fit residues: 4.3027 Evaluate side-chains 17 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 13 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 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 23 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 0.1980 chunk 18 optimal weight: 0.2980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2557 Z= 0.229 Angle : 0.590 7.103 3500 Z= 0.292 Chirality : 0.040 0.124 443 Planarity : 0.004 0.049 409 Dihedral : 3.372 13.952 341 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.85 % Allowed : 15.93 % Favored : 82.22 % 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: 0.21 (0.51), residues: 312 helix: 0.73 (0.35), residues: 246 sheet: None (None), residues: 0 loop : -1.90 (0.83), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 383 PHE 0.012 0.001 PHE A 385 TYR 0.006 0.001 TYR A 135 ARG 0.001 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 18 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 13 time to evaluate : 0.263 Fit side-chains REVERT: A 439 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7433 (t80) outliers start: 5 outliers final: 4 residues processed: 18 average time/residue: 0.1256 time to fit residues: 3.0175 Evaluate side-chains 18 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 13 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 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 7 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 0.3980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3231 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= 0.200 Angle : 0.580 8.135 3500 Z= 0.283 Chirality : 0.039 0.122 443 Planarity : 0.004 0.049 409 Dihedral : 3.274 13.484 341 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.22 % Allowed : 16.30 % 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: 0.48 (0.51), residues: 312 helix: 0.85 (0.35), residues: 249 sheet: None (None), residues: 0 loop : -1.62 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 383 PHE 0.017 0.001 PHE A 450 TYR 0.007 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 19 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 13 time to evaluate : 0.374 Fit side-chains REVERT: A 439 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7405 (t80) outliers start: 6 outliers final: 4 residues processed: 18 average time/residue: 0.1545 time to fit residues: 3.7186 Evaluate side-chains 18 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 13 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 360 ILE Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 452 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.0270 chunk 14 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3324 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= 0.164 Angle : 0.559 8.948 3500 Z= 0.270 Chirality : 0.039 0.113 443 Planarity : 0.004 0.049 409 Dihedral : 3.191 13.907 341 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.11 % Allowed : 18.15 % Favored : 80.74 % 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: 0.70 (0.51), residues: 312 helix: 1.06 (0.35), residues: 246 sheet: None (None), residues: 0 loop : -1.67 (0.83), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 230 PHE 0.011 0.001 PHE A 385 TYR 0.005 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 17 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 14 time to evaluate : 0.286 Fit side-chains REVERT: A 439 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.7438 (t80) outliers start: 3 outliers final: 2 residues processed: 17 average time/residue: 0.1731 time to fit residues: 3.7392 Evaluate side-chains 16 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 13 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE 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 15 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 0.0570 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3419 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= 0.171 Angle : 0.576 8.886 3500 Z= 0.275 Chirality : 0.039 0.119 443 Planarity : 0.004 0.049 409 Dihedral : 3.241 13.853 341 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.74 % Allowed : 18.52 % Favored : 80.74 % 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: 0.88 (0.51), residues: 312 helix: 1.20 (0.35), residues: 246 sheet: None (None), residues: 0 loop : -1.67 (0.83), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 230 PHE 0.011 0.001 PHE A 385 TYR 0.004 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 15 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 13 time to evaluate : 0.287 Fit side-chains REVERT: A 439 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.7448 (t80) outliers start: 2 outliers final: 1 residues processed: 15 average time/residue: 0.1440 time to fit residues: 2.9048 Evaluate side-chains 15 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 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 439 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 0.0270 chunk 30 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3520 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= 0.171 Angle : 0.586 9.326 3500 Z= 0.278 Chirality : 0.039 0.112 443 Planarity : 0.004 0.049 409 Dihedral : 3.247 13.681 341 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % 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: 0.94 (0.51), residues: 312 helix: 1.29 (0.35), residues: 244 sheet: None (None), residues: 0 loop : -1.74 (0.83), residues: 68 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 0.004 0.001 TYR A 377 ARG 0.000 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 fitting. rotamer outliers: 5 poor density : 13 time to evaluate : 0.287 Fit side-chains REVERT: A 439 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.7474 (t80) outliers start: 5 outliers final: 3 residues processed: 18 average time/residue: 0.1339 time to fit residues: 3.2211 Evaluate side-chains 17 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 13 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE 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 15 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.0050 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2557 Z= 0.167 Angle : 0.576 9.378 3500 Z= 0.275 Chirality : 0.039 0.113 443 Planarity : 0.004 0.049 409 Dihedral : 3.253 13.621 341 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.48 % Allowed : 17.78 % Favored : 80.74 % 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: 0.95 (0.51), residues: 312 helix: 1.25 (0.35), residues: 245 sheet: None (None), residues: 0 loop : -1.60 (0.82), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 383 PHE 0.021 0.001 PHE A 450 TYR 0.005 0.001 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 16 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 12 time to evaluate : 0.299 Fit side-chains REVERT: A 439 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.7481 (t80) outliers start: 4 outliers final: 3 residues processed: 16 average time/residue: 0.1465 time to fit residues: 3.1294 Evaluate side-chains 16 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 12 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE 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: 0.0980 chunk 18 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.062147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.053306 restraints weight = 12155.151| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.53 r_work: 0.3006 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3693 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= 0.167 Angle : 0.569 9.366 3500 Z= 0.272 Chirality : 0.039 0.112 443 Planarity : 0.004 0.049 409 Dihedral : 3.250 13.641 341 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.48 % Allowed : 17.78 % Favored : 80.74 % 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: 1.02 (0.51), residues: 312 helix: 1.28 (0.35), residues: 245 sheet: None (None), residues: 0 loop : -1.52 (0.83), residues: 67 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 985.62 seconds wall clock time: 18 minutes 5.88 seconds (1085.88 seconds total)