Starting phenix.real_space_refine on Wed Mar 5 14:17:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bc5_12139/03_2025/7bc5_12139.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bc5_12139/03_2025/7bc5_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/cci-nas-00/data/ceres_data/7bc5_12139/03_2025/7bc5_12139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bc5_12139/03_2025/7bc5_12139.map" model { file = "/net/cci-nas-00/data/ceres_data/7bc5_12139/03_2025/7bc5_12139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bc5_12139/03_2025/7bc5_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-5624/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: 2.39, per 1000 atoms: 1.99 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 165.9 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: 0.14 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: 0.23 Time building geometry restraints manager: 0.34 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: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.660 Find NCS groups from input model: 0.010 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.880 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.145 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: 0.1426 time to fit residues: 6.4804 Evaluate side-chains 36 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. 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: 10.0000 chunk 9 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.198711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.194839 restraints weight = 2407.647| |-----------------------------------------------------------------------------| r_work (start): 0.4509 rms_B_bonded: 0.85 r_work: 0.4482 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.4437 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5884 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 to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.148 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 50 average time/residue: 0.0967 time to fit residues: 5.5966 Evaluate side-chains 48 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 6 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.199780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.196424 restraints weight = 2294.703| |-----------------------------------------------------------------------------| r_work (start): 0.4530 rms_B_bonded: 0.73 r_work: 0.4505 rms_B_bonded: 1.12 restraints_weight: 0.5000 r_work: 0.4455 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.4455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5860 moved from start: 0.3334 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= 0.208 Angle : 0.700 8.040 1646 Z= 0.330 Chirality : 0.042 0.119 188 Planarity : 0.005 0.035 214 Dihedral : 6.364 39.724 167 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 5.34 % Allowed : 25.95 % Favored : 68.70 % 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: -4.23 (0.53), residues: 159 helix: -3.21 (0.40), residues: 82 sheet: None (None), residues: 0 loop : -2.23 (0.63), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 252 HIS 0.001 0.001 HIS A 150 PHE 0.008 0.002 PHE A 215 TYR 0.001 0.000 TYR A 247 ARG 0.001 0.000 ARG A 274 *********************** 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 50 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.134 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 46 average time/residue: 0.1067 time to fit residues: 5.5832 Evaluate side-chains 45 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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: 9.9990 chunk 5 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.0370 chunk 0 optimal weight: 30.0000 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 overall best weight: 4.0066 ------------------------------------------------------------------------------- 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 = 0.4558 r_free = 0.4558 target = 0.198471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.194990 restraints weight = 2370.393| |-----------------------------------------------------------------------------| r_work (start): 0.4523 rms_B_bonded: 0.81 r_work: 0.4495 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.4444 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.4444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5893 moved from start: 0.3811 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= 0.203 Angle : 0.697 8.497 1646 Z= 0.324 Chirality : 0.042 0.111 188 Planarity : 0.004 0.029 214 Dihedral : 6.024 35.251 167 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 6.11 % Allowed : 29.77 % Favored : 64.12 % 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: -3.69 (0.57), residues: 159 helix: -2.74 (0.46), residues: 81 sheet: None (None), residues: 0 loop : -2.01 (0.65), residues: 78 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 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 45 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.149 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 41 average time/residue: 0.0890 time to fit residues: 4.3037 Evaluate side-chains 43 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 294 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 14 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.4581 r_free = 0.4581 target = 0.200524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.197695 restraints weight = 2389.860| |-----------------------------------------------------------------------------| r_work (start): 0.4546 rms_B_bonded: 0.68 r_work: 0.4524 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.4478 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.4478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5819 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1220 Z= 0.188 Angle : 0.667 7.631 1646 Z= 0.310 Chirality : 0.041 0.099 188 Planarity : 0.004 0.027 214 Dihedral : 5.732 33.852 167 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 7.63 % Allowed : 30.53 % Favored : 61.83 % 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: -3.29 (0.59), residues: 159 helix: -2.41 (0.49), residues: 81 sheet: None (None), residues: 0 loop : -1.82 (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 0.011 0.002 PHE A 215 TYR 0.001 0.000 TYR A 247 ARG 0.001 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 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 47 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.146 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 43 average time/residue: 0.0804 time to fit residues: 4.1974 Evaluate side-chains 44 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 0.0770 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 40.0000 chunk 7 optimal weight: 20.0000 chunk 1 optimal weight: 0.2980 chunk 5 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 overall best weight: 2.8744 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.200361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.197062 restraints weight = 2396.941| |-----------------------------------------------------------------------------| r_work (start): 0.4547 rms_B_bonded: 0.76 r_work: 0.4520 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.4472 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.4367 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= 0.185 Angle : 0.677 9.284 1646 Z= 0.305 Chirality : 0.042 0.124 188 Planarity : 0.004 0.025 214 Dihedral : 5.276 26.687 167 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 4.58 % Allowed : 34.35 % Favored : 61.07 % 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: -2.86 (0.62), residues: 159 helix: -2.06 (0.52), residues: 81 sheet: None (None), residues: 0 loop : -1.61 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 252 HIS 0.002 0.001 HIS A 150 PHE 0.010 0.002 PHE A 215 TYR 0.001 0.000 TYR A 247 ARG 0.001 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.126 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 41 average time/residue: 0.0691 time to fit residues: 3.4233 Evaluate side-chains 43 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.126 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 4 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 2 optimal weight: 30.0000 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.195419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.192123 restraints weight = 2400.038| |-----------------------------------------------------------------------------| r_work (start): 0.4508 rms_B_bonded: 0.75 r_work: 0.4483 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.4433 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5946 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 1220 Z= 0.262 Angle : 0.669 5.970 1646 Z= 0.322 Chirality : 0.043 0.117 188 Planarity : 0.004 0.024 214 Dihedral : 5.831 29.532 167 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 8.40 % Allowed : 31.30 % 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: -2.95 (0.64), residues: 159 helix: -2.26 (0.52), residues: 81 sheet: None (None), residues: 0 loop : -1.49 (0.75), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 252 HIS 0.002 0.001 HIS A 150 PHE 0.009 0.002 PHE A 239 TYR 0.002 0.001 TYR A 247 ARG 0.001 0.000 ARG A 245 *********************** 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 52 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.145 Fit side-chains REVERT: A 202 THR cc_start: 0.5658 (OUTLIER) cc_final: 0.5401 (p) outliers start: 11 outliers final: 9 residues processed: 46 average time/residue: 0.0861 time to fit residues: 4.6635 Evaluate side-chains 52 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 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 184 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 278 ASP 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 5 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 12 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.4511 r_free = 0.4511 target = 0.191882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.188260 restraints weight = 2461.361| |-----------------------------------------------------------------------------| r_work (start): 0.4467 rms_B_bonded: 0.87 r_work: 0.4439 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.4381 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 1220 Z= 0.321 Angle : 0.729 6.333 1646 Z= 0.359 Chirality : 0.046 0.152 188 Planarity : 0.004 0.023 214 Dihedral : 6.502 31.631 167 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 8.40 % Allowed : 33.59 % Favored : 58.02 % 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: -3.12 (0.63), residues: 159 helix: -2.49 (0.49), residues: 83 sheet: None (None), residues: 0 loop : -1.41 (0.76), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 252 HIS 0.002 0.001 HIS A 150 PHE 0.009 0.002 PHE A 215 TYR 0.002 0.001 TYR A 292 ARG 0.002 0.000 ARG A 245 *********************** 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 53 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.148 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 47 average time/residue: 0.1201 time to fit residues: 6.4016 Evaluate side-chains 45 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 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 14 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.4557 r_free = 0.4557 target = 0.197114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.193962 restraints weight = 2380.987| |-----------------------------------------------------------------------------| r_work (start): 0.4521 rms_B_bonded: 0.75 r_work: 0.4494 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.4443 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1220 Z= 0.180 Angle : 0.650 5.493 1646 Z= 0.314 Chirality : 0.041 0.120 188 Planarity : 0.004 0.023 214 Dihedral : 5.772 26.231 167 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 5.34 % Allowed : 36.64 % Favored : 58.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.64), residues: 159 helix: -2.47 (0.49), residues: 89 sheet: None (None), residues: 0 loop : -1.29 (0.77), 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 0.012 0.002 PHE A 215 TYR 0.008 0.001 TYR A 247 ARG 0.002 0.001 ARG A 229 *********************** 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 48 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.130 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 45 average time/residue: 0.0982 time to fit residues: 5.0830 Evaluate side-chains 46 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 8 optimal weight: 4.9990 chunk 2 optimal weight: 0.0020 chunk 6 optimal weight: 0.0000 chunk 13 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 3 optimal weight: 0.0980 chunk 9 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 12 optimal weight: 0.0570 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 overall best weight: 1.0312 ------------------------------------------------------------------------------- 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 = 0.4589 r_free = 0.4589 target = 0.201980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.198852 restraints weight = 2362.762| |-----------------------------------------------------------------------------| r_work (start): 0.4556 rms_B_bonded: 0.76 r_work: 0.4531 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.4481 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.4481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5748 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 1220 Z= 0.153 Angle : 0.623 4.784 1646 Z= 0.297 Chirality : 0.041 0.120 188 Planarity : 0.004 0.024 214 Dihedral : 5.275 21.251 167 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.82 % Allowed : 37.40 % Favored : 58.78 % 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: -2.98 (0.63), residues: 159 helix: -2.23 (0.51), residues: 89 sheet: None (None), residues: 0 loop : -1.42 (0.73), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 252 HIS 0.000 0.000 HIS A 150 PHE 0.010 0.002 PHE A 215 TYR 0.023 0.004 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 42 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.148 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 38 average time/residue: 0.1014 time to fit residues: 4.4638 Evaluate side-chains 39 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 287 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 12 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 30.0000 chunk 1 optimal weight: 30.0000 chunk 3 optimal weight: 0.0670 chunk 15 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.0370 chunk 8 optimal weight: 4.9990 overall best weight: 1.8202 ------------------------------------------------------------------------------- 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 = 0.4582 r_free = 0.4582 target = 0.200879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.197652 restraints weight = 2380.402| |-----------------------------------------------------------------------------| r_work (start): 0.4548 rms_B_bonded: 0.78 r_work: 0.4523 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.4477 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5750 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1220 Z= 0.172 Angle : 0.643 4.911 1646 Z= 0.306 Chirality : 0.042 0.151 188 Planarity : 0.004 0.023 214 Dihedral : 5.127 18.099 167 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % 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: -2.84 (0.63), residues: 159 helix: -2.07 (0.52), residues: 89 sheet: None (None), residues: 0 loop : -1.43 (0.72), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 252 HIS 0.000 0.000 HIS A 150 PHE 0.009 0.001 PHE A 215 TYR 0.021 0.003 TYR A 247 ARG 0.003 0.000 ARG A 258 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1183.10 seconds wall clock time: 21 minutes 3.77 seconds (1263.77 seconds total)