Starting phenix.real_space_refine on Fri Dec 27 14:57:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a03_15046/12_2024/8a03_15046.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a03_15046/12_2024/8a03_15046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a03_15046/12_2024/8a03_15046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a03_15046/12_2024/8a03_15046.map" model { file = "/net/cci-nas-00/data/ceres_data/8a03_15046/12_2024/8a03_15046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a03_15046/12_2024/8a03_15046.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 3495 2.51 5 N 885 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5511 Number of models: 1 Model: "" Number of chains: 1 Chain: "K" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Restraints were copied for chains: J, L Time building chain proxies: 3.31, per 1000 atoms: 0.60 Number of scatterers: 5511 At special positions: 0 Unit cell: (96.72, 101.68, 57.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 1116 8.00 N 885 7.00 C 3495 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: 1.42 Conformation dependent library (CDL) restraints added in 658.3 milliseconds 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 18 sheets defined 10.5% alpha, 38.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'L' and resid 31 through 35 Processing helix chain 'L' and resid 60 through 66 Processing helix chain 'L' and resid 178 through 190 removed outlier: 3.686A pdb=" N ILE L 189 " --> pdb=" O LEU L 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 31 through 35 Processing helix chain 'K' and resid 60 through 66 Processing helix chain 'K' and resid 178 through 190 removed outlier: 3.687A pdb=" N ILE K 189 " --> pdb=" O LEU K 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 35 Processing helix chain 'J' and resid 60 through 66 Processing helix chain 'J' and resid 178 through 190 removed outlier: 3.686A pdb=" N ILE J 189 " --> pdb=" O LEU J 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 2 through 7 removed outlier: 5.738A pdb=" N LYS L 2 " --> pdb=" O GLY L 119 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY L 119 " --> pdb=" O LYS L 2 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA L 4 " --> pdb=" O LEU L 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 15 through 17 removed outlier: 7.221A pdb=" N ILE L 40 " --> pdb=" O ASN L 56 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASN L 56 " --> pdb=" O ILE L 40 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE L 42 " --> pdb=" O LEU L 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 93 through 94 removed outlier: 5.139A pdb=" N SER L 93 " --> pdb=" O THR L 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'L' and resid 128 through 137 removed outlier: 5.323A pdb=" N ASN L 230 " --> pdb=" O THR L 157 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG L 234 " --> pdb=" O LEU L 153 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU L 153 " --> pdb=" O ARG L 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 143 through 147 removed outlier: 6.679A pdb=" N GLN L 168 " --> pdb=" O VAL L 217 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE L 219 " --> pdb=" O SER L 166 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER L 166 " --> pdb=" O ILE L 219 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE L 221 " --> pdb=" O ASP L 164 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP L 164 " --> pdb=" O ILE L 221 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS L 223 " --> pdb=" O VAL L 162 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL L 162 " --> pdb=" O LYS L 223 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL L 175 " --> pdb=" O TYR L 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 194 through 195 Processing sheet with id=AA7, first strand: chain 'K' and resid 2 through 7 removed outlier: 5.738A pdb=" N LYS K 2 " --> pdb=" O GLY K 119 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY K 119 " --> pdb=" O LYS K 2 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA K 4 " --> pdb=" O LEU K 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 15 through 17 removed outlier: 7.220A pdb=" N ILE K 40 " --> pdb=" O ASN K 56 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASN K 56 " --> pdb=" O ILE K 40 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE K 42 " --> pdb=" O LEU K 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 93 through 94 removed outlier: 5.137A pdb=" N SER K 93 " --> pdb=" O THR K 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 128 through 137 removed outlier: 5.323A pdb=" N ASN K 230 " --> pdb=" O THR K 157 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG K 234 " --> pdb=" O LEU K 153 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU K 153 " --> pdb=" O ARG K 234 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 143 through 147 removed outlier: 6.679A pdb=" N GLN K 168 " --> pdb=" O VAL K 217 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE K 219 " --> pdb=" O SER K 166 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER K 166 " --> pdb=" O ILE K 219 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE K 221 " --> pdb=" O ASP K 164 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP K 164 " --> pdb=" O ILE K 221 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS K 223 " --> pdb=" O VAL K 162 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL K 162 " --> pdb=" O LYS K 223 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL K 175 " --> pdb=" O TYR K 167 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 194 through 195 Processing sheet with id=AB4, first strand: chain 'J' and resid 2 through 7 removed outlier: 5.738A pdb=" N LYS J 2 " --> pdb=" O GLY J 119 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY J 119 " --> pdb=" O LYS J 2 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA J 4 " --> pdb=" O LEU J 117 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 15 through 17 removed outlier: 7.220A pdb=" N ILE J 40 " --> pdb=" O ASN J 56 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASN J 56 " --> pdb=" O ILE J 40 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE J 42 " --> pdb=" O LEU J 54 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 93 through 94 removed outlier: 5.138A pdb=" N SER J 93 " --> pdb=" O THR J 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'J' and resid 128 through 137 removed outlier: 5.323A pdb=" N ASN J 230 " --> pdb=" O THR J 157 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG J 234 " --> pdb=" O LEU J 153 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU J 153 " --> pdb=" O ARG J 234 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 143 through 147 removed outlier: 6.678A pdb=" N GLN J 168 " --> pdb=" O VAL J 217 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE J 219 " --> pdb=" O SER J 166 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER J 166 " --> pdb=" O ILE J 219 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE J 221 " --> pdb=" O ASP J 164 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP J 164 " --> pdb=" O ILE J 221 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS J 223 " --> pdb=" O VAL J 162 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL J 162 " --> pdb=" O LYS J 223 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL J 175 " --> pdb=" O TYR J 167 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 194 through 195 210 hydrogen bonds defined for protein. 540 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1818 1.34 - 1.46: 1003 1.46 - 1.57: 2726 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 5571 Sorted by residual: bond pdb=" C VAL K 148 " pdb=" O VAL K 148 " ideal model delta sigma weight residual 1.236 1.226 0.011 1.19e-02 7.06e+03 7.90e-01 bond pdb=" C VAL L 148 " pdb=" O VAL L 148 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 7.73e-01 bond pdb=" C VAL J 148 " pdb=" O VAL J 148 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 7.54e-01 bond pdb=" CG LEU K 117 " pdb=" CD2 LEU K 117 " ideal model delta sigma weight residual 1.521 1.503 0.018 3.30e-02 9.18e+02 2.81e-01 bond pdb=" CG LEU J 117 " pdb=" CD2 LEU J 117 " ideal model delta sigma weight residual 1.521 1.504 0.017 3.30e-02 9.18e+02 2.80e-01 ... (remaining 5566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 7232 0.91 - 1.81: 242 1.81 - 2.72: 48 2.72 - 3.63: 23 3.63 - 4.53: 3 Bond angle restraints: 7548 Sorted by residual: angle pdb=" C LEU L 26 " pdb=" N SER L 27 " pdb=" CA SER L 27 " ideal model delta sigma weight residual 122.73 120.05 2.68 1.62e+00 3.81e-01 2.73e+00 angle pdb=" C LEU J 26 " pdb=" N SER J 27 " pdb=" CA SER J 27 " ideal model delta sigma weight residual 122.73 120.08 2.65 1.62e+00 3.81e-01 2.69e+00 angle pdb=" C LEU K 26 " pdb=" N SER K 27 " pdb=" CA SER K 27 " ideal model delta sigma weight residual 122.73 120.11 2.62 1.62e+00 3.81e-01 2.61e+00 angle pdb=" CA LEU K 26 " pdb=" CB LEU K 26 " pdb=" CG LEU K 26 " ideal model delta sigma weight residual 116.30 120.83 -4.53 3.50e+00 8.16e-02 1.68e+00 angle pdb=" CA LEU L 26 " pdb=" CB LEU L 26 " pdb=" CG LEU L 26 " ideal model delta sigma weight residual 116.30 120.81 -4.51 3.50e+00 8.16e-02 1.66e+00 ... (remaining 7543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3108 17.97 - 35.94: 246 35.94 - 53.91: 45 53.91 - 71.87: 18 71.87 - 89.84: 3 Dihedral angle restraints: 3420 sinusoidal: 1329 harmonic: 2091 Sorted by residual: dihedral pdb=" CA GLN J 75 " pdb=" CB GLN J 75 " pdb=" CG GLN J 75 " pdb=" CD GLN J 75 " ideal model delta sinusoidal sigma weight residual -60.00 -106.76 46.76 3 1.50e+01 4.44e-03 8.39e+00 dihedral pdb=" CA GLN L 75 " pdb=" CB GLN L 75 " pdb=" CG GLN L 75 " pdb=" CD GLN L 75 " ideal model delta sinusoidal sigma weight residual -60.00 -106.73 46.73 3 1.50e+01 4.44e-03 8.38e+00 dihedral pdb=" CA GLN K 75 " pdb=" CB GLN K 75 " pdb=" CG GLN K 75 " pdb=" CD GLN K 75 " ideal model delta sinusoidal sigma weight residual -60.00 -106.68 46.68 3 1.50e+01 4.44e-03 8.37e+00 ... (remaining 3417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 593 0.027 - 0.054: 173 0.054 - 0.081: 59 0.081 - 0.108: 76 0.108 - 0.135: 35 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA ILE K 42 " pdb=" N ILE K 42 " pdb=" C ILE K 42 " pdb=" CB ILE K 42 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE J 42 " pdb=" N ILE J 42 " pdb=" C ILE J 42 " pdb=" CB ILE J 42 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE L 42 " pdb=" N ILE L 42 " pdb=" C ILE L 42 " pdb=" CB ILE L 42 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 933 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU J 178 " 0.015 5.00e-02 4.00e+02 2.20e-02 7.77e-01 pdb=" N PRO J 179 " -0.038 5.00e-02 4.00e+02 pdb=" CA PRO J 179 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO J 179 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU K 178 " 0.014 5.00e-02 4.00e+02 2.18e-02 7.62e-01 pdb=" N PRO K 179 " -0.038 5.00e-02 4.00e+02 pdb=" CA PRO K 179 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO K 179 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU L 178 " -0.014 5.00e-02 4.00e+02 2.18e-02 7.60e-01 pdb=" N PRO L 179 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO L 179 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO L 179 " -0.012 5.00e-02 4.00e+02 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 2046 2.90 - 3.40: 4445 3.40 - 3.90: 8664 3.90 - 4.40: 9263 4.40 - 4.90: 17482 Nonbonded interactions: 41900 Sorted by model distance: nonbonded pdb=" N GLY J 22 " pdb=" O ILE J 120 " model vdw 2.399 3.120 nonbonded pdb=" N GLY L 22 " pdb=" O ILE L 120 " model vdw 2.399 3.120 nonbonded pdb=" N GLY K 22 " pdb=" O ILE K 120 " model vdw 2.399 3.120 nonbonded pdb=" N ASP J 207 " pdb=" OD1 ASP J 207 " model vdw 2.421 3.120 nonbonded pdb=" N ASP L 207 " pdb=" OD1 ASP L 207 " model vdw 2.422 3.120 ... (remaining 41895 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 Found NCS groups: ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.430 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 : 0.002 0.018 5571 Z= 0.110 Angle : 0.437 4.533 7548 Z= 0.231 Chirality : 0.044 0.135 936 Planarity : 0.002 0.022 960 Dihedral : 14.179 89.842 2064 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.33), residues: 711 helix: 1.61 (0.71), residues: 66 sheet: 1.39 (0.31), residues: 315 loop : -0.85 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 118 PHE 0.004 0.001 PHE L 231 TYR 0.005 0.001 TYR L 43 ARG 0.003 0.001 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.651 Fit side-chains REVERT: L 38 GLU cc_start: 0.8123 (mp0) cc_final: 0.7697 (mp0) REVERT: L 122 GLU cc_start: 0.7407 (pt0) cc_final: 0.7192 (pt0) REVERT: L 152 ASP cc_start: 0.7491 (p0) cc_final: 0.7201 (p0) REVERT: K 100 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7666 (mt-10) REVERT: J 101 SER cc_start: 0.8415 (m) cc_final: 0.8003 (p) REVERT: J 152 ASP cc_start: 0.7273 (p0) cc_final: 0.7040 (p0) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1586 time to fit residues: 24.5692 Evaluate side-chains 79 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 0.0010 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 125 GLN L 225 GLN K 225 GLN J 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5571 Z= 0.248 Angle : 0.518 5.147 7548 Z= 0.275 Chirality : 0.047 0.146 936 Planarity : 0.003 0.030 960 Dihedral : 3.680 10.710 750 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.90 % Allowed : 6.67 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.33), residues: 711 helix: 0.65 (0.65), residues: 72 sheet: 1.38 (0.32), residues: 312 loop : -0.98 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 118 PHE 0.008 0.001 PHE J 142 TYR 0.019 0.002 TYR L 43 ARG 0.006 0.001 ARG K 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.709 Fit side-chains REVERT: L 152 ASP cc_start: 0.7390 (p0) cc_final: 0.7090 (p0) REVERT: J 101 SER cc_start: 0.8456 (m) cc_final: 0.8163 (p) outliers start: 12 outliers final: 11 residues processed: 77 average time/residue: 0.1427 time to fit residues: 15.5338 Evaluate side-chains 74 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 168 GLN Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain J residue 202 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 55 optimal weight: 0.1980 chunk 21 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 47 optimal weight: 0.0570 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 134 GLN J 225 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 5571 Z= 0.131 Angle : 0.439 4.134 7548 Z= 0.236 Chirality : 0.046 0.130 936 Planarity : 0.003 0.024 960 Dihedral : 3.423 10.909 750 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.27 % Allowed : 9.52 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.33), residues: 711 helix: 0.89 (0.66), residues: 72 sheet: 1.45 (0.32), residues: 306 loop : -0.99 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 118 PHE 0.005 0.001 PHE J 142 TYR 0.014 0.001 TYR L 43 ARG 0.006 0.001 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.641 Fit side-chains REVERT: L 146 ILE cc_start: 0.8345 (pt) cc_final: 0.7954 (mt) REVERT: J 101 SER cc_start: 0.8473 (m) cc_final: 0.8131 (p) REVERT: J 163 SER cc_start: 0.8864 (t) cc_final: 0.8581 (p) outliers start: 8 outliers final: 7 residues processed: 87 average time/residue: 0.1358 time to fit residues: 16.9956 Evaluate side-chains 86 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 168 GLN Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 127 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 66 optimal weight: 0.0170 chunk 59 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 75 GLN K 75 GLN J 16 GLN J 75 GLN J 134 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5571 Z= 0.261 Angle : 0.518 4.479 7548 Z= 0.278 Chirality : 0.047 0.146 936 Planarity : 0.003 0.032 960 Dihedral : 3.846 12.205 750 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.54 % Allowed : 11.90 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.33), residues: 711 helix: 0.41 (0.63), residues: 72 sheet: 1.07 (0.32), residues: 336 loop : -1.30 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 118 PHE 0.007 0.001 PHE K 142 TYR 0.018 0.001 TYR L 43 ARG 0.008 0.001 ARG K 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.594 Fit side-chains REVERT: K 152 ASP cc_start: 0.7543 (p0) cc_final: 0.7318 (p0) REVERT: J 101 SER cc_start: 0.8523 (m) cc_final: 0.8228 (p) outliers start: 16 outliers final: 14 residues processed: 75 average time/residue: 0.1545 time to fit residues: 16.0270 Evaluate side-chains 72 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 75 GLN Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 75 GLN Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain J residue 202 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5571 Z= 0.276 Angle : 0.514 4.733 7548 Z= 0.276 Chirality : 0.047 0.139 936 Planarity : 0.003 0.030 960 Dihedral : 3.922 12.872 750 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.22 % Allowed : 12.86 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.32), residues: 711 helix: 0.33 (0.64), residues: 72 sheet: 1.27 (0.32), residues: 306 loop : -1.24 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 118 PHE 0.006 0.001 PHE K 142 TYR 0.018 0.001 TYR L 43 ARG 0.007 0.001 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.684 Fit side-chains REVERT: L 168 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: K 152 ASP cc_start: 0.7558 (p0) cc_final: 0.7326 (p0) REVERT: K 220 GLU cc_start: 0.8169 (tt0) cc_final: 0.7788 (tt0) REVERT: J 101 SER cc_start: 0.8537 (m) cc_final: 0.8271 (p) REVERT: J 149 GLN cc_start: 0.7871 (tt0) cc_final: 0.7629 (tt0) outliers start: 14 outliers final: 12 residues processed: 68 average time/residue: 0.1268 time to fit residues: 12.7159 Evaluate side-chains 74 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain J residue 202 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 75 GLN J 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 5571 Z= 0.435 Angle : 0.616 5.168 7548 Z= 0.327 Chirality : 0.050 0.149 936 Planarity : 0.003 0.037 960 Dihedral : 4.432 14.719 750 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.33 % Allowed : 12.86 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.32), residues: 711 helix: -0.07 (0.62), residues: 72 sheet: 1.03 (0.32), residues: 306 loop : -1.47 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS L 118 PHE 0.008 0.001 PHE K 142 TYR 0.012 0.002 TYR K 115 ARG 0.005 0.001 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.685 Fit side-chains REVERT: L 101 SER cc_start: 0.8627 (OUTLIER) cc_final: 0.8329 (p) REVERT: L 165 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8244 (tt) REVERT: L 168 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: K 220 GLU cc_start: 0.8067 (tt0) cc_final: 0.7721 (tt0) REVERT: J 38 GLU cc_start: 0.8393 (mp0) cc_final: 0.8092 (mp0) REVERT: J 101 SER cc_start: 0.8675 (m) cc_final: 0.8409 (p) outliers start: 21 outliers final: 14 residues processed: 73 average time/residue: 0.1124 time to fit residues: 12.1745 Evaluate side-chains 66 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 75 GLN Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 202 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5571 Z= 0.214 Angle : 0.499 4.342 7548 Z= 0.271 Chirality : 0.047 0.140 936 Planarity : 0.003 0.029 960 Dihedral : 4.055 14.236 750 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.54 % Allowed : 13.49 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.32), residues: 711 helix: 0.26 (0.64), residues: 72 sheet: 1.05 (0.32), residues: 306 loop : -1.38 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 118 PHE 0.005 0.001 PHE K 142 TYR 0.018 0.001 TYR L 43 ARG 0.006 0.001 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.770 Fit side-chains REVERT: L 101 SER cc_start: 0.8601 (OUTLIER) cc_final: 0.8297 (p) REVERT: L 165 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8166 (tt) REVERT: L 168 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: K 220 GLU cc_start: 0.8098 (tt0) cc_final: 0.7713 (tt0) REVERT: J 101 SER cc_start: 0.8608 (m) cc_final: 0.8316 (p) REVERT: J 149 GLN cc_start: 0.7853 (tt0) cc_final: 0.7610 (tt0) outliers start: 16 outliers final: 12 residues processed: 64 average time/residue: 0.1247 time to fit residues: 11.8252 Evaluate side-chains 69 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 202 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5571 Z= 0.165 Angle : 0.463 5.247 7548 Z= 0.252 Chirality : 0.046 0.132 936 Planarity : 0.003 0.024 960 Dihedral : 3.759 13.352 750 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.90 % Allowed : 14.60 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.32), residues: 711 helix: 0.55 (0.65), residues: 72 sheet: 1.12 (0.32), residues: 306 loop : -1.29 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 118 PHE 0.004 0.001 PHE K 142 TYR 0.018 0.001 TYR L 43 ARG 0.005 0.001 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.660 Fit side-chains REVERT: L 101 SER cc_start: 0.8585 (m) cc_final: 0.8284 (p) REVERT: L 165 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8132 (tt) REVERT: L 168 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: K 101 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8204 (p) REVERT: K 220 GLU cc_start: 0.8084 (tt0) cc_final: 0.7691 (tt0) REVERT: J 38 GLU cc_start: 0.8303 (mp0) cc_final: 0.8092 (mp0) REVERT: J 101 SER cc_start: 0.8513 (m) cc_final: 0.8236 (p) REVERT: J 149 GLN cc_start: 0.7910 (tt0) cc_final: 0.7670 (tt0) outliers start: 12 outliers final: 6 residues processed: 70 average time/residue: 0.1304 time to fit residues: 13.2440 Evaluate side-chains 72 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 165 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5571 Z= 0.193 Angle : 0.492 7.424 7548 Z= 0.267 Chirality : 0.046 0.145 936 Planarity : 0.003 0.024 960 Dihedral : 3.826 13.258 750 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.38 % Allowed : 14.92 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.32), residues: 711 helix: 0.52 (0.64), residues: 72 sheet: 1.14 (0.32), residues: 306 loop : -1.24 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 118 PHE 0.004 0.001 PHE K 142 TYR 0.007 0.001 TYR K 43 ARG 0.005 0.001 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.572 Fit side-chains REVERT: L 101 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8286 (p) REVERT: L 165 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8127 (tt) REVERT: L 168 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7955 (tt0) REVERT: K 101 SER cc_start: 0.8724 (OUTLIER) cc_final: 0.8308 (p) REVERT: K 220 GLU cc_start: 0.8073 (tt0) cc_final: 0.7712 (tt0) REVERT: J 101 SER cc_start: 0.8528 (m) cc_final: 0.8255 (p) REVERT: J 149 GLN cc_start: 0.7925 (tt0) cc_final: 0.7689 (tt0) outliers start: 15 outliers final: 11 residues processed: 74 average time/residue: 0.1284 time to fit residues: 13.7116 Evaluate side-chains 82 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 75 GLN Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 136 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 42 optimal weight: 0.4980 chunk 33 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5571 Z= 0.169 Angle : 0.489 6.340 7548 Z= 0.266 Chirality : 0.046 0.141 936 Planarity : 0.003 0.024 960 Dihedral : 3.730 13.862 750 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.06 % Allowed : 15.08 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.32), residues: 711 helix: 0.65 (0.65), residues: 72 sheet: 1.18 (0.32), residues: 306 loop : -1.18 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS L 118 PHE 0.004 0.001 PHE K 142 TYR 0.018 0.001 TYR L 43 ARG 0.005 0.001 ARG J 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.677 Fit side-chains REVERT: L 101 SER cc_start: 0.8596 (m) cc_final: 0.8275 (p) REVERT: L 165 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8078 (tt) REVERT: L 168 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: K 101 SER cc_start: 0.8710 (m) cc_final: 0.8289 (p) REVERT: J 101 SER cc_start: 0.8521 (m) cc_final: 0.8243 (p) REVERT: J 149 GLN cc_start: 0.7905 (tt0) cc_final: 0.7676 (tt0) outliers start: 13 outliers final: 11 residues processed: 79 average time/residue: 0.1260 time to fit residues: 14.4939 Evaluate side-chains 80 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 136 SER Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 39 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.112577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.100346 restraints weight = 7661.592| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.92 r_work: 0.2995 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5571 Z= 0.213 Angle : 0.511 6.892 7548 Z= 0.277 Chirality : 0.047 0.144 936 Planarity : 0.003 0.024 960 Dihedral : 3.831 13.789 750 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.54 % Allowed : 14.76 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.32), residues: 711 helix: 0.49 (0.64), residues: 72 sheet: 1.16 (0.32), residues: 306 loop : -1.15 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 118 PHE 0.005 0.001 PHE K 142 TYR 0.018 0.001 TYR L 43 ARG 0.005 0.001 ARG J 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1292.05 seconds wall clock time: 24 minutes 28.73 seconds (1468.73 seconds total)