Starting phenix.real_space_refine on Tue Aug 4 13:08:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21or_67869/08_2026/21or_67869.cif Found real_map, /net/cci-nas-00/data/ceres_data/21or_67869/08_2026/21or_67869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21or_67869/08_2026/21or_67869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21or_67869/08_2026/21or_67869.map" model { file = "/net/cci-nas-00/data/ceres_data/21or_67869/08_2026/21or_67869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21or_67869/08_2026/21or_67869.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 19 5.16 5 C 2084 2.51 5 N 505 2.21 5 O 566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3175 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3159 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 16, 'TRANS': 397} Chain breaks: 1 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'BG6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.93, per 1000 atoms: 0.29 Number of scatterers: 3175 At special positions: 0 Unit cell: (73.984, 54.91, 72.828, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 1 15.00 O 566 8.00 N 505 7.00 C 2084 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 116.3 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 87.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 5 through 29 removed outlier: 3.537A pdb=" N TYR A 9 " --> pdb=" O GLY A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 42 Proline residue: A 36 - end of helix Processing helix chain 'A' and resid 45 through 74 Processing helix chain 'A' and resid 75 through 97 removed outlier: 3.528A pdb=" N LEU A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.526A pdb=" N GLY A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 removed outlier: 3.730A pdb=" N CYS A 121 " --> pdb=" O GLY A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 163 removed outlier: 3.937A pdb=" N SER A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 165 through 187 Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 216 through 222 Processing helix chain 'A' and resid 223 through 254 removed outlier: 3.853A pdb=" N TRP A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLN A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N PHE A 249 " --> pdb=" O ASP A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 290 Processing helix chain 'A' and resid 300 through 321 Processing helix chain 'A' and resid 327 through 357 Proline residue: A 345 - end of helix removed outlier: 3.633A pdb=" N GLY A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 380 removed outlier: 3.576A pdb=" N ASN A 374 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 392 through 414 Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' 271 hydrogen bonds defined for protein. 804 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: 0.45 Time building geometry restraints manager: 0.39 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: 869 1.34 - 1.45: 628 1.45 - 1.57: 1734 1.57 - 1.69: 1 1.69 - 1.81: 31 Bond restraints: 3263 Sorted by residual: bond pdb=" C5 BG6 A 501 " pdb=" O5 BG6 A 501 " ideal model delta sigma weight residual 1.418 1.541 -0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" C5 BG6 A 501 " pdb=" C6 BG6 A 501 " ideal model delta sigma weight residual 1.520 1.423 0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C2 BG6 A 501 " pdb=" O2 BG6 A 501 " ideal model delta sigma weight residual 1.405 1.481 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" CA ARG A 126 " pdb=" C ARG A 126 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.29e-02 6.01e+03 1.44e+01 bond pdb=" C3 BG6 A 501 " pdb=" O3 BG6 A 501 " ideal model delta sigma weight residual 1.408 1.481 -0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 3258 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 4351 2.47 - 4.94: 69 4.94 - 7.42: 18 7.42 - 9.89: 4 9.89 - 12.36: 1 Bond angle restraints: 4443 Sorted by residual: angle pdb=" CA LEU A 159 " pdb=" CB LEU A 159 " pdb=" CG LEU A 159 " ideal model delta sigma weight residual 116.30 128.66 -12.36 3.50e+00 8.16e-02 1.25e+01 angle pdb=" N THR A 143 " pdb=" CA THR A 143 " pdb=" CB THR A 143 " ideal model delta sigma weight residual 110.39 115.66 -5.27 1.66e+00 3.63e-01 1.01e+01 angle pdb=" CA GLU A 270 " pdb=" CB GLU A 270 " pdb=" CG GLU A 270 " ideal model delta sigma weight residual 114.10 120.18 -6.08 2.00e+00 2.50e-01 9.24e+00 angle pdb=" CB MET A 372 " pdb=" CG MET A 372 " pdb=" SD MET A 372 " ideal model delta sigma weight residual 112.70 121.61 -8.91 3.00e+00 1.11e-01 8.82e+00 angle pdb=" N THR A 143 " pdb=" CA THR A 143 " pdb=" C THR A 143 " ideal model delta sigma weight residual 112.54 108.96 3.58 1.22e+00 6.72e-01 8.59e+00 ... (remaining 4438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 1660 21.92 - 43.83: 172 43.83 - 65.75: 28 65.75 - 87.67: 3 87.67 - 109.58: 8 Dihedral angle restraints: 1871 sinusoidal: 697 harmonic: 1174 Sorted by residual: dihedral pdb=" C2 BG6 A 501 " pdb=" C3 BG6 A 501 " pdb=" C4 BG6 A 501 " pdb=" O4 BG6 A 501 " ideal model delta sinusoidal sigma weight residual 175.48 65.90 109.58 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C2 BG6 A 501 " pdb=" C3 BG6 A 501 " pdb=" C4 BG6 A 501 " pdb=" C5 BG6 A 501 " ideal model delta sinusoidal sigma weight residual 53.81 -55.08 108.89 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" O3 BG6 A 501 " pdb=" C3 BG6 A 501 " pdb=" C4 BG6 A 501 " pdb=" O4 BG6 A 501 " ideal model delta sinusoidal sigma weight residual -64.11 -172.82 108.71 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 1868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 380 0.045 - 0.089: 94 0.089 - 0.134: 29 0.134 - 0.179: 0 0.179 - 0.223: 1 Chirality restraints: 504 Sorted by residual: chirality pdb=" CB THR A 143 " pdb=" CA THR A 143 " pdb=" OG1 THR A 143 " pdb=" CG2 THR A 143 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C5 BG6 A 501 " pdb=" C4 BG6 A 501 " pdb=" C6 BG6 A 501 " pdb=" O5 BG6 A 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.63 0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA LEU A 159 " pdb=" N LEU A 159 " pdb=" C LEU A 159 " pdb=" CB LEU A 159 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 501 not shown) Planarity restraints: 543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 142 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C SER A 142 " -0.036 2.00e-02 2.50e+03 pdb=" O SER A 142 " 0.014 2.00e-02 2.50e+03 pdb=" N THR A 143 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 152 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO A 153 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 125 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.15e+00 pdb=" C LEU A 125 " -0.031 2.00e-02 2.50e+03 pdb=" O LEU A 125 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG A 126 " 0.010 2.00e-02 2.50e+03 ... (remaining 540 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 497 2.75 - 3.29: 3392 3.29 - 3.83: 5717 3.83 - 4.36: 6140 4.36 - 4.90: 10523 Nonbonded interactions: 26269 Sorted by model distance: nonbonded pdb=" OE1 GLN A 4 " pdb=" OH TYR A 9 " model vdw 2.214 3.040 nonbonded pdb=" O VAL A 177 " pdb=" OG SER A 180 " model vdw 2.217 3.040 nonbonded pdb=" O ALA A 95 " pdb=" NH1 ARG A 166 " model vdw 2.264 3.120 nonbonded pdb=" OD1 ASN A 27 " pdb=" ND2 ASN A 91 " model vdw 2.281 3.120 nonbonded pdb=" O SER A 63 " pdb=" OG SER A 67 " model vdw 2.290 3.040 ... (remaining 26264 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.800 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.140 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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 0.123 3263 Z= 0.275 Angle : 0.816 12.361 4443 Z= 0.394 Chirality : 0.042 0.223 504 Planarity : 0.005 0.046 543 Dihedral : 19.498 109.582 1125 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.30 % Allowed : 29.13 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.41), residues: 410 helix: 1.68 (0.28), residues: 344 sheet: None (None), residues: 0 loop : 0.70 (0.77), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 423 TYR 0.021 0.001 TYR A 225 PHE 0.012 0.001 PHE A 340 TRP 0.025 0.001 TRP A 118 HIS 0.001 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.28 ( 3263) covalent geometry : angle 0.81587 / 0.39 ( 4443) hydrogen bonds : bond 0.11880 / 8.16 ( 271) hydrogen bonds : angle 5.27844 / 3.93 ( 804) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8999 (mtt90) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.0944 time to fit residues: 14.0340 Evaluate side-chains 121 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.0570 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.116749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.102875 restraints weight = 7352.706| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 3.81 r_work: 0.3357 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3263 Z= 0.158 Angle : 0.672 7.405 4443 Z= 0.340 Chirality : 0.041 0.156 504 Planarity : 0.005 0.046 543 Dihedral : 9.345 54.535 470 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.50 % Allowed : 25.53 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.41), residues: 410 helix: 1.87 (0.28), residues: 347 sheet: None (None), residues: 0 loop : 0.86 (0.79), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 423 TYR 0.031 0.002 TYR A 225 PHE 0.013 0.001 PHE A 249 TRP 0.009 0.001 TRP A 138 HIS 0.003 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 ( 3263) covalent geometry : angle 0.67231 / 0.34 ( 4443) hydrogen bonds : bond 0.05213 / 3.34 ( 271) hydrogen bonds : angle 4.44302 / 3.30 ( 804) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 GLN cc_start: 0.8222 (pm20) cc_final: 0.8005 (pm20) REVERT: A 286 ARG cc_start: 0.8026 (mmm-85) cc_final: 0.7757 (mmt90) outliers start: 5 outliers final: 4 residues processed: 133 average time/residue: 0.0628 time to fit residues: 10.1859 Evaluate side-chains 124 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 328 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.116339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.102116 restraints weight = 7450.092| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.91 r_work: 0.3343 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3263 Z= 0.159 Angle : 0.635 6.924 4443 Z= 0.327 Chirality : 0.039 0.147 504 Planarity : 0.005 0.044 543 Dihedral : 6.121 57.365 466 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.10 % Allowed : 27.03 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.41), residues: 410 helix: 1.81 (0.27), residues: 347 sheet: None (None), residues: 0 loop : 0.85 (0.78), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 423 TYR 0.015 0.001 TYR A 225 PHE 0.012 0.001 PHE A 340 TRP 0.009 0.001 TRP A 138 HIS 0.002 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 ( 3263) covalent geometry : angle 0.63493 / 0.33 ( 4443) hydrogen bonds : bond 0.05182 / 3.33 ( 271) hydrogen bonds : angle 4.38050 / 3.26 ( 804) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.8799 (tp) cc_final: 0.8576 (tp) REVERT: A 73 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7934 (tm-30) REVERT: A 127 LYS cc_start: 0.9204 (tptm) cc_final: 0.8847 (tptm) REVERT: A 218 GLN cc_start: 0.8277 (pm20) cc_final: 0.8071 (pm20) REVERT: A 257 GLN cc_start: 0.7923 (mm110) cc_final: 0.7578 (mm-40) REVERT: A 286 ARG cc_start: 0.8060 (mmm-85) cc_final: 0.7860 (mmt90) outliers start: 7 outliers final: 6 residues processed: 128 average time/residue: 0.0694 time to fit residues: 10.7135 Evaluate side-chains 130 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 332 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 34 optimal weight: 0.0670 chunk 14 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 0.0050 overall best weight: 0.4332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.117743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.103829 restraints weight = 7363.453| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.81 r_work: 0.3378 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3263 Z= 0.141 Angle : 0.612 6.022 4443 Z= 0.316 Chirality : 0.039 0.149 504 Planarity : 0.005 0.045 543 Dihedral : 5.565 57.339 466 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.00 % Allowed : 26.73 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.41), residues: 410 helix: 1.84 (0.28), residues: 348 sheet: None (None), residues: 0 loop : 0.89 (0.79), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 423 TYR 0.017 0.001 TYR A 225 PHE 0.012 0.001 PHE A 340 TRP 0.009 0.001 TRP A 138 HIS 0.002 0.000 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 ( 3263) covalent geometry : angle 0.61210 / 0.32 ( 4443) hydrogen bonds : bond 0.04928 / 3.18 ( 271) hydrogen bonds : angle 4.28498 / 3.19 ( 804) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8641 (tt0) cc_final: 0.8310 (tt0) REVERT: A 127 LYS cc_start: 0.9203 (tptm) cc_final: 0.8830 (tptm) REVERT: A 233 TYR cc_start: 0.9144 (t80) cc_final: 0.8864 (t80) REVERT: A 286 ARG cc_start: 0.8033 (mmm-85) cc_final: 0.7825 (mmt90) REVERT: A 288 MET cc_start: 0.7796 (ttm) cc_final: 0.7557 (tpp) REVERT: A 423 ARG cc_start: 0.7709 (ttp-110) cc_final: 0.7451 (ttp-110) outliers start: 10 outliers final: 9 residues processed: 132 average time/residue: 0.0640 time to fit residues: 10.4140 Evaluate side-chains 131 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 TYR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 332 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 0.0050 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.117979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.103862 restraints weight = 7265.696| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.88 r_work: 0.3372 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3263 Z= 0.144 Angle : 0.616 8.185 4443 Z= 0.318 Chirality : 0.039 0.156 504 Planarity : 0.005 0.044 543 Dihedral : 5.414 54.899 466 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.00 % Allowed : 27.33 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.41), residues: 410 helix: 1.80 (0.28), residues: 349 sheet: None (None), residues: 0 loop : 1.04 (0.80), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 77 TYR 0.019 0.001 TYR A 225 PHE 0.014 0.001 PHE A 249 TRP 0.009 0.001 TRP A 138 HIS 0.002 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 3263) covalent geometry : angle 0.61613 / 0.32 ( 4443) hydrogen bonds : bond 0.04876 / 3.15 ( 271) hydrogen bonds : angle 4.29490 / 3.20 ( 804) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLN cc_start: 0.8299 (tm-30) cc_final: 0.7892 (tm-30) REVERT: A 127 LYS cc_start: 0.9191 (tptm) cc_final: 0.8818 (tptm) REVERT: A 233 TYR cc_start: 0.9141 (t80) cc_final: 0.8857 (t80) REVERT: A 270 GLU cc_start: 0.8761 (tp30) cc_final: 0.8522 (tp30) REVERT: A 332 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8507 (mp) REVERT: A 423 ARG cc_start: 0.7753 (ttp-110) cc_final: 0.7518 (ttp-110) outliers start: 10 outliers final: 6 residues processed: 131 average time/residue: 0.0584 time to fit residues: 9.5218 Evaluate side-chains 130 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 TYR Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 332 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.117602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.103639 restraints weight = 7366.917| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.84 r_work: 0.3353 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3263 Z= 0.154 Angle : 0.637 7.192 4443 Z= 0.334 Chirality : 0.040 0.146 504 Planarity : 0.005 0.044 543 Dihedral : 5.273 51.876 466 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.00 % Allowed : 28.53 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.41), residues: 410 helix: 1.80 (0.28), residues: 347 sheet: None (None), residues: 0 loop : 0.87 (0.80), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.022 0.001 TYR A 225 PHE 0.024 0.002 PHE A 108 TRP 0.007 0.001 TRP A 138 HIS 0.002 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 3263) covalent geometry : angle 0.63662 / 0.33 ( 4443) hydrogen bonds : bond 0.04914 / 3.18 ( 271) hydrogen bonds : angle 4.35423 / 3.25 ( 804) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: A 233 TYR cc_start: 0.9180 (t80) cc_final: 0.8897 (t80) REVERT: A 270 GLU cc_start: 0.8808 (tp30) cc_final: 0.8521 (tp30) REVERT: A 288 MET cc_start: 0.7826 (ttm) cc_final: 0.7544 (tpp) REVERT: A 332 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8507 (mp) outliers start: 10 outliers final: 7 residues processed: 125 average time/residue: 0.0402 time to fit residues: 6.3219 Evaluate side-chains 130 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 TYR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 332 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.114989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.100942 restraints weight = 7606.095| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.81 r_work: 0.3329 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3263 Z= 0.172 Angle : 0.693 8.979 4443 Z= 0.355 Chirality : 0.041 0.146 504 Planarity : 0.005 0.043 543 Dihedral : 5.193 48.278 466 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.70 % Allowed : 28.83 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.41), residues: 410 helix: 1.76 (0.28), residues: 345 sheet: None (None), residues: 0 loop : 0.84 (0.78), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 423 TYR 0.019 0.001 TYR A 225 PHE 0.014 0.002 PHE A 108 TRP 0.009 0.001 TRP A 138 HIS 0.003 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 ( 3263) covalent geometry : angle 0.69275 / 0.36 ( 4443) hydrogen bonds : bond 0.05034 / 3.27 ( 271) hydrogen bonds : angle 4.41767 / 3.31 ( 804) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.114 Fit side-chains revert: symmetry clash REVERT: A 73 GLN cc_start: 0.8343 (tm-30) cc_final: 0.7926 (tm-30) REVERT: A 233 TYR cc_start: 0.9165 (t80) cc_final: 0.8928 (t80) REVERT: A 270 GLU cc_start: 0.8894 (tp30) cc_final: 0.8604 (tp30) REVERT: A 332 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8467 (mp) REVERT: A 423 ARG cc_start: 0.7720 (ttp-110) cc_final: 0.7372 (ttp80) outliers start: 9 outliers final: 5 residues processed: 126 average time/residue: 0.0521 time to fit residues: 8.2287 Evaluate side-chains 127 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 332 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.115528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.101481 restraints weight = 7536.728| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.85 r_work: 0.3336 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3263 Z= 0.165 Angle : 0.694 9.645 4443 Z= 0.358 Chirality : 0.042 0.144 504 Planarity : 0.005 0.043 543 Dihedral : 5.140 46.673 466 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.40 % Allowed : 29.13 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.41), residues: 410 helix: 1.67 (0.28), residues: 345 sheet: None (None), residues: 0 loop : 0.80 (0.77), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 423 TYR 0.024 0.001 TYR A 225 PHE 0.015 0.001 PHE A 108 TRP 0.008 0.001 TRP A 138 HIS 0.003 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 3263) covalent geometry : angle 0.69433 / 0.36 ( 4443) hydrogen bonds : bond 0.05046 / 3.26 ( 271) hydrogen bonds : angle 4.50505 / 3.39 ( 804) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: A 73 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7838 (tm-30) REVERT: A 233 TYR cc_start: 0.9160 (t80) cc_final: 0.8926 (t80) REVERT: A 270 GLU cc_start: 0.8938 (tp30) cc_final: 0.8682 (tp30) REVERT: A 332 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8452 (mp) outliers start: 8 outliers final: 5 residues processed: 125 average time/residue: 0.0627 time to fit residues: 9.7257 Evaluate side-chains 128 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 332 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.114270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.100408 restraints weight = 7519.530| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.74 r_work: 0.3337 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3263 Z= 0.166 Angle : 0.742 10.690 4443 Z= 0.374 Chirality : 0.042 0.157 504 Planarity : 0.005 0.043 543 Dihedral : 5.119 46.208 466 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.80 % Allowed : 30.03 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.41), residues: 410 helix: 1.71 (0.28), residues: 345 sheet: None (None), residues: 0 loop : 0.77 (0.79), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 423 TYR 0.020 0.001 TYR A 225 PHE 0.013 0.001 PHE A 14 TRP 0.008 0.001 TRP A 138 HIS 0.003 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 ( 3263) covalent geometry : angle 0.74229 / 0.37 ( 4443) hydrogen bonds : bond 0.05102 / 3.30 ( 271) hydrogen bonds : angle 4.53601 / 3.42 ( 804) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: A 73 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7833 (tm-30) REVERT: A 233 TYR cc_start: 0.9139 (t80) cc_final: 0.8903 (t80) REVERT: A 270 GLU cc_start: 0.8959 (tp30) cc_final: 0.8699 (tp30) REVERT: A 332 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8456 (mp) REVERT: A 423 ARG cc_start: 0.7737 (ttp-110) cc_final: 0.7321 (ttp80) outliers start: 6 outliers final: 3 residues processed: 122 average time/residue: 0.0596 time to fit residues: 8.9924 Evaluate side-chains 125 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 0.0170 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 overall best weight: 0.5220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.117272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.103141 restraints weight = 7382.892| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 3.86 r_work: 0.3363 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3263 Z= 0.156 Angle : 0.753 11.261 4443 Z= 0.383 Chirality : 0.043 0.201 504 Planarity : 0.005 0.043 543 Dihedral : 5.097 46.662 466 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.50 % Allowed : 30.93 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.42), residues: 410 helix: 1.72 (0.28), residues: 346 sheet: None (None), residues: 0 loop : 0.87 (0.80), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 423 TYR 0.020 0.001 TYR A 225 PHE 0.032 0.001 PHE A 181 TRP 0.009 0.001 TRP A 393 HIS 0.002 0.000 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 ( 3263) covalent geometry : angle 0.75308 / 0.38 ( 4443) hydrogen bonds : bond 0.05054 / 3.25 ( 271) hydrogen bonds : angle 4.56786 / 3.45 ( 804) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 73 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7789 (tm-30) REVERT: A 233 TYR cc_start: 0.9130 (t80) cc_final: 0.8897 (t80) REVERT: A 270 GLU cc_start: 0.8975 (tp30) cc_final: 0.8717 (tp30) REVERT: A 332 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8452 (mp) REVERT: A 423 ARG cc_start: 0.7704 (ttp-110) cc_final: 0.7341 (ttp80) outliers start: 5 outliers final: 3 residues processed: 125 average time/residue: 0.0506 time to fit residues: 7.8760 Evaluate side-chains 129 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.117028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.102834 restraints weight = 7527.732| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.88 r_work: 0.3355 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3263 Z= 0.165 Angle : 0.767 11.398 4443 Z= 0.389 Chirality : 0.042 0.155 504 Planarity : 0.005 0.042 543 Dihedral : 5.109 46.822 466 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.80 % Allowed : 30.33 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.42), residues: 410 helix: 1.74 (0.28), residues: 345 sheet: None (None), residues: 0 loop : 0.80 (0.78), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 423 TYR 0.023 0.001 TYR A 225 PHE 0.013 0.001 PHE A 14 TRP 0.010 0.001 TRP A 393 HIS 0.002 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 ( 3263) covalent geometry : angle 0.76686 / 0.39 ( 4443) hydrogen bonds : bond 0.05075 / 3.27 ( 271) hydrogen bonds : angle 4.62872 / 3.51 ( 804) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 907.01 seconds wall clock time: 16 minutes 15.09 seconds (975.09 seconds total)