Starting phenix.real_space_refine on Mon Sep 23 11:32:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc5_12139/09_2024/7bc5_12139.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc5_12139/09_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_12139/09_2024/7bc5_12139.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc5_12139/09_2024/7bc5_12139.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc5_12139/09_2024/7bc5_12139.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc5_12139/09_2024/7bc5_12139.cif" } 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. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 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: 1.32, per 1000 atoms: 1.10 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 157.9 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: 0.13 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: 0.26 Time building geometry restraints manager: 2.66 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: 0.00 - 2.49: 1589 2.49 - 4.98: 48 4.98 - 7.47: 7 7.47 - 9.96: 1 9.96 - 12.45: 1 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 3.040 nonbonded pdb=" O SER A 178 " pdb=" OG SER A 178 " model vdw 2.340 3.040 nonbonded pdb=" OH TYR A 247 " pdb=" OD2 ASP A 286 " model vdw 2.381 3.040 nonbonded pdb=" O ARG A 251 " pdb=" NH1 ARG A 251 " model vdw 2.408 3.120 nonbonded pdb=" O PRO A 139 " pdb=" NE ARG A 258 " model vdw 2.409 3.120 ... (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: 4.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 11.100 Find NCS groups from input model: 0.020 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.070 ------------------------------------------------------------------------------- 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 : 0.153 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: 0.1462 time to fit residues: 6.6692 Evaluate side-chains 36 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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: 4.9990 chunk 12 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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: 0.6272 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 1220 Z= 0.256 Angle : 0.757 8.112 1646 Z= 0.363 Chirality : 0.043 0.114 188 Planarity : 0.006 0.036 214 Dihedral : 6.720 41.388 167 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 17.30 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: -4.60 (0.50), residues: 159 helix: -3.55 (0.40), residues: 78 sheet: None (None), residues: 0 loop : -2.48 (0.56), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 252 HIS 0.002 0.001 HIS A 155 PHE 0.010 0.002 PHE A 215 TYR 0.006 0.001 TYR A 292 ARG 0.003 0.001 ARG A 274 *********************** 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 56 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.141 Fit side-chains REVERT: A 206 GLU cc_start: 0.6562 (mp0) cc_final: 0.6138 (mp0) REVERT: A 228 ASN cc_start: 0.8268 (m110) cc_final: 0.7598 (t0) outliers start: 9 outliers final: 8 residues processed: 50 average time/residue: 0.0975 time to fit residues: 5.6011 Evaluate side-chains 50 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.139 ------------------------------------------------------------------------------- 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: 9.9990 chunk 1 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 8 optimal weight: 0.0970 chunk 0 optimal weight: 5.9990 overall best weight: 4.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 1220 Z= 0.202 Angle : 0.706 8.769 1646 Z= 0.330 Chirality : 0.042 0.119 188 Planarity : 0.005 0.032 214 Dihedral : 6.416 40.044 167 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 5.34 % Allowed : 26.72 % 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: -4.26 (0.53), residues: 159 helix: -3.25 (0.40), residues: 82 sheet: None (None), residues: 0 loop : -2.24 (0.63), residues: 77 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 0.002 PHE A 215 TYR 0.001 0.000 TYR A 247 ARG 0.001 0.000 ARG A 229 *********************** 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: 7 poor density : 44 time to evaluate : 0.144 Fit side-chains REVERT: A 206 GLU cc_start: 0.6288 (mp0) cc_final: 0.6080 (mp0) REVERT: A 228 ASN cc_start: 0.8383 (m110) cc_final: 0.7660 (t0) outliers start: 7 outliers final: 6 residues processed: 47 average time/residue: 0.0904 time to fit residues: 4.9347 Evaluate side-chains 46 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 6 optimal weight: 8.9990 chunk 13 optimal weight: 40.0000 chunk 10 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 7 optimal weight: 0.0770 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 overall best weight: 5.4146 ------------------------------------------------------------------------------- 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: 0.6319 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 1220 Z= 0.246 Angle : 0.735 8.578 1646 Z= 0.344 Chirality : 0.043 0.111 188 Planarity : 0.004 0.029 214 Dihedral : 6.431 37.755 167 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 6.11 % Allowed : 31.30 % Favored : 62.60 % 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: -3.74 (0.57), residues: 159 helix: -2.84 (0.45), residues: 81 sheet: None (None), residues: 0 loop : -1.97 (0.67), residues: 78 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 0.008 0.002 PHE A 215 TYR 0.002 0.001 TYR A 292 ARG 0.001 0.000 ARG A 274 *********************** 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 49 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.145 Fit side-chains REVERT: A 228 ASN cc_start: 0.8409 (m110) cc_final: 0.7702 (t0) outliers start: 8 outliers final: 7 residues processed: 45 average time/residue: 0.1064 time to fit residues: 5.4695 Evaluate side-chains 46 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 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: 0.0020 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 14 optimal weight: 0.0670 chunk 11 optimal weight: 9.9990 chunk 13 optimal weight: 30.0000 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 overall best weight: 2.6132 ------------------------------------------------------------------------------- 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: 0.6273 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1220 Z= 0.175 Angle : 0.678 7.297 1646 Z= 0.318 Chirality : 0.041 0.106 188 Planarity : 0.004 0.025 214 Dihedral : 5.907 34.531 167 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 6.87 % Allowed : 32.82 % 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: -3.42 (0.59), residues: 159 helix: -2.53 (0.48), residues: 81 sheet: None (None), residues: 0 loop : -1.87 (0.66), residues: 78 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 0.012 0.003 PHE A 215 TYR 0.001 0.000 TYR A 292 ARG 0.001 0.000 ARG A 274 *********************** 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 46 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 228 ASN cc_start: 0.8395 (m110) cc_final: 0.7695 (t0) outliers start: 9 outliers final: 6 residues processed: 41 average time/residue: 0.0723 time to fit residues: 3.6055 Evaluate side-chains 43 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.112 ------------------------------------------------------------------------------- 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 287 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 3 optimal weight: 9.9990 chunk 2 optimal weight: 30.0000 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 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 150 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 1220 Z= 0.257 Angle : 0.723 7.406 1646 Z= 0.339 Chirality : 0.044 0.116 188 Planarity : 0.004 0.025 214 Dihedral : 6.118 32.569 167 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % 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: -3.18 (0.61), residues: 159 helix: -2.43 (0.49), residues: 81 sheet: None (None), residues: 0 loop : -1.63 (0.71), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 252 HIS 0.004 0.002 HIS A 150 PHE 0.012 0.003 PHE A 215 TYR 0.001 0.000 TYR A 292 ARG 0.001 0.000 ARG A 245 *********************** 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 48 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: A 228 ASN cc_start: 0.8432 (m110) cc_final: 0.7764 (t0) outliers start: 8 outliers final: 7 residues processed: 44 average time/residue: 0.0835 time to fit residues: 4.3327 Evaluate side-chains 48 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 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 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 294 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 11 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1220 Z= 0.196 Angle : 0.679 8.346 1646 Z= 0.315 Chirality : 0.042 0.110 188 Planarity : 0.004 0.025 214 Dihedral : 5.587 27.331 167 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % 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 : 0.00 % 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: -2.95 (0.63), residues: 159 helix: -2.20 (0.52), residues: 81 sheet: None (None), residues: 0 loop : -1.56 (0.72), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 252 HIS 0.001 0.001 HIS A 150 PHE 0.011 0.002 PHE A 215 TYR 0.001 0.000 TYR A 247 ARG 0.001 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 50 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 228 ASN cc_start: 0.8313 (m110) cc_final: 0.7750 (t0) REVERT: A 231 MET cc_start: 0.7184 (tpt) cc_final: 0.6837 (mmm) outliers start: 9 outliers final: 7 residues processed: 47 average time/residue: 0.0874 time to fit residues: 4.8577 Evaluate side-chains 48 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 287 SER Chi-restraints excluded: chain A residue 294 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 11 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 30.0000 chunk 2 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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: 0.6295 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1220 Z= 0.187 Angle : 0.628 5.591 1646 Z= 0.300 Chirality : 0.041 0.109 188 Planarity : 0.004 0.025 214 Dihedral : 5.378 25.268 167 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 5.34 % Allowed : 35.11 % Favored : 59.54 % 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: -3.13 (0.63), residues: 159 helix: -2.37 (0.50), residues: 87 sheet: None (None), residues: 0 loop : -1.50 (0.75), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 252 HIS 0.001 0.000 HIS A 150 PHE 0.009 0.002 PHE A 215 TYR 0.008 0.001 TYR A 247 ARG 0.002 0.000 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 50 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 228 ASN cc_start: 0.8337 (m110) cc_final: 0.7792 (t0) REVERT: A 231 MET cc_start: 0.7173 (tpt) cc_final: 0.6895 (mmm) REVERT: A 239 PHE cc_start: 0.5832 (t80) cc_final: 0.5135 (t80) outliers start: 7 outliers final: 7 residues processed: 47 average time/residue: 0.1081 time to fit residues: 5.8419 Evaluate side-chains 49 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 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 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 294 SER 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: 30.0000 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 15 optimal weight: 0.2980 chunk 2 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- 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: 0.6310 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 1220 Z= 0.220 Angle : 0.656 5.581 1646 Z= 0.317 Chirality : 0.043 0.121 188 Planarity : 0.004 0.024 214 Dihedral : 5.548 22.666 167 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 5.34 % Allowed : 35.11 % Favored : 59.54 % 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: -3.10 (0.64), residues: 159 helix: -2.44 (0.49), residues: 89 sheet: None (None), residues: 0 loop : -1.30 (0.78), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 252 HIS 0.001 0.001 HIS A 150 PHE 0.008 0.002 PHE A 215 TYR 0.007 0.001 TYR A 247 ARG 0.001 0.000 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 49 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.144 Fit side-chains REVERT: A 228 ASN cc_start: 0.8143 (m110) cc_final: 0.7618 (t0) REVERT: A 231 MET cc_start: 0.7050 (tpt) cc_final: 0.6828 (mmm) REVERT: A 239 PHE cc_start: 0.5811 (t80) cc_final: 0.5186 (t80) outliers start: 7 outliers final: 7 residues processed: 46 average time/residue: 0.0984 time to fit residues: 5.2393 Evaluate side-chains 49 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 287 SER Chi-restraints excluded: chain A residue 294 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 0 optimal weight: 30.0000 chunk 6 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 0.0670 chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 2 optimal weight: 0.2980 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 0.0070 chunk 11 optimal weight: 20.0000 overall best weight: 1.0138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 1220 Z= 0.151 Angle : 0.589 4.905 1646 Z= 0.281 Chirality : 0.040 0.124 188 Planarity : 0.004 0.024 214 Dihedral : 4.642 15.325 167 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.05 % Allowed : 36.64 % Favored : 60.31 % 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 (0.63), residues: 159 helix: -2.15 (0.51), residues: 90 sheet: None (None), residues: 0 loop : -1.52 (0.72), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 252 HIS 0.000 0.000 HIS A 150 PHE 0.007 0.001 PHE A 215 TYR 0.004 0.001 TYR A 247 ARG 0.003 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 48 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.148 Fit side-chains REVERT: A 228 ASN cc_start: 0.8041 (m110) cc_final: 0.7585 (t0) REVERT: A 239 PHE cc_start: 0.5677 (t80) cc_final: 0.5081 (t80) outliers start: 4 outliers final: 4 residues processed: 45 average time/residue: 0.1294 time to fit residues: 6.5091 Evaluate side-chains 45 residues out of total 131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 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 188 LEU Chi-restraints excluded: chain A residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 13 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 5 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 0.0470 chunk 7 optimal weight: 0.0670 chunk 6 optimal weight: 20.0000 overall best weight: 3.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.197922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.194289 restraints weight = 2366.723| |-----------------------------------------------------------------------------| r_work (start): 0.4516 rms_B_bonded: 0.82 r_work: 0.4490 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.4440 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.4440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1220 Z= 0.178 Angle : 0.600 5.010 1646 Z= 0.288 Chirality : 0.042 0.113 188 Planarity : 0.004 0.022 214 Dihedral : 4.983 16.395 167 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 3.05 % Allowed : 35.11 % Favored : 61.83 % 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: -3.00 (0.63), residues: 159 helix: -2.24 (0.50), residues: 89 sheet: None (None), residues: 0 loop : -1.45 (0.75), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 252 HIS 0.001 0.000 HIS A 150 PHE 0.007 0.002 PHE A 215 TYR 0.008 0.001 TYR A 247 ARG 0.002 0.000 ARG A 258 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 942.05 seconds wall clock time: 17 minutes 19.45 seconds (1039.45 seconds total)