Starting phenix.real_space_refine on Sun Mar 10 14:17:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v22_31634/03_2024/7v22_31634.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v22_31634/03_2024/7v22_31634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v22_31634/03_2024/7v22_31634.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v22_31634/03_2024/7v22_31634.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v22_31634/03_2024/7v22_31634.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v22_31634/03_2024/7v22_31634.pdb" } resolution = 3.38 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= 0.046 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 5 5.16 5 C 1278 2.51 5 N 321 2.21 5 O 354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 1958 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1958 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 13, 'TRANS': 226} Chain breaks: 3 Time building chain proxies: 1.65, per 1000 atoms: 0.84 Number of scatterers: 1958 At special positions: 0 Unit cell: (50.76, 70.2, 60.48, 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 5 16.00 O 354 8.00 N 321 7.00 C 1278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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: 0.78 Conformation dependent library (CDL) restraints added in 327.2 milliseconds 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 458 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.065A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.579A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 172 removed outlier: 4.420A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 157 removed outlier: 6.242A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) 61 hydrogen bonds defined for protein. 156 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: 0.47 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 609 1.34 - 1.46: 535 1.46 - 1.58: 863 1.58 - 1.70: 0 1.70 - 1.82: 6 Bond restraints: 2013 Sorted by residual: bond pdb=" CA ASN A 121 " pdb=" CB ASN A 121 " ideal model delta sigma weight residual 1.532 1.550 -0.018 1.82e-02 3.02e+03 1.03e+00 bond pdb=" CB PRO A 82 " pdb=" CG PRO A 82 " ideal model delta sigma weight residual 1.492 1.531 -0.039 5.00e-02 4.00e+02 6.19e-01 bond pdb=" N PHE A 106 " pdb=" CA PHE A 106 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.32e-02 5.74e+03 5.75e-01 bond pdb=" CA GLU A 96 " pdb=" CB GLU A 96 " ideal model delta sigma weight residual 1.532 1.542 -0.010 1.36e-02 5.41e+03 5.45e-01 bond pdb=" CA PRO A 39 " pdb=" C PRO A 39 " ideal model delta sigma weight residual 1.528 1.519 0.009 1.20e-02 6.94e+03 5.16e-01 ... (remaining 2008 not shown) Histogram of bond angle deviations from ideal: 100.83 - 107.45: 76 107.45 - 114.08: 1086 114.08 - 120.70: 760 120.70 - 127.33: 795 127.33 - 133.95: 23 Bond angle restraints: 2740 Sorted by residual: angle pdb=" CA GLU A 96 " pdb=" CB GLU A 96 " pdb=" CG GLU A 96 " ideal model delta sigma weight residual 114.10 119.87 -5.77 2.00e+00 2.50e-01 8.34e+00 angle pdb=" CA ALA A 123 " pdb=" C ALA A 123 " pdb=" N THR A 124 " ideal model delta sigma weight residual 119.71 116.59 3.12 1.17e+00 7.31e-01 7.11e+00 angle pdb=" N ILE A 100 " pdb=" CA ILE A 100 " pdb=" C ILE A 100 " ideal model delta sigma weight residual 112.96 110.33 2.63 1.00e+00 1.00e+00 6.92e+00 angle pdb=" N ALA A 123 " pdb=" CA ALA A 123 " pdb=" C ALA A 123 " ideal model delta sigma weight residual 114.62 111.70 2.92 1.14e+00 7.69e-01 6.58e+00 angle pdb=" N GLY A 219 " pdb=" CA GLY A 219 " pdb=" C GLY A 219 " ideal model delta sigma weight residual 112.14 115.37 -3.23 1.29e+00 6.01e-01 6.27e+00 ... (remaining 2735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 1050 17.06 - 34.11: 98 34.11 - 51.17: 18 51.17 - 68.22: 6 68.22 - 85.27: 2 Dihedral angle restraints: 1174 sinusoidal: 466 harmonic: 708 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 49.21 43.79 1 1.00e+01 1.00e-02 2.67e+01 dihedral pdb=" CA ASP A 290 " pdb=" CB ASP A 290 " pdb=" CG ASP A 290 " pdb=" OD1 ASP A 290 " ideal model delta sinusoidal sigma weight residual -30.00 -84.89 54.89 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASN A 121 " pdb=" CB ASN A 121 " pdb=" CG ASN A 121 " pdb=" OD1 ASN A 121 " ideal model delta sinusoidal sigma weight residual 120.00 -173.55 -66.45 2 2.00e+01 2.50e-03 1.01e+01 ... (remaining 1171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 169 0.027 - 0.053: 78 0.053 - 0.079: 31 0.079 - 0.105: 15 0.105 - 0.132: 10 Chirality restraints: 303 Sorted by residual: chirality pdb=" CA GLU A 96 " pdb=" N GLU A 96 " pdb=" C GLU A 96 " pdb=" CB GLU A 96 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE A 119 " pdb=" N ILE A 119 " pdb=" C ILE A 119 " pdb=" CB ILE A 119 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.42e-01 chirality pdb=" CA VAL A 227 " pdb=" N VAL A 227 " pdb=" C VAL A 227 " pdb=" CB VAL A 227 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.00e-01 ... (remaining 300 not shown) Planarity restraints: 349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 96 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.31e+00 pdb=" CD GLU A 96 " 0.020 2.00e-02 2.50e+03 pdb=" OE1 GLU A 96 " -0.007 2.00e-02 2.50e+03 pdb=" OE2 GLU A 96 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 121 " 0.005 2.00e-02 2.50e+03 1.06e-02 1.12e+00 pdb=" C ASN A 121 " -0.018 2.00e-02 2.50e+03 pdb=" O ASN A 121 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN A 122 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 208 " -0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO A 209 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 209 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 209 " -0.015 5.00e-02 4.00e+02 ... (remaining 346 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 297 2.77 - 3.30: 1796 3.30 - 3.83: 3018 3.83 - 4.37: 3623 4.37 - 4.90: 6515 Nonbonded interactions: 15249 Sorted by model distance: nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.236 2.440 nonbonded pdb=" O ASN A 121 " pdb=" ND2 ASN A 121 " model vdw 2.334 2.520 nonbonded pdb=" O ASP A 80 " pdb=" OH TYR A 265 " model vdw 2.366 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" NZ LYS A 195 " model vdw 2.451 2.520 nonbonded pdb=" NZ LYS A 187 " pdb=" O LEU A 212 " model vdw 2.461 2.520 ... (remaining 15244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 12.940 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.760 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 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 : 0.003 0.039 2013 Z= 0.182 Angle : 0.662 7.133 2740 Z= 0.378 Chirality : 0.042 0.132 303 Planarity : 0.003 0.026 349 Dihedral : 14.097 85.274 710 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.07 % Favored : 87.50 % Rotamer: Outliers : 0.46 % Allowed : 0.92 % Favored : 98.62 % 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: -2.81 (0.53), residues: 232 helix: None (None), residues: 0 sheet: -1.00 (0.51), residues: 96 loop : -2.63 (0.52), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 104 HIS 0.002 0.000 HIS A 207 PHE 0.012 0.001 PHE A 106 TYR 0.014 0.001 TYR A 266 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.239 Fit side-chains REVERT: A 265 TYR cc_start: 0.8186 (p90) cc_final: 0.7903 (p90) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.1707 time to fit residues: 9.9168 Evaluate side-chains 40 residues out of total 217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 134 GLN A 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2013 Z= 0.243 Angle : 0.627 7.193 2740 Z= 0.326 Chirality : 0.045 0.151 303 Planarity : 0.004 0.024 349 Dihedral : 4.472 14.616 261 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.07 % Favored : 87.50 % Rotamer: Outliers : 0.92 % Allowed : 11.06 % Favored : 88.02 % 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: -2.67 (0.52), residues: 232 helix: None (None), residues: 0 sheet: -0.88 (0.50), residues: 96 loop : -2.56 (0.51), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 64 HIS 0.003 0.001 HIS A 207 PHE 0.015 0.002 PHE A 157 TYR 0.015 0.001 TYR A 266 ARG 0.003 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.238 Fit side-chains REVERT: A 96 GLU cc_start: 0.8246 (pp20) cc_final: 0.7910 (pp20) REVERT: A 169 GLU cc_start: 0.7988 (tp30) cc_final: 0.7760 (tp30) REVERT: A 200 TYR cc_start: 0.7580 (m-80) cc_final: 0.6944 (m-80) REVERT: A 205 SER cc_start: 0.8668 (p) cc_final: 0.8432 (p) REVERT: A 228 ASP cc_start: 0.6365 (p0) cc_final: 0.6071 (p0) REVERT: A 265 TYR cc_start: 0.8175 (p90) cc_final: 0.7793 (p90) outliers start: 2 outliers final: 1 residues processed: 39 average time/residue: 0.1872 time to fit residues: 8.2861 Evaluate side-chains 37 residues out of total 217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 17 optimal weight: 0.0970 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2013 Z= 0.200 Angle : 0.574 6.711 2740 Z= 0.297 Chirality : 0.043 0.149 303 Planarity : 0.003 0.019 349 Dihedral : 4.446 16.077 261 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.43 % Allowed : 13.79 % Favored : 85.78 % Rotamer: Outliers : 1.84 % Allowed : 10.60 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.53), residues: 232 helix: None (None), residues: 0 sheet: -0.63 (0.52), residues: 96 loop : -2.62 (0.50), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 104 HIS 0.002 0.001 HIS A 207 PHE 0.011 0.001 PHE A 106 TYR 0.013 0.001 TYR A 266 ARG 0.003 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.237 Fit side-chains REVERT: A 96 GLU cc_start: 0.8196 (pp20) cc_final: 0.7686 (pp20) REVERT: A 202 LYS cc_start: 0.8497 (mttm) cc_final: 0.7972 (mtmm) outliers start: 4 outliers final: 1 residues processed: 41 average time/residue: 0.1933 time to fit residues: 8.9608 Evaluate side-chains 37 residues out of total 217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 13 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2013 Z= 0.206 Angle : 0.576 6.490 2740 Z= 0.298 Chirality : 0.043 0.148 303 Planarity : 0.003 0.020 349 Dihedral : 4.435 15.815 261 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.43 % Allowed : 13.79 % Favored : 85.78 % Rotamer: Outliers : 2.30 % Allowed : 11.52 % Favored : 86.18 % 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: -2.42 (0.54), residues: 232 helix: None (None), residues: 0 sheet: -0.55 (0.53), residues: 96 loop : -2.53 (0.51), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 104 HIS 0.002 0.001 HIS A 207 PHE 0.011 0.001 PHE A 106 TYR 0.011 0.001 TYR A 266 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.237 Fit side-chains REVERT: A 96 GLU cc_start: 0.8087 (pp20) cc_final: 0.7472 (pp20) REVERT: A 200 TYR cc_start: 0.7577 (m-80) cc_final: 0.6928 (m-80) REVERT: A 202 LYS cc_start: 0.8512 (mttm) cc_final: 0.7971 (mtmm) REVERT: A 228 ASP cc_start: 0.6455 (p0) cc_final: 0.5943 (p0) outliers start: 5 outliers final: 4 residues processed: 41 average time/residue: 0.1818 time to fit residues: 8.4953 Evaluate side-chains 40 residues out of total 217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 chunk 19 optimal weight: 0.0020 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 245 HIS A 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2013 Z= 0.205 Angle : 0.579 6.427 2740 Z= 0.296 Chirality : 0.044 0.153 303 Planarity : 0.003 0.020 349 Dihedral : 4.466 15.638 261 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.43 % Allowed : 13.79 % Favored : 85.78 % Rotamer: Outliers : 2.30 % Allowed : 13.82 % Favored : 83.87 % 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: -2.37 (0.54), residues: 232 helix: None (None), residues: 0 sheet: -0.46 (0.54), residues: 96 loop : -2.55 (0.50), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 104 HIS 0.002 0.001 HIS A 207 PHE 0.012 0.001 PHE A 106 TYR 0.012 0.001 TYR A 266 ARG 0.004 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.233 Fit side-chains REVERT: A 96 GLU cc_start: 0.8169 (pp20) cc_final: 0.7779 (pp20) REVERT: A 202 LYS cc_start: 0.8526 (mttm) cc_final: 0.8078 (mtmm) outliers start: 5 outliers final: 5 residues processed: 42 average time/residue: 0.1858 time to fit residues: 8.9273 Evaluate side-chains 40 residues out of total 217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 245 HIS A 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 2013 Z= 0.300 Angle : 0.637 6.721 2740 Z= 0.326 Chirality : 0.046 0.175 303 Planarity : 0.004 0.026 349 Dihedral : 4.815 15.155 261 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.43 % Allowed : 14.22 % Favored : 85.34 % Rotamer: Outliers : 4.15 % Allowed : 14.75 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.54), residues: 232 helix: None (None), residues: 0 sheet: -0.56 (0.54), residues: 96 loop : -2.49 (0.51), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 104 HIS 0.002 0.001 HIS A 49 PHE 0.012 0.002 PHE A 86 TYR 0.015 0.001 TYR A 266 ARG 0.004 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.174 Fit side-chains REVERT: A 96 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7688 (pp20) REVERT: A 200 TYR cc_start: 0.7647 (m-80) cc_final: 0.7096 (m-80) REVERT: A 228 ASP cc_start: 0.6686 (p0) cc_final: 0.6122 (p0) outliers start: 9 outliers final: 7 residues processed: 43 average time/residue: 0.1289 time to fit residues: 6.3820 Evaluate side-chains 42 residues out of total 217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 0.0030 chunk 14 optimal weight: 0.0970 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 overall best weight: 0.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 245 HIS A 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2013 Z= 0.166 Angle : 0.580 7.314 2740 Z= 0.295 Chirality : 0.043 0.147 303 Planarity : 0.003 0.019 349 Dihedral : 4.563 16.547 261 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.50 % Favored : 87.07 % Rotamer: Outliers : 2.30 % Allowed : 17.05 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.55), residues: 232 helix: None (None), residues: 0 sheet: -0.50 (0.54), residues: 96 loop : -2.43 (0.51), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 258 HIS 0.001 0.000 HIS A 207 PHE 0.014 0.001 PHE A 106 TYR 0.008 0.001 TYR A 266 ARG 0.003 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.228 Fit side-chains REVERT: A 96 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7623 (pp20) REVERT: A 200 TYR cc_start: 0.7566 (m-80) cc_final: 0.6935 (m-80) REVERT: A 202 LYS cc_start: 0.8475 (mttm) cc_final: 0.8091 (mtmm) REVERT: A 228 ASP cc_start: 0.6388 (p0) cc_final: 0.6079 (p0) outliers start: 5 outliers final: 3 residues processed: 41 average time/residue: 0.1942 time to fit residues: 9.0147 Evaluate side-chains 41 residues out of total 217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 213 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 0.0980 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 245 HIS A 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2013 Z= 0.229 Angle : 0.600 7.521 2740 Z= 0.304 Chirality : 0.044 0.152 303 Planarity : 0.003 0.021 349 Dihedral : 4.575 15.730 261 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.43 % Allowed : 13.36 % Favored : 86.21 % Rotamer: Outliers : 2.76 % Allowed : 17.05 % Favored : 80.18 % 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: -2.27 (0.55), residues: 232 helix: None (None), residues: 0 sheet: -0.50 (0.54), residues: 96 loop : -2.38 (0.51), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 258 HIS 0.002 0.001 HIS A 207 PHE 0.011 0.001 PHE A 106 TYR 0.011 0.001 TYR A 266 ARG 0.003 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.339 Fit side-chains REVERT: A 96 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7661 (pp20) REVERT: A 202 LYS cc_start: 0.8516 (mttm) cc_final: 0.8120 (mtmm) REVERT: A 237 ARG cc_start: 0.8114 (mtm110) cc_final: 0.7865 (mtm180) outliers start: 6 outliers final: 5 residues processed: 40 average time/residue: 0.2513 time to fit residues: 11.4431 Evaluate side-chains 42 residues out of total 217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 213 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 1 optimal weight: 0.1980 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 2 optimal weight: 0.0370 chunk 7 optimal weight: 0.3980 overall best weight: 0.1858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 2013 Z= 0.159 Angle : 0.622 8.027 2740 Z= 0.322 Chirality : 0.044 0.145 303 Planarity : 0.003 0.017 349 Dihedral : 4.378 16.518 261 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.64 % Favored : 87.93 % Rotamer: Outliers : 2.30 % Allowed : 17.97 % Favored : 79.72 % 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: -2.20 (0.55), residues: 232 helix: None (None), residues: 0 sheet: -0.39 (0.55), residues: 96 loop : -2.38 (0.51), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 258 HIS 0.001 0.000 HIS A 207 PHE 0.015 0.001 PHE A 106 TYR 0.006 0.001 TYR A 266 ARG 0.005 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.239 Fit side-chains REVERT: A 96 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7611 (pp20) REVERT: A 202 LYS cc_start: 0.8570 (mttm) cc_final: 0.8051 (mtmm) outliers start: 5 outliers final: 4 residues processed: 42 average time/residue: 0.2152 time to fit residues: 10.0836 Evaluate side-chains 39 residues out of total 217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.0770 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 0.0470 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 2013 Z= 0.230 Angle : 0.635 7.631 2740 Z= 0.328 Chirality : 0.044 0.149 303 Planarity : 0.004 0.027 349 Dihedral : 4.460 15.879 261 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.43 % Allowed : 13.36 % Favored : 86.21 % Rotamer: Outliers : 2.76 % Allowed : 17.05 % Favored : 80.18 % 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: -2.30 (0.54), residues: 232 helix: None (None), residues: 0 sheet: -0.45 (0.54), residues: 96 loop : -2.46 (0.50), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.001 0.001 HIS A 207 PHE 0.012 0.001 PHE A 157 TYR 0.011 0.001 TYR A 266 ARG 0.004 0.000 ARG A 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.230 Fit side-chains REVERT: A 96 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7349 (pp20) REVERT: A 202 LYS cc_start: 0.8518 (mttm) cc_final: 0.8012 (mtmm) outliers start: 6 outliers final: 4 residues processed: 40 average time/residue: 0.1971 time to fit residues: 8.8689 Evaluate side-chains 41 residues out of total 217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 218 GLN A 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.148679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111052 restraints weight = 2632.148| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.15 r_work: 0.3203 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2013 Z= 0.258 Angle : 0.654 7.735 2740 Z= 0.333 Chirality : 0.045 0.149 303 Planarity : 0.004 0.025 349 Dihedral : 4.636 15.516 261 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.43 % Allowed : 13.36 % Favored : 86.21 % Rotamer: Outliers : 1.84 % Allowed : 18.89 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.53), residues: 232 helix: None (None), residues: 0 sheet: -0.60 (0.54), residues: 95 loop : -2.58 (0.49), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 258 HIS 0.002 0.001 HIS A 207 PHE 0.012 0.002 PHE A 86 TYR 0.012 0.001 TYR A 266 ARG 0.003 0.001 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1214.89 seconds wall clock time: 23 minutes 21.00 seconds (1401.00 seconds total)