Starting phenix.real_space_refine on Fri Apr 5 12:02:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc5_12139/04_2024/7bc5_12139.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc5_12139/04_2024/7bc5_12139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc5_12139/04_2024/7bc5_12139.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc5_12139/04_2024/7bc5_12139.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc5_12139/04_2024/7bc5_12139.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc5_12139/04_2024/7bc5_12139.pdb" } resolution = 3.1 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= 0.010 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 3 5.16 5 C 757 2.51 5 N 206 2.21 5 O 234 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 140": "OD1" <-> "OD2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A ASP 201": "OD1" <-> "OD2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 260": "OD1" <-> "OD2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ASP 286": "OD1" <-> "OD2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 1200 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1200 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 9, 'TRANS': 151} Time building chain proxies: 1.27, per 1000 atoms: 1.06 Number of scatterers: 1200 At special positions: 0 Unit cell: (58.575, 54.315, 45.795, 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 3 16.00 O 234 8.00 N 206 7.00 C 757 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: 0.39 Conformation dependent library (CDL) restraints added in 331.9 milliseconds 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 288 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 0 sheets defined 53.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 149 through 157 removed outlier: 3.833A pdb=" N LEU A 157 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 180 through 188 removed outlier: 3.663A pdb=" N LEU A 185 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 removed outlier: 4.205A pdb=" N ALA A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLN A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 234 removed outlier: 3.923A pdb=" N ASN A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 251 removed outlier: 3.614A pdb=" N ALA A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.760A pdb=" N GLU A 283 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 293 removed outlier: 3.552A pdb=" N CYS A 288 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) 37 hydrogen bonds defined for protein. 102 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: 0.22 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 392 1.34 - 1.46: 140 1.46 - 1.57: 683 1.57 - 1.69: 0 1.69 - 1.80: 5 Bond restraints: 1220 Sorted by residual: bond pdb=" CG ARG A 274 " pdb=" CD ARG A 274 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.14e+00 bond pdb=" CG LEU A 264 " pdb=" CD1 LEU A 264 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 bond pdb=" CB GLN A 249 " pdb=" CG GLN A 249 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.08e+00 bond pdb=" CB PHE A 192 " pdb=" CG PHE A 192 " ideal model delta sigma weight residual 1.502 1.479 0.023 2.30e-02 1.89e+03 9.61e-01 bond pdb=" C MET A 235 " pdb=" N PRO A 236 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.22e-01 ... (remaining 1215 not shown) Histogram of bond angle deviations from ideal: 98.14 - 105.29: 32 105.29 - 112.44: 583 112.44 - 119.60: 473 119.60 - 126.75: 544 126.75 - 133.90: 14 Bond angle restraints: 1646 Sorted by residual: angle pdb=" C PRO A 165 " pdb=" N LEU A 166 " pdb=" CA LEU A 166 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 angle pdb=" CA LEU A 166 " pdb=" CB LEU A 166 " pdb=" CG LEU A 166 " ideal model delta sigma weight residual 116.30 128.75 -12.45 3.50e+00 8.16e-02 1.27e+01 angle pdb=" CA LEU A 207 " pdb=" CB LEU A 207 " pdb=" CG LEU A 207 " ideal model delta sigma weight residual 116.30 126.08 -9.78 3.50e+00 8.16e-02 7.80e+00 angle pdb=" C THR A 195 " pdb=" CA THR A 195 " pdb=" CB THR A 195 " ideal model delta sigma weight residual 108.88 112.72 -3.84 1.50e+00 4.44e-01 6.56e+00 angle pdb=" N SER A 194 " pdb=" CA SER A 194 " pdb=" C SER A 194 " ideal model delta sigma weight residual 110.80 116.15 -5.35 2.13e+00 2.20e-01 6.30e+00 ... (remaining 1641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.50: 629 14.50 - 29.00: 79 29.00 - 43.49: 34 43.49 - 57.99: 6 57.99 - 72.49: 2 Dihedral angle restraints: 750 sinusoidal: 300 harmonic: 450 Sorted by residual: dihedral pdb=" CA GLY A 193 " pdb=" C GLY A 193 " pdb=" N SER A 194 " pdb=" CA SER A 194 " ideal model delta harmonic sigma weight residual -180.00 -124.03 -55.97 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA GLN A 222 " pdb=" C GLN A 222 " pdb=" N THR A 223 " pdb=" CA THR A 223 " ideal model delta harmonic sigma weight residual 180.00 156.23 23.77 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLU A 206 " pdb=" C GLU A 206 " pdb=" N LEU A 207 " pdb=" CA LEU A 207 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 95 0.034 - 0.067: 55 0.067 - 0.101: 28 0.101 - 0.134: 8 0.134 - 0.168: 2 Chirality restraints: 188 Sorted by residual: chirality pdb=" CB VAL A 243 " pdb=" CA VAL A 243 " pdb=" CG1 VAL A 243 " pdb=" CG2 VAL A 243 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CG LEU A 275 " pdb=" CB LEU A 275 " pdb=" CD1 LEU A 275 " pdb=" CD2 LEU A 275 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA PRO A 199 " pdb=" N PRO A 199 " pdb=" C PRO A 199 " pdb=" CB PRO A 199 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 185 not shown) Planarity restraints: 214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 211 " 0.013 2.00e-02 2.50e+03 1.57e-02 4.30e+00 pdb=" CG PHE A 211 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 211 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 211 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 211 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 211 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 211 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 166 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C LEU A 166 " -0.030 2.00e-02 2.50e+03 pdb=" O LEU A 166 " 0.011 2.00e-02 2.50e+03 pdb=" N SER A 167 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 193 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C GLY A 193 " -0.030 2.00e-02 2.50e+03 pdb=" O GLY A 193 " 0.011 2.00e-02 2.50e+03 pdb=" N SER A 194 " 0.010 2.00e-02 2.50e+03 ... (remaining 211 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 380 2.83 - 3.35: 1054 3.35 - 3.87: 1922 3.87 - 4.38: 2218 4.38 - 4.90: 3472 Nonbonded interactions: 9046 Sorted by model distance: nonbonded pdb=" O ARG A 229 " pdb=" OG SER A 233 " model vdw 2.314 2.440 nonbonded pdb=" O SER A 178 " pdb=" OG SER A 178 " model vdw 2.340 2.440 nonbonded pdb=" OH TYR A 247 " pdb=" OD2 ASP A 286 " model vdw 2.381 2.440 nonbonded pdb=" O ARG A 251 " pdb=" NH1 ARG A 251 " model vdw 2.408 2.520 nonbonded pdb=" O PRO A 139 " pdb=" NE ARG A 258 " model vdw 2.409 2.520 ... (remaining 9041 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: 4.250 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: 20.380 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.960 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 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 : 0.005 0.055 1220 Z= 0.308 Angle : 1.045 12.451 1646 Z= 0.509 Chirality : 0.053 0.168 188 Planarity : 0.007 0.040 214 Dihedral : 15.919 72.490 462 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.76 % Allowed : 10.69 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.66 % 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: -5.64 (0.43), residues: 159 helix: -4.45 (0.28), residues: 77 sheet: None (None), residues: 0 loop : -3.00 (0.51), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 252 HIS 0.004 0.002 HIS A 150 PHE 0.036 0.004 PHE A 211 TYR 0.005 0.001 TYR A 247 ARG 0.017 0.002 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.125 Fit side-chains REVERT: A 183 GLU cc_start: 0.7862 (tt0) cc_final: 0.7067 (mm-30) REVERT: A 228 ASN cc_start: 0.8306 (m110) cc_final: 0.7599 (t0) outliers start: 1 outliers final: 0 residues processed: 41 average time/residue: 0.1392 time to fit residues: 6.3170 Evaluate side-chains 36 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 13 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 30.0000 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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: 0.6302 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 1220 Z= 0.277 Angle : 0.762 8.375 1646 Z= 0.364 Chirality : 0.043 0.126 188 Planarity : 0.005 0.038 214 Dihedral : 6.927 42.792 167 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 6.87 % Allowed : 18.32 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.66 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.47 (0.53), residues: 159 helix: -3.54 (0.41), residues: 76 sheet: None (None), residues: 0 loop : -2.35 (0.60), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 252 HIS 0.003 0.002 HIS A 150 PHE 0.011 0.002 PHE A 239 TYR 0.005 0.001 TYR A 292 ARG 0.003 0.001 ARG A 245 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.155 Fit side-chains REVERT: A 206 GLU cc_start: 0.6111 (mp0) cc_final: 0.5714 (mp0) REVERT: A 228 ASN cc_start: 0.8410 (m110) cc_final: 0.7669 (t0) outliers start: 9 outliers final: 8 residues processed: 47 average time/residue: 0.0735 time to fit residues: 4.1592 Evaluate side-chains 49 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 294 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 13 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 1220 Z= 0.238 Angle : 0.729 8.215 1646 Z= 0.344 Chirality : 0.042 0.126 188 Planarity : 0.005 0.038 214 Dihedral : 6.652 40.313 167 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 6.87 % Allowed : 25.19 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.66 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.54), residues: 159 helix: -3.30 (0.40), residues: 82 sheet: None (None), residues: 0 loop : -2.19 (0.65), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 252 HIS 0.003 0.001 HIS A 150 PHE 0.010 0.003 PHE A 215 TYR 0.002 0.001 TYR A 292 ARG 0.002 0.001 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 228 ASN cc_start: 0.8416 (m110) cc_final: 0.7653 (t0) outliers start: 9 outliers final: 8 residues processed: 45 average time/residue: 0.0852 time to fit residues: 4.5084 Evaluate side-chains 48 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 294 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 11 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 1220 Z= 0.218 Angle : 0.704 8.516 1646 Z= 0.328 Chirality : 0.041 0.108 188 Planarity : 0.005 0.029 214 Dihedral : 6.209 36.407 167 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 6.11 % Allowed : 33.59 % Favored : 60.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.66 % 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: -3.75 (0.59), residues: 159 helix: -2.89 (0.46), residues: 82 sheet: None (None), residues: 0 loop : -1.90 (0.69), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 252 HIS 0.003 0.002 HIS A 150 PHE 0.007 0.002 PHE A 239 TYR 0.002 0.001 TYR A 247 ARG 0.002 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.144 Fit side-chains REVERT: A 228 ASN cc_start: 0.8404 (m110) cc_final: 0.7639 (t0) REVERT: A 258 ARG cc_start: 0.5952 (mtp85) cc_final: 0.5273 (ttp-110) outliers start: 8 outliers final: 6 residues processed: 49 average time/residue: 0.1119 time to fit residues: 6.2174 Evaluate side-chains 50 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 294 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 7 optimal weight: 7.9990 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 1220 Z= 0.215 Angle : 0.676 7.769 1646 Z= 0.317 Chirality : 0.042 0.103 188 Planarity : 0.005 0.029 214 Dihedral : 6.103 35.495 167 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 6.87 % Allowed : 33.59 % Favored : 59.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.66 % 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: -3.55 (0.58), residues: 159 helix: -2.81 (0.47), residues: 78 sheet: None (None), residues: 0 loop : -1.80 (0.66), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 252 HIS 0.004 0.001 HIS A 150 PHE 0.012 0.003 PHE A 215 TYR 0.003 0.001 TYR A 247 ARG 0.002 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.135 Fit side-chains REVERT: A 228 ASN cc_start: 0.8393 (m110) cc_final: 0.7659 (t0) outliers start: 9 outliers final: 7 residues processed: 45 average time/residue: 0.1162 time to fit residues: 5.9130 Evaluate side-chains 46 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 294 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 0.0020 chunk 1 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 13 optimal weight: 30.0000 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 overall best weight: 2.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1220 Z= 0.174 Angle : 0.610 6.376 1646 Z= 0.289 Chirality : 0.040 0.112 188 Planarity : 0.004 0.027 214 Dihedral : 5.455 28.140 167 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 6.87 % Allowed : 35.11 % Favored : 58.02 % 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: -3.25 (0.61), residues: 159 helix: -2.57 (0.49), residues: 78 sheet: None (None), residues: 0 loop : -1.62 (0.69), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 252 HIS 0.003 0.001 HIS A 150 PHE 0.009 0.002 PHE A 215 TYR 0.003 0.001 TYR A 247 ARG 0.003 0.001 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.143 Fit side-chains REVERT: A 228 ASN cc_start: 0.8294 (m110) cc_final: 0.7606 (t0) outliers start: 9 outliers final: 8 residues processed: 47 average time/residue: 0.1155 time to fit residues: 6.1228 Evaluate side-chains 47 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 299 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 11 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 50.0000 chunk 14 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.0670 overall best weight: 2.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 1220 Z= 0.160 Angle : 0.583 5.782 1646 Z= 0.279 Chirality : 0.040 0.116 188 Planarity : 0.004 0.026 214 Dihedral : 5.151 24.436 167 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 6.11 % Allowed : 35.88 % Favored : 58.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.63), residues: 159 helix: -2.27 (0.51), residues: 78 sheet: None (None), residues: 0 loop : -1.44 (0.71), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 252 HIS 0.002 0.001 HIS A 150 PHE 0.008 0.001 PHE A 215 TYR 0.003 0.001 TYR A 247 ARG 0.003 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.141 Fit side-chains REVERT: A 228 ASN cc_start: 0.8259 (m110) cc_final: 0.7601 (t0) outliers start: 8 outliers final: 6 residues processed: 44 average time/residue: 0.1004 time to fit residues: 5.0907 Evaluate side-chains 45 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 11 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 HIS ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 1220 Z= 0.205 Angle : 0.605 5.481 1646 Z= 0.296 Chirality : 0.042 0.118 188 Planarity : 0.004 0.025 214 Dihedral : 5.468 23.298 167 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 8.40 % Allowed : 34.35 % Favored : 57.25 % 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: -3.06 (0.63), residues: 159 helix: -2.38 (0.50), residues: 84 sheet: None (None), residues: 0 loop : -1.44 (0.73), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 252 HIS 0.003 0.001 HIS A 150 PHE 0.008 0.002 PHE A 239 TYR 0.002 0.001 TYR A 292 ARG 0.004 0.001 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.151 Fit side-chains REVERT: A 228 ASN cc_start: 0.8299 (m110) cc_final: 0.7627 (t0) outliers start: 11 outliers final: 9 residues processed: 45 average time/residue: 0.0990 time to fit residues: 5.1836 Evaluate side-chains 47 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 299 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 10 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 3 optimal weight: 0.4980 chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1220 Z= 0.201 Angle : 0.612 5.470 1646 Z= 0.294 Chirality : 0.042 0.116 188 Planarity : 0.004 0.023 214 Dihedral : 5.438 21.876 167 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 7.63 % Allowed : 35.88 % Favored : 56.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.64), residues: 159 helix: -2.30 (0.50), residues: 84 sheet: None (None), residues: 0 loop : -1.40 (0.75), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 252 HIS 0.001 0.001 HIS A 150 PHE 0.006 0.001 PHE A 215 TYR 0.002 0.001 TYR A 292 ARG 0.003 0.001 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.137 Fit side-chains REVERT: A 228 ASN cc_start: 0.8194 (m110) cc_final: 0.7604 (t0) outliers start: 10 outliers final: 9 residues processed: 46 average time/residue: 0.0918 time to fit residues: 4.8069 Evaluate side-chains 47 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 299 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 0 optimal weight: 40.0000 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 0.0980 chunk 3 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 30.0000 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.5427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 1220 Z= 0.213 Angle : 0.625 5.084 1646 Z= 0.299 Chirality : 0.042 0.123 188 Planarity : 0.004 0.025 214 Dihedral : 5.499 21.364 167 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 7.63 % Allowed : 35.88 % Favored : 56.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.66), residues: 159 helix: -2.00 (0.53), residues: 79 sheet: None (None), residues: 0 loop : -1.28 (0.75), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 252 HIS 0.002 0.001 HIS A 150 PHE 0.008 0.001 PHE A 215 TYR 0.003 0.001 TYR A 292 ARG 0.004 0.001 ARG A 258 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.101 Fit side-chains REVERT: A 228 ASN cc_start: 0.8189 (m110) cc_final: 0.7600 (t0) REVERT: A 239 PHE cc_start: 0.5402 (t80) cc_final: 0.5180 (t80) outliers start: 10 outliers final: 10 residues processed: 43 average time/residue: 0.0742 time to fit residues: 3.6916 Evaluate side-chains 47 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 299 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 13 optimal weight: 30.0000 chunk 14 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 0.0470 overall best weight: 5.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** 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 = 0.4475 r_free = 0.4475 target = 0.189176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.186039 restraints weight = 2418.057| |-----------------------------------------------------------------------------| r_work (start): 0.4439 rms_B_bonded: 0.78 r_work: 0.4413 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.4367 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.4367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6040 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 1220 Z= 0.240 Angle : 0.660 6.041 1646 Z= 0.316 Chirality : 0.043 0.126 188 Planarity : 0.004 0.024 214 Dihedral : 5.701 22.291 167 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 7.63 % Allowed : 35.11 % Favored : 57.25 % 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: -3.06 (0.63), residues: 159 helix: -2.36 (0.50), residues: 86 sheet: None (None), residues: 0 loop : -1.42 (0.74), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 252 HIS 0.002 0.001 HIS A 150 PHE 0.008 0.002 PHE A 239 TYR 0.003 0.001 TYR A 292 ARG 0.003 0.001 ARG A 258 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 906.98 seconds wall clock time: 18 minutes 35.94 seconds (1115.94 seconds total)