Starting phenix.real_space_refine on Fri Aug 2 12:30:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v85_43023/08_2024/8v85_43023_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v85_43023/08_2024/8v85_43023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v85_43023/08_2024/8v85_43023.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v85_43023/08_2024/8v85_43023.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v85_43023/08_2024/8v85_43023_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v85_43023/08_2024/8v85_43023_neut.cif" } resolution = 2.9 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 8 5.16 5 C 986 2.51 5 N 268 2.21 5 O 277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 1539 Number of models: 1 Model: "" Number of chains: 1 Chain: "3" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1539 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 10, 'TRANS': 186} Time building chain proxies: 1.40, per 1000 atoms: 0.91 Number of scatterers: 1539 At special positions: 0 Unit cell: (59.4, 59.4, 52.92, 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 8 16.00 O 277 8.00 N 268 7.00 C 986 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: 0.52 Conformation dependent library (CDL) restraints added in 281.7 milliseconds 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 368 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 1 sheets defined 57.9% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain '3' and resid 146 through 155 Processing helix chain '3' and resid 161 through 173 Proline residue: 3 169 - end of helix Processing helix chain '3' and resid 188 through 199 Proline residue: 3 194 - end of helix Processing helix chain '3' and resid 216 through 232 Processing helix chain '3' and resid 246 through 256 Processing helix chain '3' and resid 264 through 276 Processing helix chain '3' and resid 278 through 282 removed outlier: 4.164A pdb=" N SER 3 281 " --> pdb=" O ASP 3 278 " (cutoff:3.500A) Processing helix chain '3' and resid 289 through 297 Processing helix chain '3' and resid 298 through 309 removed outlier: 3.548A pdb=" N GLU 3 304 " --> pdb=" O GLU 3 300 " (cutoff:3.500A) Processing helix chain '3' and resid 323 through 334 Processing sheet with id=AA1, first strand: chain '3' and resid 238 through 241 removed outlier: 6.138A pdb=" N VAL 3 239 " --> pdb=" O ILE 3 262 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA 3 210 " --> pdb=" O ILE 3 261 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA 3 263 " --> pdb=" O ALA 3 210 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE 3 212 " --> pdb=" O ALA 3 263 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL 3 211 " --> pdb=" O VAL 3 286 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASP 3 288 " --> pdb=" O VAL 3 211 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU 3 213 " --> pdb=" O ASP 3 288 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL 3 285 " --> pdb=" O LEU 3 316 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N PHE 3 318 " --> pdb=" O VAL 3 285 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHE 3 287 " --> pdb=" O PHE 3 318 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE 3 177 " --> pdb=" O THR 3 315 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 210 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: 0.38 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 506 1.34 - 1.46: 262 1.46 - 1.57: 779 1.57 - 1.69: 0 1.69 - 1.80: 16 Bond restraints: 1563 Sorted by residual: bond pdb=" CA THR 3 312 " pdb=" CB THR 3 312 " ideal model delta sigma weight residual 1.522 1.530 -0.008 1.32e-02 5.74e+03 3.59e-01 bond pdb=" CA THR 3 312 " pdb=" C THR 3 312 " ideal model delta sigma weight residual 1.530 1.524 0.006 1.10e-02 8.26e+03 2.91e-01 bond pdb=" C LYS 3 198 " pdb=" N LEU 3 199 " ideal model delta sigma weight residual 1.331 1.338 -0.007 1.25e-02 6.40e+03 2.85e-01 bond pdb=" CA ILE 3 168 " pdb=" C ILE 3 168 " ideal model delta sigma weight residual 1.520 1.524 -0.004 8.80e-03 1.29e+04 2.21e-01 bond pdb=" CA LEU 3 193 " pdb=" C LEU 3 193 " ideal model delta sigma weight residual 1.520 1.526 -0.006 1.23e-02 6.61e+03 2.01e-01 ... (remaining 1558 not shown) Histogram of bond angle deviations from ideal: 100.38 - 106.55: 50 106.55 - 112.72: 846 112.72 - 118.88: 415 118.88 - 125.05: 783 125.05 - 131.22: 14 Bond angle restraints: 2108 Sorted by residual: angle pdb=" C ALA 3 263 " pdb=" N THR 3 264 " pdb=" CA THR 3 264 " ideal model delta sigma weight residual 120.94 127.58 -6.64 1.90e+00 2.77e-01 1.22e+01 angle pdb=" N GLY 3 244 " pdb=" CA GLY 3 244 " pdb=" C GLY 3 244 " ideal model delta sigma weight residual 115.08 112.16 2.92 1.19e+00 7.06e-01 6.04e+00 angle pdb=" CA PHE 3 298 " pdb=" C PHE 3 298 " pdb=" O PHE 3 298 " ideal model delta sigma weight residual 119.23 116.51 2.72 1.54e+00 4.22e-01 3.11e+00 angle pdb=" CA THR 3 312 " pdb=" C THR 3 312 " pdb=" N ARG 3 313 " ideal model delta sigma weight residual 114.76 116.67 -1.91 1.14e+00 7.69e-01 2.80e+00 angle pdb=" CA THR 3 312 " pdb=" C THR 3 312 " pdb=" O THR 3 312 " ideal model delta sigma weight residual 122.64 120.61 2.03 1.25e+00 6.40e-01 2.64e+00 ... (remaining 2103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.18: 847 9.18 - 18.35: 91 18.35 - 27.53: 18 27.53 - 36.71: 6 36.71 - 45.88: 6 Dihedral angle restraints: 968 sinusoidal: 403 harmonic: 565 Sorted by residual: dihedral pdb=" N LYS 3 155 " pdb=" CA LYS 3 155 " pdb=" CB LYS 3 155 " pdb=" CG LYS 3 155 " ideal model delta sinusoidal sigma weight residual -180.00 -134.12 -45.88 3 1.50e+01 4.44e-03 8.24e+00 dihedral pdb=" N LYS 3 228 " pdb=" CA LYS 3 228 " pdb=" CB LYS 3 228 " pdb=" CG LYS 3 228 " ideal model delta sinusoidal sigma weight residual -60.00 -103.18 43.18 3 1.50e+01 4.44e-03 7.76e+00 dihedral pdb=" CA ALA 3 263 " pdb=" C ALA 3 263 " pdb=" N THR 3 264 " pdb=" CA THR 3 264 " ideal model delta harmonic sigma weight residual 180.00 166.40 13.60 0 5.00e+00 4.00e-02 7.39e+00 ... (remaining 965 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.027: 162 0.027 - 0.054: 49 0.054 - 0.081: 19 0.081 - 0.107: 13 0.107 - 0.134: 8 Chirality restraints: 251 Sorted by residual: chirality pdb=" CA ILE 3 261 " pdb=" N ILE 3 261 " pdb=" C ILE 3 261 " pdb=" CB ILE 3 261 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE 3 212 " pdb=" N ILE 3 212 " pdb=" C ILE 3 212 " pdb=" CB ILE 3 212 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA VAL 3 178 " pdb=" N VAL 3 178 " pdb=" C VAL 3 178 " pdb=" CB VAL 3 178 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 248 not shown) Planarity restraints: 269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR 3 161 " -0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO 3 162 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO 3 162 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO 3 162 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE 3 168 " 0.016 5.00e-02 4.00e+02 2.45e-02 9.62e-01 pdb=" N PRO 3 169 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO 3 169 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO 3 169 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE 3 191 " 0.006 2.00e-02 2.50e+03 5.13e-03 4.61e-01 pdb=" CG PHE 3 191 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE 3 191 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE 3 191 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE 3 191 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE 3 191 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE 3 191 " 0.001 2.00e-02 2.50e+03 ... (remaining 266 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 499 2.85 - 3.37: 1485 3.37 - 3.88: 2523 3.88 - 4.39: 2831 4.39 - 4.90: 4700 Nonbonded interactions: 12038 Sorted by model distance: nonbonded pdb=" O ASP 3 245 " pdb=" NH2 ARG 3 267 " model vdw 2.342 3.120 nonbonded pdb=" NH2 ARG 3 209 " pdb=" OD2 ASP 3 259 " model vdw 2.364 3.120 nonbonded pdb=" OE1 GLN 3 250 " pdb=" NE ARG 3 267 " model vdw 2.407 3.120 nonbonded pdb=" N GLN 3 301 " pdb=" OE1 GLN 3 301 " model vdw 2.439 3.120 nonbonded pdb=" O ILE 3 163 " pdb=" OG1 THR 3 167 " model vdw 2.486 3.040 ... (remaining 12033 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: 2.750 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: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 11.310 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1091 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 0.020 1563 Z= 0.119 Angle : 0.504 6.641 2108 Z= 0.280 Chirality : 0.041 0.134 251 Planarity : 0.003 0.025 269 Dihedral : 8.921 45.882 600 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: 1.33 (0.61), residues: 195 helix: 1.64 (0.52), residues: 108 sheet: 0.27 (0.76), residues: 39 loop : -0.15 (0.89), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS 3 270 PHE 0.012 0.001 PHE 3 191 TYR 0.006 0.001 TYR 3 284 ARG 0.002 0.000 ARG 3 341 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.186 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 1.5846 time to fit residues: 37.0726 Evaluate side-chains 14 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 16 optimal weight: 30.0000 chunk 14 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 50.0000 chunk 5 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 17 optimal weight: 30.0000 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 150 ASN 3 159 GLN 3 202 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1436 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1563 Z= 0.243 Angle : 0.656 5.388 2108 Z= 0.329 Chirality : 0.045 0.169 251 Planarity : 0.005 0.031 269 Dihedral : 4.403 14.351 210 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.33 % Allowed : 8.14 % Favored : 89.53 % 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: 0.53 (0.60), residues: 195 helix: 0.84 (0.50), residues: 107 sheet: 0.04 (0.87), residues: 38 loop : -0.15 (0.86), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS 3 202 PHE 0.013 0.002 PHE 3 268 TYR 0.005 0.002 TYR 3 284 ARG 0.007 0.001 ARG 3 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 15 time to evaluate : 0.188 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 17 average time/residue: 1.0629 time to fit residues: 18.5993 Evaluate side-chains 16 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 14 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 324 ASN Chi-restraints excluded: chain 3 residue 336 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 17 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 11 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 16 optimal weight: 40.0000 chunk 4 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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: 0.1529 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1563 Z= 0.209 Angle : 0.588 6.191 2108 Z= 0.290 Chirality : 0.042 0.146 251 Planarity : 0.005 0.047 269 Dihedral : 4.448 15.891 210 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.33 % Allowed : 11.05 % Favored : 86.63 % 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: 0.18 (0.61), residues: 195 helix: 0.77 (0.52), residues: 107 sheet: -0.65 (0.95), residues: 28 loop : -0.45 (0.83), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS 3 202 PHE 0.008 0.001 PHE 3 230 TYR 0.002 0.001 TYR 3 284 ARG 0.008 0.001 ARG 3 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 15 time to evaluate : 0.187 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 18 average time/residue: 1.2914 time to fit residues: 23.7863 Evaluate side-chains 16 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 14 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 324 ASN Chi-restraints excluded: chain 3 residue 336 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 30.0000 chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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: 0.1755 moved from start: 0.7188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 1563 Z= 0.277 Angle : 0.757 9.909 2108 Z= 0.363 Chirality : 0.044 0.158 251 Planarity : 0.006 0.053 269 Dihedral : 5.134 17.790 210 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 25.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.16 % Allowed : 9.88 % Favored : 88.95 % 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: 0.18 (0.65), residues: 195 helix: 0.44 (0.53), residues: 105 sheet: -0.68 (0.96), residues: 37 loop : 0.52 (0.93), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS 3 202 PHE 0.015 0.002 PHE 3 224 TYR 0.012 0.006 TYR 3 284 ARG 0.005 0.001 ARG 3 292 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.165 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 19 average time/residue: 1.1655 time to fit residues: 22.6699 Evaluate side-chains 16 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 14 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 324 ASN Chi-restraints excluded: chain 3 residue 336 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 30.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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: 0.1663 moved from start: 0.7397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1563 Z= 0.184 Angle : 0.652 9.684 2108 Z= 0.305 Chirality : 0.042 0.134 251 Planarity : 0.005 0.031 269 Dihedral : 4.588 16.212 210 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.16 % Allowed : 12.79 % Favored : 86.05 % 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: -0.26 (0.62), residues: 195 helix: 0.58 (0.54), residues: 107 sheet: -0.83 (1.15), residues: 26 loop : -1.02 (0.74), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS 3 202 PHE 0.007 0.001 PHE 3 294 TYR 0.009 0.002 TYR 3 284 ARG 0.003 0.001 ARG 3 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.190 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 17 average time/residue: 1.0371 time to fit residues: 18.1425 Evaluate side-chains 14 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 336 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 chunk 3 optimal weight: 30.0000 chunk 12 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- 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: 0.1745 moved from start: 0.7978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1563 Z= 0.226 Angle : 0.683 9.596 2108 Z= 0.332 Chirality : 0.042 0.140 251 Planarity : 0.005 0.036 269 Dihedral : 4.676 15.766 210 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.16 % Allowed : 14.53 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.64), residues: 195 helix: 0.64 (0.54), residues: 104 sheet: -1.28 (0.90), residues: 38 loop : -0.02 (0.86), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS 3 202 PHE 0.008 0.001 PHE 3 294 TYR 0.008 0.003 TYR 3 284 ARG 0.004 0.001 ARG 3 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.191 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 16 average time/residue: 1.1139 time to fit residues: 18.3326 Evaluate side-chains 14 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 336 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 14 optimal weight: 30.0000 chunk 16 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 0.1980 chunk 5 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- 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: 0.1767 moved from start: 0.8611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1563 Z= 0.241 Angle : 0.766 12.195 2108 Z= 0.357 Chirality : 0.043 0.154 251 Planarity : 0.005 0.034 269 Dihedral : 4.733 15.916 210 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.33 % Allowed : 15.12 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.63), residues: 195 helix: 0.34 (0.54), residues: 105 sheet: -1.60 (0.92), residues: 36 loop : -0.12 (0.84), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS 3 270 PHE 0.008 0.001 PHE 3 294 TYR 0.006 0.002 TYR 3 284 ARG 0.004 0.001 ARG 3 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 14 time to evaluate : 0.180 Fit side-chains REVERT: 3 253 MET cc_start: -0.2597 (tpt) cc_final: -0.3098 (ppp) REVERT: 3 275 MET cc_start: 0.1657 (pmm) cc_final: 0.1262 (pmm) outliers start: 4 outliers final: 1 residues processed: 17 average time/residue: 1.3202 time to fit residues: 22.9834 Evaluate side-chains 14 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 336 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 0.0770 chunk 11 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 13 optimal weight: 0.0670 chunk 2 optimal weight: 0.9980 overall best weight: 2.2280 ------------------------------------------------------------------------------- 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: 0.1698 moved from start: 0.8486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1563 Z= 0.199 Angle : 0.749 12.039 2108 Z= 0.352 Chirality : 0.043 0.127 251 Planarity : 0.004 0.029 269 Dihedral : 4.403 14.691 210 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.74 % Allowed : 16.28 % Favored : 81.98 % 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: -0.34 (0.63), residues: 195 helix: 0.42 (0.53), residues: 105 sheet: -1.63 (0.92), residues: 35 loop : -0.13 (0.84), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS 3 202 PHE 0.019 0.002 PHE 3 230 TYR 0.003 0.001 TYR 3 284 ARG 0.003 0.000 ARG 3 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 0.189 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 16 average time/residue: 1.1433 time to fit residues: 18.8180 Evaluate side-chains 16 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 336 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 8.9990 chunk 15 optimal weight: 20.0000 chunk 6 optimal weight: 50.0000 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 50.0000 chunk 12 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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: 0.1805 moved from start: 0.9230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 1563 Z= 0.249 Angle : 0.888 16.204 2108 Z= 0.405 Chirality : 0.045 0.143 251 Planarity : 0.004 0.027 269 Dihedral : 4.659 15.860 210 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 26.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.58 % Allowed : 18.02 % Favored : 81.40 % 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: -0.32 (0.63), residues: 195 helix: 0.38 (0.54), residues: 105 sheet: -1.47 (0.94), residues: 34 loop : -0.14 (0.85), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS 3 202 PHE 0.017 0.002 PHE 3 230 TYR 0.003 0.001 TYR 3 284 ARG 0.004 0.001 ARG 3 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.185 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 15 average time/residue: 1.2109 time to fit residues: 18.6625 Evaluate side-chains 15 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 336 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 4 optimal weight: 30.0000 chunk 15 optimal weight: 9.9990 chunk 17 optimal weight: 40.0000 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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: 0.1881 moved from start: 1.0190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 1563 Z= 0.295 Angle : 0.918 13.603 2108 Z= 0.436 Chirality : 0.048 0.171 251 Planarity : 0.006 0.040 269 Dihedral : 5.334 19.260 210 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 32.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.58 % Allowed : 18.60 % Favored : 80.81 % 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: -0.86 (0.61), residues: 195 helix: -0.08 (0.53), residues: 105 sheet: -1.71 (0.90), residues: 34 loop : -0.33 (0.83), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS 3 202 PHE 0.014 0.002 PHE 3 230 TYR 0.004 0.002 TYR 3 284 ARG 0.004 0.001 ARG 3 154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.151 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 1.2510 time to fit residues: 20.5336 Evaluate side-chains 16 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 336 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 30.0000 chunk 3 optimal weight: 30.0000 chunk 9 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 17 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.4824 r_free = 0.4824 target = 0.108832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.098921 restraints weight = 21276.777| |-----------------------------------------------------------------------------| r_work (start): 0.4704 rms_B_bonded: 10.83 r_work (final): 0.4704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2620 moved from start: 1.0416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1563 Z= 0.246 Angle : 0.849 13.213 2108 Z= 0.401 Chirality : 0.045 0.177 251 Planarity : 0.005 0.029 269 Dihedral : 5.116 16.669 210 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 26.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.58 % Allowed : 19.77 % Favored : 79.65 % 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: -1.13 (0.61), residues: 195 helix: -0.21 (0.51), residues: 106 sheet: -1.94 (0.87), residues: 34 loop : -0.55 (0.85), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS 3 202 PHE 0.013 0.002 PHE 3 230 TYR 0.005 0.002 TYR 3 284 ARG 0.002 0.001 ARG 3 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1005.08 seconds wall clock time: 18 minutes 24.14 seconds (1104.14 seconds total)