Starting phenix.real_space_refine on Mon Jun 24 12:45:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v85_43023/06_2024/8v85_43023_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v85_43023/06_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_43023/06_2024/8v85_43023.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v85_43023/06_2024/8v85_43023.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v85_43023/06_2024/8v85_43023_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v85_43023/06_2024/8v85_43023_neut.pdb" } 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: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 1.33, per 1000 atoms: 0.86 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: 1.44 Conformation dependent library (CDL) restraints added in 273.2 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: 0.18 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: 0.35 Time building geometry restraints manager: 1.50 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 2.520 nonbonded pdb=" NH2 ARG 3 209 " pdb=" OD2 ASP 3 259 " model vdw 2.364 2.520 nonbonded pdb=" OE1 GLN 3 250 " pdb=" NE ARG 3 267 " model vdw 2.407 2.520 nonbonded pdb=" N GLN 3 301 " pdb=" OE1 GLN 3 301 " model vdw 2.439 2.520 nonbonded pdb=" O ILE 3 163 " pdb=" OG1 THR 3 167 " model vdw 2.486 2.440 ... (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: 2.930 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: 12.680 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.320 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:10.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.990 ------------------------------------------------------------------------------- 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 : 0.181 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 1.5624 time to fit residues: 36.5481 Evaluate side-chains 14 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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: 20.0000 chunk 14 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 202 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1413 moved from start: 0.3610 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= 0.214 Angle : 0.604 4.995 2108 Z= 0.305 Chirality : 0.043 0.169 251 Planarity : 0.004 0.027 269 Dihedral : 4.196 14.333 210 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.91 % Allowed : 7.56 % 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: 0.68 (0.59), residues: 195 helix: 0.91 (0.50), residues: 107 sheet: 0.50 (0.84), residues: 38 loop : -0.36 (0.86), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS 3 270 PHE 0.013 0.002 PHE 3 268 TYR 0.004 0.001 TYR 3 284 ARG 0.004 0.001 ARG 3 182 *********************** 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 20 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 15 time to evaluate : 0.178 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 18 average time/residue: 1.0491 time to fit residues: 19.4162 Evaluate side-chains 17 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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: 0.6980 chunk 12 optimal weight: 30.0000 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 11 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 30.0000 chunk 4 optimal weight: 40.0000 chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 159 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1579 moved from start: 0.5448 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= 0.203 Angle : 0.593 5.414 2108 Z= 0.298 Chirality : 0.043 0.150 251 Planarity : 0.005 0.040 269 Dihedral : 4.586 15.553 210 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.33 % Allowed : 10.47 % Favored : 87.21 % 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 (0.62), residues: 195 helix: 0.69 (0.52), residues: 107 sheet: -0.21 (0.89), residues: 38 loop : -0.38 (0.89), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.002 HIS 3 202 PHE 0.012 0.001 PHE 3 294 TYR 0.005 0.002 TYR 3 284 ARG 0.007 0.001 ARG 3 292 *********************** 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 21 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 17 time to evaluate : 0.181 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 20 average time/residue: 1.3969 time to fit residues: 28.5049 Evaluate side-chains 18 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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: 20.0000 chunk 7 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 12 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 16 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1759 moved from start: 0.7137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 1563 Z= 0.253 Angle : 0.767 11.708 2108 Z= 0.363 Chirality : 0.044 0.162 251 Planarity : 0.006 0.041 269 Dihedral : 5.059 18.147 210 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 31.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.33 % Allowed : 9.88 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.40 (0.61), residues: 195 helix: 0.27 (0.52), residues: 106 sheet: -0.68 (1.08), residues: 28 loop : -0.76 (0.77), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS 3 270 PHE 0.012 0.002 PHE 3 224 TYR 0.008 0.003 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: 4 poor density : 16 time to evaluate : 0.165 Fit side-chains REVERT: 3 253 MET cc_start: -0.2796 (tpt) cc_final: -0.3280 (ppp) REVERT: 3 275 MET cc_start: 0.1269 (OUTLIER) cc_final: 0.0493 (pmm) outliers start: 4 outliers final: 3 residues processed: 17 average time/residue: 0.8836 time to fit residues: 15.5072 Evaluate side-chains 19 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 15 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 191 PHE Chi-restraints excluded: chain 3 residue 275 MET 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: 0.5980 chunk 18 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 30.0000 chunk 6 optimal weight: 50.0000 chunk 9 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1704 moved from start: 0.7357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1563 Z= 0.176 Angle : 0.661 10.927 2108 Z= 0.305 Chirality : 0.042 0.144 251 Planarity : 0.004 0.029 269 Dihedral : 4.541 17.384 210 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.16 % Allowed : 12.21 % 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: -0.43 (0.61), residues: 195 helix: 0.33 (0.52), residues: 106 sheet: -0.69 (1.18), residues: 26 loop : -0.95 (0.74), residues: 63 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 0.002 0.001 TYR 3 284 ARG 0.002 0.000 ARG 3 237 *********************** 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 19 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 17 time to evaluate : 0.173 Fit side-chains REVERT: 3 195 MET cc_start: 0.0756 (mmt) cc_final: 0.0096 (tpt) REVERT: 3 275 MET cc_start: 0.1047 (pmm) cc_final: 0.0801 (pmm) outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 1.0253 time to fit residues: 18.9786 Evaluate side-chains 16 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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: 30.0000 chunk 15 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 3 optimal weight: 50.0000 chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1976 moved from start: 0.9893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 1563 Z= 0.353 Angle : 0.900 12.580 2108 Z= 0.430 Chirality : 0.047 0.165 251 Planarity : 0.006 0.040 269 Dihedral : 5.964 21.736 210 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 46.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.49 % Allowed : 13.95 % 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: -1.18 (0.59), residues: 195 helix: -0.41 (0.50), residues: 105 sheet: -1.32 (1.00), residues: 34 loop : -0.74 (0.75), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS 3 270 PHE 0.012 0.002 PHE 3 224 TYR 0.008 0.002 TYR 3 284 ARG 0.005 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 23 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 17 time to evaluate : 0.181 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 20 average time/residue: 1.2559 time to fit residues: 25.6722 Evaluate side-chains 19 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 15 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 149 LEU Chi-restraints excluded: chain 3 residue 191 PHE Chi-restraints excluded: chain 3 residue 324 ASN 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: 20.0000 chunk 16 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 40.0000 chunk 13 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1891 moved from start: 1.0062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1563 Z= 0.237 Angle : 0.718 9.702 2108 Z= 0.348 Chirality : 0.045 0.154 251 Planarity : 0.005 0.046 269 Dihedral : 5.491 20.264 210 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 36.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.74 % Allowed : 16.86 % 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: -1.14 (0.60), residues: 195 helix: -0.20 (0.52), residues: 104 sheet: -1.58 (0.94), residues: 35 loop : -0.85 (0.75), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS 3 202 PHE 0.009 0.001 PHE 3 230 TYR 0.005 0.002 TYR 3 284 ARG 0.004 0.001 ARG 3 237 *********************** 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 20 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 17 time to evaluate : 0.168 Fit side-chains REVERT: 3 195 MET cc_start: 0.0842 (mmt) cc_final: 0.0501 (tpt) REVERT: 3 253 MET cc_start: -0.2550 (tpt) cc_final: -0.2813 (ppp) REVERT: 3 275 MET cc_start: 0.0197 (OUTLIER) cc_final: -0.0331 (pmm) outliers start: 3 outliers final: 2 residues processed: 18 average time/residue: 1.0981 time to fit residues: 20.2582 Evaluate side-chains 19 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 275 MET Chi-restraints excluded: chain 3 residue 324 ASN 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: 5.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 11 optimal weight: 30.0000 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 4 optimal weight: 0.3980 chunk 13 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1891 moved from start: 1.0301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 1563 Z= 0.233 Angle : 0.765 11.623 2108 Z= 0.373 Chirality : 0.044 0.127 251 Planarity : 0.005 0.036 269 Dihedral : 5.214 18.814 210 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 35.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.74 % Allowed : 20.35 % Favored : 77.91 % 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 (0.59), residues: 195 helix: -0.17 (0.52), residues: 104 sheet: -1.77 (0.90), residues: 35 loop : -1.04 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS 3 202 PHE 0.012 0.001 PHE 3 191 TYR 0.002 0.001 TYR 3 284 ARG 0.003 0.001 ARG 3 237 *********************** 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 19 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: 3 195 MET cc_start: 0.0856 (mmt) cc_final: 0.0569 (tpt) REVERT: 3 275 MET cc_start: 0.0207 (pp-130) cc_final: -0.0310 (pmm) outliers start: 3 outliers final: 2 residues processed: 18 average time/residue: 0.9121 time to fit residues: 16.8245 Evaluate side-chains 17 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 324 ASN 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: 5.9990 chunk 15 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 11 optimal weight: 50.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1949 moved from start: 1.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 1563 Z= 0.284 Angle : 0.838 11.882 2108 Z= 0.404 Chirality : 0.048 0.190 251 Planarity : 0.005 0.030 269 Dihedral : 5.638 21.043 210 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 44.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.16 % Allowed : 22.67 % Favored : 76.16 % 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: -1.67 (0.57), residues: 195 helix: -0.53 (0.50), residues: 104 sheet: -2.02 (0.86), residues: 35 loop : -1.17 (0.71), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS 3 202 PHE 0.020 0.002 PHE 3 230 TYR 0.004 0.002 TYR 3 284 ARG 0.003 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 17 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.176 Fit side-chains REVERT: 3 195 MET cc_start: 0.1032 (mmt) cc_final: 0.0785 (tpt) REVERT: 3 253 MET cc_start: -0.0878 (ppp) cc_final: -0.1413 (tpt) REVERT: 3 275 MET cc_start: -0.0210 (pp-130) cc_final: -0.0452 (pp-130) outliers start: 2 outliers final: 2 residues processed: 16 average time/residue: 1.4786 time to fit residues: 24.1666 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 0.0030 chunk 17 optimal weight: 40.0000 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1836 moved from start: 1.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 1563 Z= 0.218 Angle : 0.793 13.261 2108 Z= 0.373 Chirality : 0.046 0.195 251 Planarity : 0.004 0.029 269 Dihedral : 5.223 23.131 210 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 31.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.16 % Allowed : 22.67 % Favored : 76.16 % 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: -1.41 (0.58), residues: 195 helix: -0.20 (0.52), residues: 104 sheet: -1.59 (1.04), residues: 25 loop : -1.67 (0.66), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS 3 202 PHE 0.024 0.002 PHE 3 230 TYR 0.003 0.002 TYR 3 284 ARG 0.002 0.000 ARG 3 217 ********************** 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: 2 poor density : 14 time to evaluate : 0.175 Fit side-chains REVERT: 3 253 MET cc_start: -0.0895 (ppp) cc_final: -0.1436 (tpt) REVERT: 3 275 MET cc_start: 0.0093 (pp-130) cc_final: -0.0574 (pmm) REVERT: 3 280 LYS cc_start: 0.1023 (tptp) cc_final: 0.0692 (tptt) outliers start: 2 outliers final: 2 residues processed: 15 average time/residue: 1.1412 time to fit residues: 17.6066 Evaluate side-chains 15 residues out of total 172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 13 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 324 ASN 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: 20.0000 chunk 12 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 17 optimal weight: 50.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 151 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 = 0.4820 r_free = 0.4820 target = 0.106565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.098201 restraints weight = 23003.110| |-----------------------------------------------------------------------------| r_work (start): 0.4674 rms_B_bonded: 9.73 r_work (final): 0.4674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2608 moved from start: 1.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 1563 Z= 0.261 Angle : 0.825 13.438 2108 Z= 0.387 Chirality : 0.047 0.186 251 Planarity : 0.005 0.029 269 Dihedral : 5.381 21.677 210 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 40.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.16 % Allowed : 22.67 % Favored : 76.16 % 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: -1.39 (0.59), residues: 195 helix: -0.15 (0.53), residues: 103 sheet: -2.17 (0.88), residues: 35 loop : -1.15 (0.69), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS 3 202 PHE 0.022 0.002 PHE 3 230 TYR 0.003 0.002 TYR 3 284 ARG 0.003 0.001 ARG 3 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1063.64 seconds wall clock time: 20 minutes 60.00 seconds (1260.00 seconds total)