Starting phenix.real_space_refine on Fri Aug 22 14:50:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrv_37791/08_2025/8wrv_37791.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrv_37791/08_2025/8wrv_37791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wrv_37791/08_2025/8wrv_37791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrv_37791/08_2025/8wrv_37791.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrv_37791/08_2025/8wrv_37791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrv_37791/08_2025/8wrv_37791.cif" } resolution = 3.28 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= 0.001 sd= 0.017 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 92 5.49 5 S 11 5.16 5 C 2479 2.51 5 N 813 2.21 5 O 1076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4471 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 580 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "D" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 166 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2537 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 3 Chain: "B" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1188 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 23, 'rna3p_pyr': 27} Link IDs: {'rna2p': 6, 'rna3p': 49} Time building chain proxies: 1.63, per 1000 atoms: 0.36 Number of scatterers: 4471 At special positions: 0 Unit cell: (60.72, 77.22, 114.84, 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 11 16.00 P 92 15.00 O 1076 8.00 N 813 7.00 C 2479 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: 0.45 Conformation dependent library (CDL) restraints added in 102.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 598 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 4 sheets defined 37.3% alpha, 20.9% beta 24 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 15 through 41 removed outlier: 3.756A pdb=" N HIS A 26 " --> pdb=" O TYR A 22 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.506A pdb=" N THR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 removed outlier: 4.118A pdb=" N SER A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.534A pdb=" N LEU A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 184 removed outlier: 3.597A pdb=" N LEU A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 199 removed outlier: 3.552A pdb=" N LEU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 237 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 removed outlier: 3.998A pdb=" N TYR A 433 " --> pdb=" O VAL A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 6 removed outlier: 5.852A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG A 428 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR A 434 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU A 426 " --> pdb=" O TYR A 434 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE A 436 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE A 424 " --> pdb=" O PHE A 436 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ASP A 438 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS A 422 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A 417 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A 407 " --> pdb=" O TYR A 417 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER A 402 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 394 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR A 408 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASN A 392 " --> pdb=" O THR A 408 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 360 through 363 removed outlier: 3.817A pdb=" N PHE A 369 " --> pdb=" O ALA A 384 " (cutoff:3.500A) 106 hydrogen bonds defined for protein. 294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 0.78 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1019 1.33 - 1.45: 1438 1.45 - 1.57: 2091 1.57 - 1.69: 181 1.69 - 1.81: 16 Bond restraints: 4745 Sorted by residual: bond pdb=" O3' A B -10 " pdb=" P G B -9 " ideal model delta sigma weight residual 1.607 1.661 -0.054 1.50e-02 4.44e+03 1.31e+01 bond pdb=" C SER A 345 " pdb=" N PRO A 346 " ideal model delta sigma weight residual 1.331 1.368 -0.037 1.31e-02 5.83e+03 8.06e+00 bond pdb=" O3' C B 14 " pdb=" P C B 15 " ideal model delta sigma weight residual 1.607 1.649 -0.042 1.50e-02 4.44e+03 7.67e+00 bond pdb=" O3' G B -36 " pdb=" P U B -35 " ideal model delta sigma weight residual 1.607 1.647 -0.040 1.50e-02 4.44e+03 7.11e+00 bond pdb=" O3' U B -35 " pdb=" P G B -34 " ideal model delta sigma weight residual 1.607 1.642 -0.035 1.50e-02 4.44e+03 5.35e+00 ... (remaining 4740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 6625 2.05 - 4.11: 178 4.11 - 6.16: 20 6.16 - 8.21: 2 8.21 - 10.27: 1 Bond angle restraints: 6826 Sorted by residual: angle pdb=" O3' C B -6 " pdb=" C3' C B -6 " pdb=" C2' C B -6 " ideal model delta sigma weight residual 113.70 107.79 5.91 1.50e+00 4.44e-01 1.55e+01 angle pdb=" O2' U B -5 " pdb=" C2' U B -5 " pdb=" C1' U B -5 " ideal model delta sigma weight residual 111.80 106.16 5.64 1.50e+00 4.44e-01 1.41e+01 angle pdb=" C4' A B -7 " pdb=" C3' A B -7 " pdb=" O3' A B -7 " ideal model delta sigma weight residual 113.00 107.73 5.27 1.50e+00 4.44e-01 1.24e+01 angle pdb=" N VAL A 395 " pdb=" CA VAL A 395 " pdb=" C VAL A 395 " ideal model delta sigma weight residual 108.46 113.41 -4.95 1.49e+00 4.50e-01 1.10e+01 angle pdb=" N PHE A 202 " pdb=" CA PHE A 202 " pdb=" C PHE A 202 " ideal model delta sigma weight residual 109.81 117.06 -7.25 2.21e+00 2.05e-01 1.08e+01 ... (remaining 6821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 2533 35.81 - 71.62: 278 71.62 - 107.43: 26 107.43 - 143.24: 2 143.24 - 179.05: 3 Dihedral angle restraints: 2842 sinusoidal: 1921 harmonic: 921 Sorted by residual: dihedral pdb=" O4' C B -6 " pdb=" C1' C B -6 " pdb=" N1 C B -6 " pdb=" C2 C B -6 " ideal model delta sinusoidal sigma weight residual 200.00 50.44 149.56 1 1.50e+01 4.44e-03 7.95e+01 dihedral pdb=" O4' U B -32 " pdb=" C1' U B -32 " pdb=" N1 U B -32 " pdb=" C2 U B -32 " ideal model delta sinusoidal sigma weight residual 200.00 53.31 146.69 1 1.50e+01 4.44e-03 7.83e+01 dihedral pdb=" O4' U B -5 " pdb=" C1' U B -5 " pdb=" N1 U B -5 " pdb=" C2 U B -5 " ideal model delta sinusoidal sigma weight residual -128.00 51.05 -179.05 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 2839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 714 0.070 - 0.141: 62 0.141 - 0.211: 21 0.211 - 0.282: 1 0.282 - 0.352: 2 Chirality restraints: 800 Sorted by residual: chirality pdb=" CA ARG A 41 " pdb=" N ARG A 41 " pdb=" C ARG A 41 " pdb=" CB ARG A 41 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA ARG A 172 " pdb=" N ARG A 172 " pdb=" C ARG A 172 " pdb=" CB ARG A 172 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C2' G B -36 " pdb=" C3' G B -36 " pdb=" O2' G B -36 " pdb=" C1' G B -36 " both_signs ideal model delta sigma weight residual False -2.75 -2.53 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 797 not shown) Planarity restraints: 547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 92 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO A 93 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 205 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.26e+00 pdb=" C SER A 205 " -0.031 2.00e-02 2.50e+03 pdb=" O SER A 205 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL A 206 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 202 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO A 203 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 203 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 203 " -0.023 5.00e-02 4.00e+02 ... (remaining 544 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1207 2.82 - 3.34: 3916 3.34 - 3.86: 8362 3.86 - 4.38: 9413 4.38 - 4.90: 13668 Nonbonded interactions: 36566 Sorted by model distance: nonbonded pdb=" NH2 ARG A 47 " pdb=" OE2 GLU A 53 " model vdw 2.301 3.120 nonbonded pdb=" O2' C B -30 " pdb=" OP2 U B -29 " model vdw 2.351 3.040 nonbonded pdb=" O2 U B -27 " pdb=" N2 G B -12 " model vdw 2.358 2.496 nonbonded pdb=" OG1 THR A 338 " pdb=" OP1 A B 5 " model vdw 2.368 3.040 nonbonded pdb=" OP1 DA C 2 " pdb=" NZ LYS A 422 " model vdw 2.397 3.120 ... (remaining 36561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 4.920 Set stop_for_unknowns flag: 0.010 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: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.530 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.030 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:1.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 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 : 0.004 0.054 4745 Z= 0.243 Angle : 0.736 10.266 6826 Z= 0.435 Chirality : 0.050 0.352 800 Planarity : 0.005 0.051 547 Dihedral : 23.712 179.047 2244 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.85 % Allowed : 0.74 % Favored : 97.41 % 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 aren not related in a simple way. whole: -1.76 (0.47), residues: 308 helix: -0.50 (0.48), residues: 109 sheet: -1.31 (0.54), residues: 77 loop : -1.51 (0.59), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 12 TYR 0.010 0.001 TYR A 22 PHE 0.021 0.001 PHE A 83 TRP 0.020 0.003 TRP A 229 HIS 0.002 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 4745) covalent geometry : angle 0.73630 ( 6826) hydrogen bonds : bond 0.16282 ( 165) hydrogen bonds : angle 7.07049 ( 412) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.136 Fit side-chains REVERT: A 102 GLU cc_start: 0.7126 (pm20) cc_final: 0.6910 (pm20) REVERT: A 437 ILE cc_start: 0.8140 (mm) cc_final: 0.7937 (mm) outliers start: 5 outliers final: 0 residues processed: 62 average time/residue: 0.1411 time to fit residues: 10.0122 Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4248 r_free = 0.4248 target = 0.181478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.143926 restraints weight = 6594.004| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.58 r_work: 0.3644 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4745 Z= 0.233 Angle : 0.687 8.462 6826 Z= 0.365 Chirality : 0.041 0.223 800 Planarity : 0.006 0.057 547 Dihedral : 25.602 178.033 1619 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.47), residues: 308 helix: 0.30 (0.47), residues: 112 sheet: -1.01 (0.56), residues: 76 loop : -1.76 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 96 TYR 0.013 0.002 TYR A 22 PHE 0.018 0.002 PHE A 369 TRP 0.010 0.002 TRP A 229 HIS 0.004 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 4745) covalent geometry : angle 0.68711 ( 6826) hydrogen bonds : bond 0.04770 ( 165) hydrogen bonds : angle 4.28432 ( 412) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.120 Fit side-chains REVERT: A 102 GLU cc_start: 0.7713 (pm20) cc_final: 0.7434 (pm20) REVERT: A 179 ARG cc_start: 0.7518 (mpp80) cc_final: 0.7171 (mtm110) REVERT: A 442 ASP cc_start: 0.6501 (p0) cc_final: 0.6167 (p0) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1283 time to fit residues: 7.9363 Evaluate side-chains 52 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.0670 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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 = 0.4201 r_free = 0.4201 target = 0.178944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.142724 restraints weight = 6508.392| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.53 r_work: 0.3608 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4745 Z= 0.226 Angle : 0.662 8.864 6826 Z= 0.354 Chirality : 0.041 0.241 800 Planarity : 0.006 0.054 547 Dihedral : 25.608 179.653 1619 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.11 % Allowed : 12.22 % Favored : 86.67 % 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 aren not related in a simple way. whole: -1.12 (0.48), residues: 308 helix: 0.59 (0.49), residues: 112 sheet: -0.98 (0.58), residues: 75 loop : -1.79 (0.58), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 356 TYR 0.012 0.002 TYR A 22 PHE 0.014 0.002 PHE A 369 TRP 0.009 0.002 TRP A 229 HIS 0.005 0.002 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 4745) covalent geometry : angle 0.66204 ( 6826) hydrogen bonds : bond 0.04570 ( 165) hydrogen bonds : angle 4.16054 ( 412) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.123 Fit side-chains REVERT: A 56 VAL cc_start: 0.6977 (p) cc_final: 0.6656 (t) REVERT: A 96 ARG cc_start: 0.8256 (mmt-90) cc_final: 0.7875 (mtp180) REVERT: A 102 GLU cc_start: 0.7677 (pm20) cc_final: 0.7358 (pm20) REVERT: A 416 ARG cc_start: 0.7901 (tpt170) cc_final: 0.7110 (tpt170) outliers start: 3 outliers final: 2 residues processed: 55 average time/residue: 0.1342 time to fit residues: 8.5276 Evaluate side-chains 54 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 15 optimal weight: 0.0060 chunk 10 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.180247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.144162 restraints weight = 6488.499| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.52 r_work: 0.3625 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4745 Z= 0.189 Angle : 0.628 8.089 6826 Z= 0.335 Chirality : 0.040 0.246 800 Planarity : 0.006 0.062 547 Dihedral : 25.374 179.725 1619 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.85 % Allowed : 12.22 % Favored : 85.93 % 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 aren not related in a simple way. whole: -0.86 (0.49), residues: 308 helix: 0.87 (0.49), residues: 113 sheet: -1.00 (0.59), residues: 75 loop : -1.61 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 404 TYR 0.011 0.001 TYR A 22 PHE 0.014 0.002 PHE A 169 TRP 0.008 0.002 TRP A 229 HIS 0.004 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 4745) covalent geometry : angle 0.62823 ( 6826) hydrogen bonds : bond 0.04337 ( 165) hydrogen bonds : angle 3.95808 ( 412) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.193 Fit side-chains REVERT: A 56 VAL cc_start: 0.6962 (p) cc_final: 0.6647 (t) REVERT: A 96 ARG cc_start: 0.8210 (mmt-90) cc_final: 0.7902 (mmm-85) REVERT: A 102 GLU cc_start: 0.7655 (pm20) cc_final: 0.7379 (pm20) REVERT: A 185 ASP cc_start: 0.7129 (t0) cc_final: 0.6734 (t0) REVERT: A 416 ARG cc_start: 0.7918 (tpt170) cc_final: 0.6671 (tpt170) outliers start: 5 outliers final: 4 residues processed: 57 average time/residue: 0.1284 time to fit residues: 8.5651 Evaluate side-chains 57 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 6 optimal weight: 0.0770 chunk 12 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.0070 chunk 35 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.180941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.144641 restraints weight = 6593.379| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.53 r_work: 0.3631 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4745 Z= 0.171 Angle : 0.620 8.615 6826 Z= 0.328 Chirality : 0.039 0.236 800 Planarity : 0.005 0.063 547 Dihedral : 25.293 179.487 1619 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.22 % Allowed : 13.70 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.49), residues: 308 helix: 1.02 (0.49), residues: 113 sheet: -1.07 (0.58), residues: 75 loop : -1.51 (0.61), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 404 TYR 0.008 0.001 TYR A 22 PHE 0.016 0.001 PHE A 169 TRP 0.009 0.002 TRP A 229 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 4745) covalent geometry : angle 0.62024 ( 6826) hydrogen bonds : bond 0.04139 ( 165) hydrogen bonds : angle 3.89316 ( 412) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.118 Fit side-chains REVERT: A 102 GLU cc_start: 0.7636 (pm20) cc_final: 0.7411 (pm20) REVERT: A 185 ASP cc_start: 0.7129 (t0) cc_final: 0.6747 (t0) REVERT: A 416 ARG cc_start: 0.7859 (tpt170) cc_final: 0.6987 (tpt170) outliers start: 6 outliers final: 5 residues processed: 56 average time/residue: 0.1268 time to fit residues: 8.2658 Evaluate side-chains 57 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.2980 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 0.0980 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.179536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.143714 restraints weight = 6661.194| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.53 r_work: 0.3619 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4745 Z= 0.204 Angle : 0.649 8.616 6826 Z= 0.342 Chirality : 0.040 0.216 800 Planarity : 0.006 0.064 547 Dihedral : 25.295 177.934 1619 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.85 % Allowed : 16.67 % Favored : 81.48 % 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 aren not related in a simple way. whole: -0.81 (0.50), residues: 308 helix: 1.01 (0.49), residues: 113 sheet: -1.12 (0.59), residues: 76 loop : -1.58 (0.61), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 404 TYR 0.010 0.002 TYR A 22 PHE 0.009 0.002 PHE A 369 TRP 0.006 0.001 TRP A 229 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 4745) covalent geometry : angle 0.64917 ( 6826) hydrogen bonds : bond 0.04441 ( 165) hydrogen bonds : angle 3.93582 ( 412) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.122 Fit side-chains REVERT: A 102 GLU cc_start: 0.7648 (pm20) cc_final: 0.7428 (pm20) REVERT: A 185 ASP cc_start: 0.7166 (t0) cc_final: 0.6793 (t0) REVERT: A 416 ARG cc_start: 0.7951 (tpt170) cc_final: 0.6960 (tpt170) outliers start: 5 outliers final: 4 residues processed: 56 average time/residue: 0.1373 time to fit residues: 8.9197 Evaluate side-chains 57 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.180589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.144922 restraints weight = 6579.069| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.50 r_work: 0.3628 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4745 Z= 0.172 Angle : 0.625 7.707 6826 Z= 0.330 Chirality : 0.039 0.214 800 Planarity : 0.005 0.064 547 Dihedral : 25.233 178.212 1619 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.59 % Allowed : 15.56 % Favored : 81.85 % 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 aren not related in a simple way. whole: -0.73 (0.50), residues: 308 helix: 1.14 (0.49), residues: 113 sheet: -1.19 (0.59), residues: 76 loop : -1.53 (0.60), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 404 TYR 0.009 0.001 TYR A 22 PHE 0.020 0.002 PHE A 169 TRP 0.007 0.002 TRP A 229 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 4745) covalent geometry : angle 0.62488 ( 6826) hydrogen bonds : bond 0.04158 ( 165) hydrogen bonds : angle 3.86470 ( 412) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.127 Fit side-chains REVERT: A 102 GLU cc_start: 0.7638 (pm20) cc_final: 0.7423 (pm20) REVERT: A 167 ARG cc_start: 0.4694 (OUTLIER) cc_final: 0.4292 (mtt180) REVERT: A 185 ASP cc_start: 0.7130 (t0) cc_final: 0.6771 (t0) REVERT: A 190 MET cc_start: 0.7862 (tpp) cc_final: 0.7577 (tpt) REVERT: A 416 ARG cc_start: 0.7903 (tpt170) cc_final: 0.6882 (tpt170) outliers start: 7 outliers final: 4 residues processed: 59 average time/residue: 0.1367 time to fit residues: 9.3023 Evaluate side-chains 58 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 167 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.1980 chunk 29 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.180566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.144785 restraints weight = 6555.285| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.52 r_work: 0.3627 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4745 Z= 0.178 Angle : 0.634 9.172 6826 Z= 0.333 Chirality : 0.039 0.215 800 Planarity : 0.006 0.064 547 Dihedral : 25.220 178.085 1619 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.22 % Allowed : 15.56 % Favored : 82.22 % 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 aren not related in a simple way. whole: -0.75 (0.50), residues: 308 helix: 1.09 (0.49), residues: 113 sheet: -1.20 (0.59), residues: 76 loop : -1.51 (0.61), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 404 TYR 0.009 0.001 TYR A 22 PHE 0.010 0.001 PHE A 169 TRP 0.006 0.001 TRP A 229 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 4745) covalent geometry : angle 0.63433 ( 6826) hydrogen bonds : bond 0.04225 ( 165) hydrogen bonds : angle 3.87617 ( 412) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.119 Fit side-chains REVERT: A 102 GLU cc_start: 0.7635 (pm20) cc_final: 0.7417 (pm20) REVERT: A 167 ARG cc_start: 0.4694 (OUTLIER) cc_final: 0.4301 (mtt180) REVERT: A 185 ASP cc_start: 0.7131 (t0) cc_final: 0.6770 (t0) REVERT: A 190 MET cc_start: 0.7871 (tpp) cc_final: 0.7624 (tpt) REVERT: A 416 ARG cc_start: 0.7915 (tpt170) cc_final: 0.6814 (tpt170) outliers start: 6 outliers final: 5 residues processed: 55 average time/residue: 0.1378 time to fit residues: 8.7606 Evaluate side-chains 56 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 430 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 17 optimal weight: 0.0270 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.180762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.144948 restraints weight = 6561.181| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.50 r_work: 0.3629 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4745 Z= 0.170 Angle : 0.625 8.643 6826 Z= 0.328 Chirality : 0.039 0.213 800 Planarity : 0.006 0.064 547 Dihedral : 25.201 178.089 1619 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.85 % Allowed : 16.30 % Favored : 81.85 % 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 aren not related in a simple way. whole: -0.68 (0.50), residues: 308 helix: 1.20 (0.49), residues: 113 sheet: -1.21 (0.59), residues: 76 loop : -1.48 (0.61), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 404 TYR 0.009 0.001 TYR A 22 PHE 0.011 0.001 PHE A 169 TRP 0.006 0.001 TRP A 229 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 4745) covalent geometry : angle 0.62454 ( 6826) hydrogen bonds : bond 0.04159 ( 165) hydrogen bonds : angle 3.85143 ( 412) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.117 Fit side-chains REVERT: A 102 GLU cc_start: 0.7638 (pm20) cc_final: 0.7429 (pm20) REVERT: A 167 ARG cc_start: 0.4706 (OUTLIER) cc_final: 0.4309 (mtt180) REVERT: A 185 ASP cc_start: 0.7140 (t0) cc_final: 0.6779 (t0) REVERT: A 190 MET cc_start: 0.7858 (tpp) cc_final: 0.7610 (tpt) REVERT: A 416 ARG cc_start: 0.7902 (tpt170) cc_final: 0.6813 (tpt170) outliers start: 5 outliers final: 4 residues processed: 55 average time/residue: 0.1397 time to fit residues: 8.8674 Evaluate side-chains 55 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 167 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 0.0370 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 21 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.3258 ------------------------------------------------------------------------------- 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 = 0.4235 r_free = 0.4235 target = 0.181575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.145852 restraints weight = 6543.335| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.51 r_work: 0.3644 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4745 Z= 0.141 Angle : 0.616 8.751 6826 Z= 0.323 Chirality : 0.038 0.209 800 Planarity : 0.005 0.063 547 Dihedral : 25.174 178.449 1619 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.85 % Allowed : 16.67 % Favored : 81.48 % 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 aren not related in a simple way. whole: -0.63 (0.50), residues: 308 helix: 1.28 (0.49), residues: 113 sheet: -1.23 (0.59), residues: 76 loop : -1.45 (0.61), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 404 TYR 0.006 0.001 TYR A 22 PHE 0.008 0.001 PHE A 369 TRP 0.008 0.001 TRP A 229 HIS 0.001 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 4745) covalent geometry : angle 0.61621 ( 6826) hydrogen bonds : bond 0.04024 ( 165) hydrogen bonds : angle 3.80710 ( 412) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.131 Fit side-chains REVERT: A 102 GLU cc_start: 0.7631 (pm20) cc_final: 0.7425 (pm20) REVERT: A 185 ASP cc_start: 0.7146 (t0) cc_final: 0.6798 (t0) REVERT: A 190 MET cc_start: 0.7845 (tpp) cc_final: 0.7600 (tpt) REVERT: A 416 ARG cc_start: 0.7855 (tpt170) cc_final: 0.6788 (tpt170) outliers start: 5 outliers final: 4 residues processed: 54 average time/residue: 0.1224 time to fit residues: 7.7715 Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.1980 chunk 8 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 0.0050 chunk 24 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 overall best weight: 0.3394 ------------------------------------------------------------------------------- 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 = 0.4243 r_free = 0.4243 target = 0.182193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.146382 restraints weight = 6586.859| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.50 r_work: 0.3653 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4745 Z= 0.144 Angle : 0.610 9.139 6826 Z= 0.320 Chirality : 0.037 0.208 800 Planarity : 0.005 0.064 547 Dihedral : 25.133 178.437 1619 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.48 % Allowed : 16.67 % Favored : 81.85 % 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 aren not related in a simple way. whole: -0.55 (0.50), residues: 308 helix: 1.40 (0.49), residues: 113 sheet: -1.23 (0.59), residues: 76 loop : -1.45 (0.61), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 404 TYR 0.007 0.001 TYR A 22 PHE 0.008 0.001 PHE A 369 TRP 0.007 0.001 TRP A 229 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 4745) covalent geometry : angle 0.61015 ( 6826) hydrogen bonds : bond 0.03989 ( 165) hydrogen bonds : angle 3.77474 ( 412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1650.12 seconds wall clock time: 28 minutes 58.08 seconds (1738.08 seconds total)