Starting phenix.real_space_refine on Mon Feb 10 19:27:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bc5_12139/02_2025/7bc5_12139.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bc5_12139/02_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_12139/02_2025/7bc5_12139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bc5_12139/02_2025/7bc5_12139.map" model { file = "/net/cci-nas-00/data/ceres_data/7bc5_12139/02_2025/7bc5_12139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bc5_12139/02_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-5592/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: 3.23, per 1000 atoms: 2.69 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: 0.29 Conformation dependent library (CDL) restraints added in 164.5 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: 0.15 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: 0.24 Time building geometry restraints manager: 0.35 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: 4.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.830 Find NCS groups from input model: 0.010 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.290 ------------------------------------------------------------------------------- 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: 0.1444 time to fit residues: 6.5778 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 : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- 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 = 35)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.194899 restraints weight = 2407.647| |-----------------------------------------------------------------------------| r_work (start): 0.4513 rms_B_bonded: 0.84 r_work: 0.4485 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.4439 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5863 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 : 0.139 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 50 average time/residue: 0.0964 time to fit residues: 5.6003 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 : 0.153 ------------------------------------------------------------------------------- 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: 30.0000 chunk 8 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 7 optimal weight: 0.0470 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- 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 = 0.4575 r_free = 0.4575 target = 0.201506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.198089 restraints weight = 2285.345| |-----------------------------------------------------------------------------| r_work (start): 0.4544 rms_B_bonded: 0.74 r_work: 0.4519 rms_B_bonded: 1.12 restraints_weight: 0.5000 r_work: 0.4476 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.4476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.3269 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= 0.186 Angle : 0.689 8.029 1646 Z= 0.323 Chirality : 0.042 0.117 188 Planarity : 0.005 0.034 214 Dihedral : 6.176 38.311 167 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.58 % Allowed : 27.48 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.66 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.54), residues: 159 helix: -3.13 (0.42), residues: 81 sheet: None (None), residues: 0 loop : -2.29 (0.62), residues: 78 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 0.001 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 49 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.152 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 45 average time/residue: 0.1127 time to fit residues: 5.7629 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 : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 11 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 7 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 overall best weight: 4.5186 ------------------------------------------------------------------------------- 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 = 0.4552 r_free = 0.4552 target = 0.197809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.194256 restraints weight = 2370.879| |-----------------------------------------------------------------------------| r_work (start): 0.4514 rms_B_bonded: 0.81 r_work: 0.4487 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.4439 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 1220 Z= 0.223 Angle : 0.711 7.942 1646 Z= 0.333 Chirality : 0.042 0.114 188 Planarity : 0.004 0.031 214 Dihedral : 6.161 36.255 167 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 6.87 % Allowed : 29.77 % Favored : 63.36 % 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 (0.45), residues: 81 sheet: None (None), residues: 0 loop : -2.02 (0.65), 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 0.007 0.002 PHE A 239 TYR 0.001 0.001 TYR A 292 ARG 0.001 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.127 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 42 average time/residue: 0.0799 time to fit residues: 3.9574 Evaluate side-chains 46 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 294 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 14 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 5 optimal weight: 0.0050 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 overall best weight: 2.1400 ------------------------------------------------------------------------------- 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 = 0.4601 r_free = 0.4601 target = 0.202697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.199521 restraints weight = 2388.255| |-----------------------------------------------------------------------------| r_work (start): 0.4568 rms_B_bonded: 0.74 r_work: 0.4542 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.4494 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.4494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5757 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1220 Z= 0.156 Angle : 0.641 7.827 1646 Z= 0.298 Chirality : 0.040 0.098 188 Planarity : 0.004 0.028 214 Dihedral : 5.459 31.685 167 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 6.87 % Allowed : 31.30 % 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: -3.23 (0.59), residues: 159 helix: -2.27 (0.51), residues: 81 sheet: None (None), residues: 0 loop : -1.91 (0.65), residues: 78 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 0.001 0.000 TYR A 292 ARG 0.002 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.139 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 43 average time/residue: 0.0734 time to fit residues: 3.8265 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 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: 4.9990 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 7 optimal weight: 0.1980 chunk 1 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 = 0.4586 r_free = 0.4586 target = 0.201104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.198036 restraints weight = 2407.968| |-----------------------------------------------------------------------------| r_work (start): 0.4556 rms_B_bonded: 0.74 r_work: 0.4531 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.4486 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.4486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5806 moved from start: 0.4315 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= 0.192 Angle : 0.676 9.019 1646 Z= 0.307 Chirality : 0.042 0.101 188 Planarity : 0.004 0.027 214 Dihedral : 5.389 29.831 167 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 5.34 % Allowed : 32.06 % Favored : 62.60 % 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: -2.96 (0.61), residues: 159 helix: -2.04 (0.53), residues: 81 sheet: None (None), residues: 0 loop : -1.79 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 252 HIS 0.002 0.001 HIS A 150 PHE 0.011 0.002 PHE A 215 TYR 0.002 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: 7 poor density : 38 time to evaluate : 0.137 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 41 average time/residue: 0.0754 time to fit residues: 3.7426 Evaluate side-chains 44 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 4 optimal weight: 9.9990 chunk 6 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 overall best weight: 3.8386 ------------------------------------------------------------------------------- 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 = 0.4576 r_free = 0.4576 target = 0.199416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.196198 restraints weight = 2400.951| |-----------------------------------------------------------------------------| r_work (start): 0.4543 rms_B_bonded: 0.76 r_work: 0.4519 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.4471 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.4471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5852 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 1220 Z= 0.206 Angle : 0.632 5.918 1646 Z= 0.301 Chirality : 0.042 0.116 188 Planarity : 0.004 0.023 214 Dihedral : 5.459 29.231 167 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 6.87 % Allowed : 32.06 % 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: -2.96 (0.62), residues: 159 helix: -2.13 (0.52), residues: 81 sheet: None (None), residues: 0 loop : -1.67 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 252 HIS 0.003 0.001 HIS A 150 PHE 0.011 0.002 PHE A 215 TYR 0.001 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 48 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.147 Fit side-chains REVERT: A 202 THR cc_start: 0.5801 (OUTLIER) cc_final: 0.5589 (p) outliers start: 9 outliers final: 8 residues processed: 45 average time/residue: 0.0941 time to fit residues: 4.9544 Evaluate side-chains 46 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASP 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 202 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 294 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 0.0770 chunk 10 optimal weight: 2.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- 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 = 0.4613 r_free = 0.4613 target = 0.203906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.200788 restraints weight = 2443.063| |-----------------------------------------------------------------------------| r_work (start): 0.4578 rms_B_bonded: 0.78 r_work: 0.4554 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.4505 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.4505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5748 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 1220 Z= 0.153 Angle : 0.593 5.464 1646 Z= 0.281 Chirality : 0.040 0.116 188 Planarity : 0.004 0.023 214 Dihedral : 4.847 24.859 167 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 6.11 % Allowed : 32.06 % Favored : 61.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.63), residues: 159 helix: -2.07 (0.54), residues: 82 sheet: None (None), residues: 0 loop : -1.56 (0.70), residues: 77 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 0.010 0.002 PHE A 215 TYR 0.002 0.000 TYR A 292 ARG 0.002 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.151 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 41 average time/residue: 0.0809 time to fit residues: 4.0018 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 : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 294 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 14 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 2 optimal weight: 0.3980 chunk 1 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 overall best weight: 5.6788 ------------------------------------------------------------------------------- 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 = 0.4534 r_free = 0.4534 target = 0.195466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.192289 restraints weight = 2401.647| |-----------------------------------------------------------------------------| r_work (start): 0.4498 rms_B_bonded: 0.80 r_work: 0.4472 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.4426 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5967 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 1220 Z= 0.301 Angle : 0.716 7.091 1646 Z= 0.340 Chirality : 0.046 0.137 188 Planarity : 0.004 0.023 214 Dihedral : 5.771 28.988 167 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 6.87 % Allowed : 29.77 % Favored : 63.36 % 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: -2.68 (0.65), residues: 159 helix: -2.04 (0.53), residues: 80 sheet: None (None), residues: 0 loop : -1.37 (0.74), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 252 HIS 0.008 0.003 HIS A 150 PHE 0.012 0.003 PHE A 215 TYR 0.003 0.001 TYR A 247 ARG 0.002 0.000 ARG A 245 *********************** 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 54 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.150 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 50 average time/residue: 0.0974 time to fit residues: 5.6208 Evaluate side-chains 52 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 294 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 0.0070 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 30.0000 chunk 10 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 12 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 overall best weight: 4.6006 ------------------------------------------------------------------------------- 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 = 0.4549 r_free = 0.4549 target = 0.195782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.192123 restraints weight = 2387.394| |-----------------------------------------------------------------------------| r_work (start): 0.4507 rms_B_bonded: 0.92 r_work: 0.4478 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.4424 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.4424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 moved from start: 0.5231 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= 0.257 Angle : 0.697 7.619 1646 Z= 0.329 Chirality : 0.045 0.119 188 Planarity : 0.004 0.023 214 Dihedral : 5.656 26.058 167 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 5.34 % Allowed : 33.59 % 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: -2.73 (0.65), residues: 159 helix: -2.11 (0.52), residues: 80 sheet: None (None), residues: 0 loop : -1.36 (0.74), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 252 HIS 0.010 0.003 HIS A 150 PHE 0.012 0.002 PHE A 215 TYR 0.005 0.001 TYR A 247 ARG 0.003 0.001 ARG A 258 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.152 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 46 average time/residue: 0.1009 time to fit residues: 5.4174 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 : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 294 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 12 optimal weight: 0.0170 chunk 5 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 13 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 overall best weight: 5.4026 ------------------------------------------------------------------------------- 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 = 0.4536 r_free = 0.4536 target = 0.194452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.190843 restraints weight = 2405.766| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 0.89 r_work: 0.4462 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.4410 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6009 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 1220 Z= 0.299 Angle : 0.742 8.091 1646 Z= 0.350 Chirality : 0.047 0.129 188 Planarity : 0.004 0.023 214 Dihedral : 5.922 27.232 167 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 6.11 % Allowed : 33.59 % Favored : 60.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.63), residues: 159 helix: -2.50 (0.49), residues: 86 sheet: None (None), residues: 0 loop : -1.33 (0.76), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 252 HIS 0.008 0.003 HIS A 150 PHE 0.011 0.003 PHE A 215 TYR 0.007 0.001 TYR A 247 ARG 0.003 0.001 ARG A 258 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1200.24 seconds wall clock time: 21 minutes 57.47 seconds (1317.47 seconds total)