Starting phenix.real_space_refine on Tue Aug 4 16:17:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wb4_65833/08_2026/9wb4_65833.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wb4_65833/08_2026/9wb4_65833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wb4_65833/08_2026/9wb4_65833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wb4_65833/08_2026/9wb4_65833.map" model { file = "/net/cci-nas-00/data/ceres_data/9wb4_65833/08_2026/9wb4_65833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wb4_65833/08_2026/9wb4_65833.cif" } resolution = 3.32 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= 0.011 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 75 5.49 5 S 15 5.16 5 C 2678 2.51 5 N 812 2.21 5 O 1142 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: 4722 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1382 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain: "B" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 973 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain: "C" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 780 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "R" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1587 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 36} Link IDs: {'rna2p': 8, 'rna3p': 66} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.12, per 1000 atoms: 0.24 Number of scatterers: 4722 At special positions: 0 Unit cell: (88.32, 73.92, 132.48, 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 15 16.00 P 75 15.00 O 1142 8.00 N 812 7.00 C 2678 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: 0.24 Conformation dependent library (CDL) restraints added in 86.1 milliseconds 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 730 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 11.4% alpha, 47.7% beta 25 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 3 through 14 Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.685A pdb=" N ILE A 90 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.775A pdb=" N GLN A 145 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS A 146 " --> pdb=" O THR A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.558A pdb=" N TYR A 177 " --> pdb=" O LYS A 174 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 178 " --> pdb=" O LYS A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 178' Processing helix chain 'B' and resid 30 through 34 removed outlier: 3.622A pdb=" N SER B 33 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR B 34 " --> pdb=" O PHE B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 34' Processing helix chain 'C' and resid 26 through 30 removed outlier: 3.643A pdb=" N ASP C 29 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.798A pdb=" N ASP C 81 " --> pdb=" O GLN C 78 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU C 82 " --> pdb=" O ALA C 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 78 through 82' Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 20 removed outlier: 3.519A pdb=" N LEU A 28 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A 34 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU A 72 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP A 58 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP A 78 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 56 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 126 removed outlier: 6.980A pdb=" N MET A 120 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE A 135 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY A 122 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 133 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ARG A 133 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ALA A 171 " --> pdb=" O HIS A 160 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N HIS A 160 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU A 150 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA A 99 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 115 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER A 105 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 10 Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.098A pdb=" N ARG B 40 " --> pdb=" O TRP B 49 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N TRP B 49 " --> pdb=" O ARG B 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 13 through 14 removed outlier: 4.339A pdb=" N VAL B 117 " --> pdb=" O ARG B 100 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 9 through 11 removed outlier: 3.596A pdb=" N THR C 104 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 17 through 23 Processing sheet with id=AA8, first strand: chain 'C' and resid 44 through 47 removed outlier: 6.848A pdb=" N TRP C 34 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR C 94 " --> pdb=" O ASP C 91 " (cutoff:3.500A) 126 hydrogen bonds defined for protein. 315 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 0.46 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1206 1.33 - 1.45: 1328 1.45 - 1.57: 2262 1.57 - 1.69: 148 1.69 - 1.81: 22 Bond restraints: 4966 Sorted by residual: bond pdb=" CA ARG A 84 " pdb=" C ARG A 84 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.24e-02 6.50e+03 1.17e+01 bond pdb=" P A R 13 " pdb=" O5' A R 13 " ideal model delta sigma weight residual 1.593 1.620 -0.027 1.00e-02 1.00e+04 7.37e+00 bond pdb=" O3' U R 60 " pdb=" P G R 61 " ideal model delta sigma weight residual 1.607 1.579 0.028 1.20e-02 6.94e+03 5.48e+00 bond pdb=" P G R 12 " pdb=" O5' G R 12 " ideal model delta sigma weight residual 1.593 1.616 -0.023 1.00e-02 1.00e+04 5.31e+00 bond pdb=" P A R 13 " pdb=" OP2 A R 13 " ideal model delta sigma weight residual 1.485 1.527 -0.042 2.00e-02 2.50e+03 4.45e+00 ... (remaining 4961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 6674 1.71 - 3.41: 352 3.41 - 5.12: 37 5.12 - 6.83: 14 6.83 - 8.54: 2 Bond angle restraints: 7079 Sorted by residual: angle pdb=" CA THR C 104 " pdb=" C THR C 104 " pdb=" O THR C 104 " ideal model delta sigma weight residual 120.36 124.63 -4.27 1.08e+00 8.57e-01 1.56e+01 angle pdb=" C3' U R 14 " pdb=" O3' U R 14 " pdb=" P G R 15 " ideal model delta sigma weight residual 119.70 124.29 -4.59 1.20e+00 6.94e-01 1.46e+01 angle pdb=" C1' C R 57 " pdb=" N1 C R 57 " pdb=" C2 C R 57 " ideal model delta sigma weight residual 118.80 122.61 -3.81 1.10e+00 8.26e-01 1.20e+01 angle pdb=" C2' A R 56 " pdb=" C1' A R 56 " pdb=" N9 A R 56 " ideal model delta sigma weight residual 112.00 115.35 -3.35 1.10e+00 8.26e-01 9.30e+00 angle pdb=" C2' G R 53 " pdb=" C1' G R 53 " pdb=" N9 G R 53 " ideal model delta sigma weight residual 112.00 115.29 -3.29 1.10e+00 8.26e-01 8.94e+00 ... (remaining 7074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.95: 2660 22.95 - 45.90: 236 45.90 - 68.84: 139 68.84 - 91.79: 22 91.79 - 114.74: 1 Dihedral angle restraints: 3058 sinusoidal: 1901 harmonic: 1157 Sorted by residual: dihedral pdb=" O4' A R 59 " pdb=" C1' A R 59 " pdb=" N9 A R 59 " pdb=" C4 A R 59 " ideal model delta sinusoidal sigma weight residual 254.00 178.29 75.71 1 1.70e+01 3.46e-03 2.50e+01 dihedral pdb=" O4' U R 60 " pdb=" C1' U R 60 " pdb=" N1 U R 60 " pdb=" C2 U R 60 " ideal model delta sinusoidal sigma weight residual 232.00 178.74 53.26 1 1.70e+01 3.46e-03 1.33e+01 dihedral pdb=" O4' A R 4 " pdb=" C1' A R 4 " pdb=" N9 A R 4 " pdb=" C4 A R 4 " ideal model delta sinusoidal sigma weight residual -106.00 -154.62 48.62 1 1.70e+01 3.46e-03 1.13e+01 ... (remaining 3055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 685 0.101 - 0.203: 161 0.203 - 0.304: 2 0.304 - 0.406: 4 0.406 - 0.507: 5 Chirality restraints: 857 Sorted by residual: chirality pdb=" P C R 82 " pdb=" OP1 C R 82 " pdb=" OP2 C R 82 " pdb=" O5' C R 82 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.43e+00 chirality pdb=" P A R 4 " pdb=" OP1 A R 4 " pdb=" OP2 A R 4 " pdb=" O5' A R 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" P C R 25 " pdb=" OP1 C R 25 " pdb=" OP2 C R 25 " pdb=" O5' C R 25 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.79e+00 ... (remaining 854 not shown) Planarity restraints: 632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 83 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C PHE A 83 " -0.066 2.00e-02 2.50e+03 pdb=" O PHE A 83 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG A 84 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 7 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO C 8 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 8 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 8 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 71 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C GLU A 71 " -0.030 2.00e-02 2.50e+03 pdb=" O GLU A 71 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 72 " 0.010 2.00e-02 2.50e+03 ... (remaining 629 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 740 2.76 - 3.30: 3870 3.30 - 3.83: 7900 3.83 - 4.37: 9545 4.37 - 4.90: 15180 Nonbonded interactions: 37235 Sorted by model distance: nonbonded pdb=" O2' U R 14 " pdb=" OP1 G R 15 " model vdw 2.227 3.040 nonbonded pdb=" OP2 C R 10 " pdb=" O2' U R 42 " model vdw 2.342 3.040 nonbonded pdb=" OH TYR C 2 " pdb=" O ASP C 25 " model vdw 2.344 3.040 nonbonded pdb=" N6 A R 36 " pdb=" O2 C R 51 " model vdw 2.366 3.120 nonbonded pdb=" NH1 ARG B 69 " pdb=" O SER B 87 " model vdw 2.371 3.120 ... (remaining 37230 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: 1.390 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.000 Process input model: 5.170 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3160 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 0.042 4966 Z= 0.394 Angle : 0.829 8.537 7079 Z= 0.519 Chirality : 0.083 0.507 857 Planarity : 0.005 0.064 632 Dihedral : 20.317 114.738 2328 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 14.87 % Favored : 85.13 % 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: 0.16 (0.43), residues: 405 helix: 1.97 (1.78), residues: 11 sheet: 1.08 (0.40), residues: 182 loop : -0.90 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 84 TYR 0.011 0.001 TYR B 97 PHE 0.011 0.001 PHE B 70 TRP 0.012 0.001 TRP C 90 HIS 0.002 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.39 ( 4966) covalent geometry : angle 0.82859 / 0.52 ( 7079) hydrogen bonds : bond 0.14654 / 9.14 ( 185) hydrogen bonds : angle 5.01367 / 3.52 ( 435) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.120 Fit side-chains REVERT: A 3 ASN cc_start: 0.5758 (m-40) cc_final: 0.5455 (m-40) REVERT: A 13 LYS cc_start: 0.7532 (mttt) cc_final: 0.7309 (mttt) REVERT: B 115 MET cc_start: -0.0195 (mtm) cc_final: -0.0441 (mtm) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1053 time to fit residues: 2.3080 Evaluate side-chains 17 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 30.0000 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 0.0060 chunk 16 optimal weight: 30.0000 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 40.0000 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 30.0000 chunk 22 optimal weight: 9.9990 chunk 37 optimal weight: 40.0000 overall best weight: 5.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 HIS ** 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 = 0.5069 r_free = 0.5069 target = 0.282155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.259066 restraints weight = 9556.487| |-----------------------------------------------------------------------------| r_work (start): 0.4792 rms_B_bonded: 2.79 r_work: 0.4453 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5520 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.351 4966 Z= 0.921 Angle : 2.066 32.458 7079 Z= 0.970 Chirality : 0.118 0.510 857 Planarity : 0.012 0.124 632 Dihedral : 23.038 146.956 1622 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.33 % Allowed : 15.74 % Favored : 81.92 % Cbeta Deviations : 0.82 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -0.28 (0.41), residues: 405 helix: -0.88 (1.15), residues: 12 sheet: 1.30 (0.41), residues: 167 loop : -1.40 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.002 ARG A 87 TYR 0.008 0.001 TYR B 82 PHE 0.058 0.007 PHE A 83 TRP 0.013 0.001 TRP C 90 HIS 0.035 0.005 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.01816 / 0.92 ( 4966) covalent geometry : angle 2.06631 / 0.97 ( 7079) hydrogen bonds : bond 0.19985 / 12.27 ( 185) hydrogen bonds : angle 6.07674 / 4.28 ( 435) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 14 time to evaluate : 0.079 Fit side-chains REVERT: A 174 LYS cc_start: -0.0473 (OUTLIER) cc_final: -0.0731 (mtpt) outliers start: 8 outliers final: 3 residues processed: 21 average time/residue: 0.0997 time to fit residues: 2.6782 Evaluate side-chains 18 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain B residue 85 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 32 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 50.0000 chunk 18 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5094 r_free = 0.5094 target = 0.286783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.259147 restraints weight = 10309.607| |-----------------------------------------------------------------------------| r_work (start): 0.4801 rms_B_bonded: 2.33 r_work: 0.4539 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5382 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.220 4966 Z= 0.396 Angle : 1.057 12.851 7079 Z= 0.541 Chirality : 0.067 0.424 857 Planarity : 0.007 0.102 632 Dihedral : 22.097 129.115 1622 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.75 % Allowed : 16.33 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -0.05 (0.41), residues: 405 helix: 0.66 (1.54), residues: 11 sheet: 1.39 (0.41), residues: 162 loop : -1.21 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 87 TYR 0.011 0.001 TYR A 60 PHE 0.035 0.003 PHE A 83 TRP 0.010 0.001 TRP C 90 HIS 0.007 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00823 / 0.40 ( 4966) covalent geometry : angle 1.05651 / 0.54 ( 7079) hydrogen bonds : bond 0.11193 / 7.27 ( 185) hydrogen bonds : angle 4.85929 / 3.48 ( 435) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 15 time to evaluate : 0.074 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 20 average time/residue: 0.0724 time to fit residues: 1.9105 Evaluate side-chains 18 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 159 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 28 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 0 optimal weight: 0.0970 chunk 14 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 chunk 38 optimal weight: 50.0000 chunk 33 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 5 optimal weight: 0.3980 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 overall best weight: 5.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4987 r_free = 0.4987 target = 0.273797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.231155 restraints weight = 9141.810| |-----------------------------------------------------------------------------| r_work (start): 0.4545 rms_B_bonded: 4.29 r_work (final): 0.4545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5274 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.482 4966 Z= 0.921 Angle : 1.968 33.124 7079 Z= 0.924 Chirality : 0.116 0.627 857 Planarity : 0.017 0.347 632 Dihedral : 24.003 113.371 1622 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.79 % Allowed : 14.87 % Favored : 81.34 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % 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: -0.22 (0.41), residues: 405 helix: -0.94 (1.55), residues: 11 sheet: 1.21 (0.41), residues: 169 loop : -1.25 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 87 TYR 0.012 0.001 TYR A 60 PHE 0.044 0.004 PHE A 83 TRP 0.013 0.002 TRP B 118 HIS 0.031 0.005 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.01934 / 0.92 ( 4966) covalent geometry : angle 1.96753 / 0.92 ( 7079) hydrogen bonds : bond 0.22715 / 15.18 ( 185) hydrogen bonds : angle 5.97759 / 4.19 ( 435) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 13 time to evaluate : 0.076 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 24 average time/residue: 0.0702 time to fit residues: 2.1689 Evaluate side-chains 21 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 13 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 94 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 2 optimal weight: 0.0980 chunk 20 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 44 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 40.0000 overall best weight: 3.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 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 = 0.5007 r_free = 0.5007 target = 0.278298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.248967 restraints weight = 9465.045| |-----------------------------------------------------------------------------| r_work (start): 0.4700 rms_B_bonded: 2.61 r_work: 0.4396 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5661 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.348 4966 Z= 0.558 Angle : 1.305 18.063 7079 Z= 0.648 Chirality : 0.080 0.447 857 Planarity : 0.010 0.177 632 Dihedral : 23.201 141.165 1622 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.50 % Allowed : 15.74 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -0.11 (0.42), residues: 405 helix: -0.90 (1.49), residues: 11 sheet: 1.42 (0.42), residues: 160 loop : -1.20 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 87 TYR 0.012 0.001 TYR A 60 PHE 0.029 0.003 PHE A 178 TRP 0.009 0.001 TRP C 90 HIS 0.008 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.01174 / 0.56 ( 4966) covalent geometry : angle 1.30507 / 0.65 ( 7079) hydrogen bonds : bond 0.14438 / 9.66 ( 185) hydrogen bonds : angle 4.99147 / 3.60 ( 435) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 13 time to evaluate : 0.106 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 25 average time/residue: 0.1005 time to fit residues: 3.1788 Evaluate side-chains 22 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 13 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain C residue 94 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 0.0970 chunk 14 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 2 optimal weight: 0.0970 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 40.0000 overall best weight: 1.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5041 r_free = 0.5041 target = 0.282576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.251339 restraints weight = 9664.558| |-----------------------------------------------------------------------------| r_work (start): 0.4725 rms_B_bonded: 2.52 r_work: 0.4461 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5572 moved from start: 0.5910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.168 4966 Z= 0.303 Angle : 0.866 10.680 7079 Z= 0.474 Chirality : 0.057 0.394 857 Planarity : 0.006 0.052 632 Dihedral : 22.648 146.024 1622 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.62 % Allowed : 17.20 % Favored : 80.17 % 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: 0.21 (0.43), residues: 405 helix: 0.17 (1.54), residues: 11 sheet: 1.29 (0.41), residues: 174 loop : -0.87 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 87 TYR 0.012 0.001 TYR A 60 PHE 0.020 0.002 PHE A 178 TRP 0.008 0.001 TRP C 90 HIS 0.013 0.002 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.30 ( 4966) covalent geometry : angle 0.86567 / 0.47 ( 7079) hydrogen bonds : bond 0.10433 / 6.94 ( 185) hydrogen bonds : angle 4.49730 / 3.27 ( 435) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 14 time to evaluate : 0.091 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 23 average time/residue: 0.0750 time to fit residues: 2.3076 Evaluate side-chains 22 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 14 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain C residue 94 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 30.0000 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 0 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5012 r_free = 0.5012 target = 0.278977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.229361 restraints weight = 9381.697| |-----------------------------------------------------------------------------| r_work (start): 0.4469 rms_B_bonded: 5.77 r_work: 0.4246 rms_B_bonded: 5.06 restraints_weight: 2.0000 r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5940 moved from start: 0.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.268 4966 Z= 0.510 Angle : 1.194 17.519 7079 Z= 0.603 Chirality : 0.076 0.410 857 Planarity : 0.006 0.045 632 Dihedral : 23.241 142.377 1622 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.37 % Allowed : 15.45 % Favored : 80.17 % 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: 0.13 (0.43), residues: 405 helix: -0.22 (1.52), residues: 11 sheet: 1.47 (0.43), residues: 160 loop : -0.96 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 87 TYR 0.013 0.001 TYR A 60 PHE 0.024 0.003 PHE A 178 TRP 0.008 0.001 TRP C 90 HIS 0.018 0.003 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.01046 / 0.51 ( 4966) covalent geometry : angle 1.19367 / 0.60 ( 7079) hydrogen bonds : bond 0.14861 / 9.85 ( 185) hydrogen bonds : angle 4.94334 / 3.59 ( 435) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 14 time to evaluate : 0.129 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 13 residues processed: 28 average time/residue: 0.1065 time to fit residues: 3.7054 Evaluate side-chains 27 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 14 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 94 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 3 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 50.0000 chunk 33 optimal weight: 40.0000 chunk 6 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 50.0000 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5028 r_free = 0.5028 target = 0.281075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.232725 restraints weight = 9500.326| |-----------------------------------------------------------------------------| r_work (start): 0.4486 rms_B_bonded: 6.21 r_work: 0.4232 rms_B_bonded: 5.79 restraints_weight: 2.0000 r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5948 moved from start: 0.6439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.238 4966 Z= 0.392 Angle : 0.994 13.527 7079 Z= 0.519 Chirality : 0.063 0.392 857 Planarity : 0.006 0.045 632 Dihedral : 22.988 145.932 1622 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.66 % Allowed : 15.45 % Favored : 79.88 % 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: 0.29 (0.43), residues: 405 helix: 0.04 (1.55), residues: 11 sheet: 1.40 (0.42), residues: 170 loop : -0.80 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 87 TYR 0.013 0.001 TYR A 60 PHE 0.014 0.002 PHE A 6 TRP 0.007 0.001 TRP C 90 HIS 0.018 0.003 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00812 / 0.39 ( 4966) covalent geometry : angle 0.99418 / 0.52 ( 7079) hydrogen bonds : bond 0.11652 / 7.81 ( 185) hydrogen bonds : angle 4.67981 / 3.41 ( 435) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 14 time to evaluate : 0.131 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 14 residues processed: 29 average time/residue: 0.0944 time to fit residues: 3.4452 Evaluate side-chains 28 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 14 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 94 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 14 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.273472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.219259 restraints weight = 8905.086| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 5.84 r_work (final): 0.4403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5702 moved from start: 0.6907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.407 4966 Z= 0.895 Angle : 1.924 28.181 7079 Z= 0.885 Chirality : 0.109 0.702 857 Planarity : 0.009 0.053 632 Dihedral : 24.147 139.231 1622 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 4.96 % Allowed : 14.87 % Favored : 80.17 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % 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: 0.13 (0.43), residues: 405 helix: -1.68 (1.40), residues: 11 sheet: 1.51 (0.44), residues: 159 loop : -0.90 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG A 87 TYR 0.017 0.001 TYR A 60 PHE 0.045 0.004 PHE A 178 TRP 0.010 0.001 TRP C 90 HIS 0.026 0.004 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.01827 / 0.89 ( 4966) covalent geometry : angle 1.92439 / 0.88 ( 7079) hydrogen bonds : bond 0.21916 / 14.64 ( 185) hydrogen bonds : angle 5.88663 / 4.21 ( 435) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 12 time to evaluate : 0.075 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 28 average time/residue: 0.0891 time to fit residues: 3.0274 Evaluate side-chains 25 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 12 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 34 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 35 optimal weight: 40.0000 chunk 28 optimal weight: 20.0000 chunk 44 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 40.0000 chunk 20 optimal weight: 50.0000 chunk 30 optimal weight: 30.0000 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.277714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.230237 restraints weight = 9285.643| |-----------------------------------------------------------------------------| r_work (start): 0.4455 rms_B_bonded: 5.60 r_work (final): 0.4455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5607 moved from start: 0.6915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.324 4966 Z= 0.567 Angle : 1.334 17.892 7079 Z= 0.656 Chirality : 0.079 0.480 857 Planarity : 0.007 0.049 632 Dihedral : 23.626 141.740 1622 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.50 % Allowed : 15.74 % Favored : 80.76 % 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: 0.16 (0.43), residues: 405 helix: -0.76 (1.48), residues: 11 sheet: 1.47 (0.43), residues: 161 loop : -0.90 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 87 TYR 0.014 0.001 TYR A 60 PHE 0.021 0.003 PHE A 178 TRP 0.007 0.001 TRP C 90 HIS 0.021 0.003 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.01176 / 0.57 ( 4966) covalent geometry : angle 1.33423 / 0.66 ( 7079) hydrogen bonds : bond 0.16373 / 11.04 ( 185) hydrogen bonds : angle 5.19930 / 3.75 ( 435) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 14 time to evaluate : 0.124 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 12 residues processed: 25 average time/residue: 0.1032 time to fit residues: 3.2364 Evaluate side-chains 26 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 14 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 50.0000 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 25 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 2 optimal weight: 0.0980 chunk 41 optimal weight: 3.9990 chunk 0 optimal weight: 0.0980 chunk 18 optimal weight: 30.0000 chunk 29 optimal weight: 0.1980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 14 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 = 0.5042 r_free = 0.5042 target = 0.282742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.230573 restraints weight = 9516.768| |-----------------------------------------------------------------------------| r_work (start): 0.4495 rms_B_bonded: 6.99 r_work: 0.4308 rms_B_bonded: 5.45 restraints_weight: 2.0000 r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5849 moved from start: 0.6824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 4966 Z= 0.216 Angle : 0.758 9.186 7079 Z= 0.432 Chirality : 0.052 0.376 857 Planarity : 0.005 0.044 632 Dihedral : 22.657 146.999 1622 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.92 % Allowed : 16.62 % Favored : 80.47 % 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: 0.36 (0.43), residues: 405 helix: 0.52 (1.54), residues: 11 sheet: 1.35 (0.42), residues: 174 loop : -0.73 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 87 TYR 0.013 0.001 TYR A 177 PHE 0.016 0.001 PHE A 6 TRP 0.006 0.001 TRP C 90 HIS 0.007 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.22 ( 4966) covalent geometry : angle 0.75850 / 0.43 ( 7079) hydrogen bonds : bond 0.10451 / 7.00 ( 185) hydrogen bonds : angle 4.55022 / 3.34 ( 435) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1439.81 seconds wall clock time: 25 minutes 17.48 seconds (1517.48 seconds total)