Starting phenix.real_space_refine on Thu Dec 7 16:28:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yv1_10940/12_2023/6yv1_10940.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yv1_10940/12_2023/6yv1_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_10940/12_2023/6yv1_10940.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yv1_10940/12_2023/6yv1_10940.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yv1_10940/12_2023/6yv1_10940.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yv1_10940/12_2023/6yv1_10940.pdb" } 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 Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 2.01, per 1000 atoms: 0.81 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 - 3.50 Amino acid : False - 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: 1.20 Conformation dependent library (CDL) restraints added in 566.3 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: 0.23 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: 0.55 Time building geometry restraints manager: 1.28 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: 100.78 - 107.44: 92 107.44 - 114.09: 1528 114.09 - 120.74: 1122 120.74 - 127.40: 731 127.40 - 134.05: 27 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 2.440 nonbonded pdb=" O LEU A 238 " pdb=" OG1 THR A 242 " model vdw 2.273 2.440 nonbonded pdb=" O VAL A 309 " pdb=" OG1 THR A 313 " model vdw 2.289 2.440 nonbonded pdb=" OH TYR A 226 " pdb=" O LEU A 424 " model vdw 2.308 2.440 nonbonded pdb=" OE1 GLU A 282 " pdb=" NH1 ARG A 296 " model vdw 2.417 2.520 ... (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: 1.590 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: 6.440 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.120 Find NCS groups from input model: 0.060 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.040 ------------------------------------------------------------------------------- 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 : 0.278 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 26 average time/residue: 0.1486 time to fit residues: 4.8315 Evaluate side-chains 14 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.284 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0285 time to fit residues: 0.4797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 236 ASN A 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1847 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= 0.185 Angle : 0.566 6.166 3500 Z= 0.280 Chirality : 0.039 0.110 443 Planarity : 0.004 0.043 409 Dihedral : 3.080 12.210 341 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.85 % Allowed : 12.22 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.04 (0.46), residues: 312 helix: -0.75 (0.32), residues: 240 sheet: None (None), residues: 0 loop : -3.02 (0.73), 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 0.013 0.001 TYR A 110 ARG 0.001 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 19 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 14 time to evaluate : 0.297 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 19 average time/residue: 0.1350 time to fit residues: 3.3999 Evaluate side-chains 14 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.274 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0381 time to fit residues: 0.4100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 0.0980 chunk 21 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2308 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= 0.167 Angle : 0.537 7.649 3500 Z= 0.260 Chirality : 0.038 0.110 443 Planarity : 0.004 0.046 409 Dihedral : 3.049 13.533 341 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.48 % Allowed : 13.70 % Favored : 84.81 % 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: 0.04 (0.35), residues: 244 sheet: None (None), residues: 0 loop : -2.75 (0.79), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 383 PHE 0.010 0.001 PHE A 385 TYR 0.008 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 18 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 14 time to evaluate : 0.280 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 16 average time/residue: 0.1419 time to fit residues: 3.0666 Evaluate side-chains 14 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.291 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0287 time to fit residues: 0.4757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 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 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2627 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= 0.174 Angle : 0.535 8.091 3500 Z= 0.258 Chirality : 0.038 0.111 443 Planarity : 0.004 0.047 409 Dihedral : 3.033 12.850 341 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.74 % Allowed : 15.93 % 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: -0.24 (0.51), residues: 312 helix: 0.52 (0.36), residues: 244 sheet: None (None), residues: 0 loop : -2.51 (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 0.005 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 16 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 14 time to evaluate : 0.282 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 15 average time/residue: 0.1828 time to fit residues: 3.4995 Evaluate side-chains 13 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.275 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2833 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= 0.206 Angle : 0.557 7.422 3500 Z= 0.272 Chirality : 0.039 0.113 443 Planarity : 0.004 0.050 409 Dihedral : 3.217 13.869 341 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.37 % Allowed : 18.15 % 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: 0.08 (0.51), residues: 312 helix: 0.65 (0.35), residues: 247 sheet: None (None), residues: 0 loop : -2.09 (0.81), 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 0.006 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 14 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.284 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 0.1511 time to fit residues: 2.6750 Evaluate side-chains 13 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.279 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3100 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= 0.219 Angle : 0.572 8.067 3500 Z= 0.277 Chirality : 0.039 0.109 443 Planarity : 0.004 0.050 409 Dihedral : 3.267 13.414 341 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.37 % Allowed : 19.63 % Favored : 80.00 % 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: 0.44 (0.51), residues: 312 helix: 0.84 (0.35), residues: 250 sheet: None (None), residues: 0 loop : -1.75 (0.86), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 383 PHE 0.017 0.001 PHE A 450 TYR 0.006 0.001 TYR A 135 ARG 0.001 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 14 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.282 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 14 average time/residue: 0.1434 time to fit residues: 2.7467 Evaluate side-chains 14 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.279 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0275 time to fit residues: 0.4063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 17 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.0970 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3192 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= 0.167 Angle : 0.542 8.662 3500 Z= 0.261 Chirality : 0.039 0.111 443 Planarity : 0.004 0.049 409 Dihedral : 3.178 13.961 341 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.37 % Allowed : 20.00 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.69 (0.51), residues: 312 helix: 1.03 (0.35), residues: 247 sheet: None (None), residues: 0 loop : -1.64 (0.84), residues: 65 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 0.001 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 14 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.285 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 14 average time/residue: 0.1455 time to fit residues: 2.7623 Evaluate side-chains 14 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.279 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0360 time to fit residues: 0.4147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 0.0980 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3303 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= 0.174 Angle : 0.565 9.041 3500 Z= 0.268 Chirality : 0.039 0.113 443 Planarity : 0.003 0.049 409 Dihedral : 3.137 13.803 341 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.74 % Allowed : 19.26 % Favored : 80.00 % 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: 1.11 (0.52), residues: 312 helix: 1.30 (0.36), residues: 246 sheet: None (None), residues: 0 loop : -1.30 (0.88), residues: 66 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 0.005 0.001 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 : 0.275 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 15 average time/residue: 0.1335 time to fit residues: 2.7281 Evaluate side-chains 15 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 13 time to evaluate : 0.268 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0336 time to fit residues: 0.4476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3410 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= 0.178 Angle : 0.564 9.235 3500 Z= 0.267 Chirality : 0.039 0.109 443 Planarity : 0.003 0.049 409 Dihedral : 3.165 13.967 341 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 18.89 % 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: 1.03 (0.52), residues: 312 helix: 1.31 (0.35), residues: 246 sheet: None (None), residues: 0 loop : -1.62 (0.84), residues: 66 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 13 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.268 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1515 time to fit residues: 2.6311 Evaluate side-chains 13 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.283 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 0.0770 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.0010 chunk 10 optimal weight: 0.0770 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2557 Z= 0.148 Angle : 0.556 9.520 3500 Z= 0.263 Chirality : 0.038 0.122 443 Planarity : 0.004 0.049 409 Dihedral : 3.084 13.914 341 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 19.26 % 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: 1.24 (0.52), residues: 312 helix: 1.39 (0.36), residues: 246 sheet: None (None), residues: 0 loop : -1.24 (0.88), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 230 PHE 0.009 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 13 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.303 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1534 time to fit residues: 2.7213 Evaluate side-chains 13 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.255 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 0.0470 chunk 29 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 31 optimal weight: 0.0000 overall best weight: 0.4682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.063237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.054288 restraints weight = 11774.719| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.44 r_work: 0.3032 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2557 Z= 0.154 Angle : 0.549 9.569 3500 Z= 0.260 Chirality : 0.038 0.113 443 Planarity : 0.003 0.049 409 Dihedral : 3.059 13.894 341 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 19.26 % 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: 1.32 (0.52), residues: 312 helix: 1.44 (0.36), residues: 246 sheet: None (None), residues: 0 loop : -1.18 (0.88), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 230 PHE 0.010 0.001 PHE A 385 TYR 0.004 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: 941.51 seconds wall clock time: 17 minutes 55.32 seconds (1075.32 seconds total)