Starting phenix.real_space_refine on Wed Jul 23 16:36:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fh5_50440/07_2025/9fh5_50440.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fh5_50440/07_2025/9fh5_50440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fh5_50440/07_2025/9fh5_50440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fh5_50440/07_2025/9fh5_50440.map" model { file = "/net/cci-nas-00/data/ceres_data/9fh5_50440/07_2025/9fh5_50440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fh5_50440/07_2025/9fh5_50440.cif" } resolution = 3.8 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= 0.344 sd= 1.454 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 S 20 5.16 5 C 1160 2.51 5 N 280 2.21 5 O 280 1.98 5 H 2040 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3780 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "B" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "C" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "D" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "E" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "F" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "G" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "H" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "I" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "J" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "K" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "L" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "M" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "N" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "O" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "P" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "Q" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "R" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "S" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "T" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Time building chain proxies: 2.25, per 1000 atoms: 0.60 Number of scatterers: 3780 At special positions: 0 Unit cell: (66.096, 57.936, 40.8, 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 20 16.00 O 280 8.00 N 280 7.00 C 1160 6.00 H 2040 1.00 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: 0.89 Conformation dependent library (CDL) restraints added in 275.1 milliseconds 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 400 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.307A pdb=" N ILE A 31 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE E 31 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE I 31 " --> pdb=" O ILE M 32 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE M 31 " --> pdb=" O ILE Q 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 removed outlier: 6.506A pdb=" N VAL A 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL E 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL I 39 " --> pdb=" O VAL M 40 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL M 39 " --> pdb=" O VAL Q 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 31 through 33 removed outlier: 6.556A pdb=" N ILE B 31 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE F 31 " --> pdb=" O ILE J 32 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE J 31 " --> pdb=" O ILE N 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 39 through 40 removed outlier: 6.642A pdb=" N VAL B 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL F 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL J 39 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL N 39 " --> pdb=" O VAL R 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 31 through 33 removed outlier: 6.519A pdb=" N ILE C 31 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE G 31 " --> pdb=" O ILE K 32 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE K 31 " --> pdb=" O ILE O 32 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE O 31 " --> pdb=" O ILE S 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.729A pdb=" N VAL C 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL G 39 " --> pdb=" O VAL K 40 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL K 39 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL O 39 " --> pdb=" O VAL S 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 31 through 33 removed outlier: 3.543A pdb=" N ILE L 32 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE P 32 " --> pdb=" O ILE L 31 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 39 through 40 removed outlier: 6.445A pdb=" N VAL D 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL H 39 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL L 39 " --> pdb=" O VAL P 40 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL P 39 " --> pdb=" O VAL T 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 8 hydrogen bonds defined for protein. 24 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: 1.22 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 2040 1.17 - 1.33: 454 1.33 - 1.49: 366 1.49 - 1.65: 860 1.65 - 1.81: 40 Bond restraints: 3760 Sorted by residual: bond pdb=" N GLY Q 37 " pdb=" H GLY Q 37 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N MET E 35 " pdb=" H MET E 35 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ILE J 32 " pdb=" H ILE J 32 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLY J 37 " pdb=" H GLY J 37 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ILE R 41 " pdb=" H ILE R 41 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 3755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 4820 1.69 - 3.38: 1353 3.38 - 5.06: 393 5.06 - 6.75: 295 6.75 - 8.44: 39 Bond angle restraints: 6900 Sorted by residual: angle pdb=" C LEU G 34 " pdb=" CA LEU G 34 " pdb=" CB LEU G 34 " ideal model delta sigma weight residual 111.73 118.96 -7.23 1.42e+00 4.96e-01 2.59e+01 angle pdb=" C LEU S 34 " pdb=" CA LEU S 34 " pdb=" CB LEU S 34 " ideal model delta sigma weight residual 111.51 119.38 -7.87 1.58e+00 4.01e-01 2.48e+01 angle pdb=" C LEU O 34 " pdb=" CA LEU O 34 " pdb=" CB LEU O 34 " ideal model delta sigma weight residual 111.51 119.02 -7.51 1.58e+00 4.01e-01 2.26e+01 angle pdb=" C LEU K 34 " pdb=" CA LEU K 34 " pdb=" CB LEU K 34 " ideal model delta sigma weight residual 111.51 118.91 -7.40 1.58e+00 4.01e-01 2.19e+01 angle pdb=" C LEU Q 34 " pdb=" CA LEU Q 34 " pdb=" CB LEU Q 34 " ideal model delta sigma weight residual 111.73 118.34 -6.61 1.42e+00 4.96e-01 2.17e+01 ... (remaining 6895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.52: 1390 14.52 - 29.03: 92 29.03 - 43.55: 20 43.55 - 58.07: 98 58.07 - 72.59: 40 Dihedral angle restraints: 1640 sinusoidal: 980 harmonic: 660 Sorted by residual: dihedral pdb=" CA GLY J 37 " pdb=" C GLY J 37 " pdb=" N GLY J 38 " pdb=" CA GLY J 38 " ideal model delta harmonic sigma weight residual -180.00 -156.64 -23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" C LEU G 34 " pdb=" N LEU G 34 " pdb=" CA LEU G 34 " pdb=" CB LEU G 34 " ideal model delta harmonic sigma weight residual -122.60 -133.60 11.00 0 2.50e+00 1.60e-01 1.94e+01 dihedral pdb=" C LEU K 34 " pdb=" N LEU K 34 " pdb=" CA LEU K 34 " pdb=" CB LEU K 34 " ideal model delta harmonic sigma weight residual -122.60 -133.38 10.78 0 2.50e+00 1.60e-01 1.86e+01 ... (remaining 1637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 155 0.066 - 0.132: 105 0.132 - 0.198: 57 0.198 - 0.264: 13 0.264 - 0.330: 10 Chirality restraints: 340 Sorted by residual: chirality pdb=" CA LEU G 34 " pdb=" N LEU G 34 " pdb=" C LEU G 34 " pdb=" CB LEU G 34 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA LEU K 34 " pdb=" N LEU K 34 " pdb=" C LEU K 34 " pdb=" CB LEU K 34 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA LEU O 34 " pdb=" N LEU O 34 " pdb=" C LEU O 34 " pdb=" CB LEU O 34 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 337 not shown) Planarity restraints: 520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 37 " 0.028 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" N GLY D 38 " -0.087 2.00e-02 2.50e+03 pdb=" CA GLY D 38 " 0.025 2.00e-02 2.50e+03 pdb=" H GLY D 38 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY H 37 " 0.027 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" N GLY H 38 " -0.085 2.00e-02 2.50e+03 pdb=" CA GLY H 38 " 0.024 2.00e-02 2.50e+03 pdb=" H GLY H 38 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY J 37 " 0.026 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" N GLY J 38 " -0.085 2.00e-02 2.50e+03 pdb=" CA GLY J 38 " 0.024 2.00e-02 2.50e+03 pdb=" H GLY J 38 " 0.034 2.00e-02 2.50e+03 ... (remaining 517 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.38: 1158 2.38 - 2.94: 8789 2.94 - 3.49: 10572 3.49 - 4.05: 13425 4.05 - 4.60: 19822 Nonbonded interactions: 53766 Sorted by model distance: nonbonded pdb=" HB VAL J 36 " pdb=" H GLY N 37 " model vdw 1.831 2.270 nonbonded pdb=" HB VAL F 36 " pdb=" H GLY J 37 " model vdw 1.833 2.270 nonbonded pdb=" O VAL H 39 " pdb=" H VAL L 40 " model vdw 1.843 2.450 nonbonded pdb=" HB VAL A 36 " pdb=" H GLY E 37 " model vdw 1.846 2.270 nonbonded pdb=" O VAL L 39 " pdb=" H VAL P 40 " model vdw 1.848 2.450 ... (remaining 53761 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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 group one per residue 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: 1.370 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: 0.070 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.570 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.010 0.028 1720 Z= 0.658 Angle : 1.973 7.873 2300 Z= 1.260 Chirality : 0.113 0.330 340 Planarity : 0.010 0.026 260 Dihedral : 9.177 23.364 540 Min Nonbonded Distance : 2.680 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 5.00 % 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: 1.74 (0.53), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.33 (0.40), residues: 240 Details of bonding type rmsd hydrogen bonds : bond 0.20338 ( 8) hydrogen bonds : angle 14.46951 ( 24) covalent geometry : bond 0.01022 ( 1720) covalent geometry : angle 1.97304 ( 2300) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 41 ILE cc_start: 0.8946 (mm) cc_final: 0.8599 (pt) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1502 time to fit residues: 12.5526 Evaluate side-chains 48 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.146104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.119373 restraints weight = 10027.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.125366 restraints weight = 5110.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.130028 restraints weight = 3109.653| |-----------------------------------------------------------------------------| r_work (final): 0.4279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 1720 Z= 0.264 Angle : 0.896 6.137 2300 Z= 0.444 Chirality : 0.066 0.148 340 Planarity : 0.003 0.008 260 Dihedral : 8.548 18.728 260 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.62 % Allowed : 17.50 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.60 (0.54), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.46 (0.41), residues: 240 Details of bonding type rmsd hydrogen bonds : bond 0.05986 ( 8) hydrogen bonds : angle 9.85234 ( 24) covalent geometry : bond 0.00556 ( 1720) covalent geometry : angle 0.89596 ( 2300) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.261 Fit side-chains REVERT: G 32 ILE cc_start: 0.9110 (mt) cc_final: 0.8796 (mp) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.1501 time to fit residues: 9.1910 Evaluate side-chains 46 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.149349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.121751 restraints weight = 9895.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.127994 restraints weight = 5134.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.132715 restraints weight = 3125.120| |-----------------------------------------------------------------------------| r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1720 Z= 0.164 Angle : 0.778 5.833 2300 Z= 0.374 Chirality : 0.065 0.146 340 Planarity : 0.002 0.007 260 Dihedral : 6.980 16.511 260 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.88 % Allowed : 21.88 % Favored : 76.25 % 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: 0.10 (0.56), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.08 (0.43), residues: 240 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 8) hydrogen bonds : angle 9.20422 ( 24) covalent geometry : bond 0.00315 ( 1720) covalent geometry : angle 0.77824 ( 2300) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.261 Fit side-chains REVERT: G 32 ILE cc_start: 0.9158 (mt) cc_final: 0.8766 (mp) REVERT: N 32 ILE cc_start: 0.8748 (mt) cc_final: 0.8424 (mp) REVERT: S 40 VAL cc_start: 0.7720 (OUTLIER) cc_final: 0.7457 (m) outliers start: 3 outliers final: 1 residues processed: 47 average time/residue: 0.1472 time to fit residues: 8.8703 Evaluate side-chains 46 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain S residue 40 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 13 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.156683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.127520 restraints weight = 9507.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.134240 restraints weight = 4931.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.139296 restraints weight = 2984.109| |-----------------------------------------------------------------------------| r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1720 Z= 0.107 Angle : 0.709 5.149 2300 Z= 0.335 Chirality : 0.067 0.143 340 Planarity : 0.002 0.006 260 Dihedral : 6.094 14.091 260 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.62 % Allowed : 23.75 % Favored : 75.62 % 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: 0.01 (0.56), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.02 (0.43), residues: 240 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 8) hydrogen bonds : angle 8.31779 ( 24) covalent geometry : bond 0.00222 ( 1720) covalent geometry : angle 0.70881 ( 2300) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.286 Fit side-chains REVERT: O 32 ILE cc_start: 0.8993 (mt) cc_final: 0.8717 (mp) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.1544 time to fit residues: 10.3911 Evaluate side-chains 48 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.159793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.130311 restraints weight = 9323.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.137383 restraints weight = 4666.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.142484 restraints weight = 2784.214| |-----------------------------------------------------------------------------| r_work (final): 0.4392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1720 Z= 0.132 Angle : 0.689 5.266 2300 Z= 0.334 Chirality : 0.065 0.137 340 Planarity : 0.002 0.006 260 Dihedral : 5.927 13.791 260 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 1.25 % Allowed : 26.25 % Favored : 72.50 % 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: -0.21 (0.56), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.15 (0.43), residues: 240 Details of bonding type rmsd hydrogen bonds : bond 0.02963 ( 8) hydrogen bonds : angle 8.45297 ( 24) covalent geometry : bond 0.00263 ( 1720) covalent geometry : angle 0.68888 ( 2300) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.285 Fit side-chains REVERT: G 32 ILE cc_start: 0.9190 (mt) cc_final: 0.8795 (mp) REVERT: N 32 ILE cc_start: 0.8752 (mt) cc_final: 0.8447 (mp) REVERT: O 32 ILE cc_start: 0.9000 (mt) cc_final: 0.8707 (mp) outliers start: 2 outliers final: 1 residues processed: 53 average time/residue: 0.1545 time to fit residues: 10.4328 Evaluate side-chains 48 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 34 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.173004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.139017 restraints weight = 9919.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.146709 restraints weight = 4783.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.151892 restraints weight = 2760.983| |-----------------------------------------------------------------------------| r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 1720 Z= 0.190 Angle : 0.703 5.470 2300 Z= 0.354 Chirality : 0.064 0.141 340 Planarity : 0.003 0.006 260 Dihedral : 6.259 15.157 260 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.88 % Allowed : 28.75 % Favored : 69.38 % 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: -1.08 (0.53), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.81 (0.40), residues: 240 Details of bonding type rmsd hydrogen bonds : bond 0.02943 ( 8) hydrogen bonds : angle 9.19472 ( 24) covalent geometry : bond 0.00374 ( 1720) covalent geometry : angle 0.70305 ( 2300) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.307 Fit side-chains REVERT: G 32 ILE cc_start: 0.9237 (mt) cc_final: 0.8839 (mp) REVERT: O 32 ILE cc_start: 0.9031 (mt) cc_final: 0.8747 (mp) outliers start: 3 outliers final: 2 residues processed: 45 average time/residue: 0.1533 time to fit residues: 8.8603 Evaluate side-chains 43 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain K residue 34 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.158414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.129176 restraints weight = 9197.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.136080 restraints weight = 4714.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.141088 restraints weight = 2825.566| |-----------------------------------------------------------------------------| r_work (final): 0.4365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1720 Z= 0.107 Angle : 0.675 6.144 2300 Z= 0.325 Chirality : 0.066 0.136 340 Planarity : 0.002 0.007 260 Dihedral : 5.667 15.050 260 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.88 % Allowed : 28.12 % Favored : 70.00 % 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: -0.87 (0.53), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.66 (0.41), residues: 240 Details of bonding type rmsd hydrogen bonds : bond 0.03194 ( 8) hydrogen bonds : angle 8.36463 ( 24) covalent geometry : bond 0.00225 ( 1720) covalent geometry : angle 0.67482 ( 2300) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.264 Fit side-chains REVERT: G 32 ILE cc_start: 0.9190 (mt) cc_final: 0.8774 (mp) REVERT: N 32 ILE cc_start: 0.8745 (mt) cc_final: 0.8434 (mp) REVERT: O 32 ILE cc_start: 0.8971 (mt) cc_final: 0.8730 (mp) outliers start: 3 outliers final: 1 residues processed: 50 average time/residue: 0.1471 time to fit residues: 9.4715 Evaluate side-chains 48 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 34 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.176536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.142357 restraints weight = 9728.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.150347 restraints weight = 4664.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.155801 restraints weight = 2677.134| |-----------------------------------------------------------------------------| r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1720 Z= 0.128 Angle : 0.681 5.749 2300 Z= 0.330 Chirality : 0.065 0.137 340 Planarity : 0.002 0.006 260 Dihedral : 5.659 15.666 260 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.25 % Allowed : 28.12 % Favored : 70.62 % 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: -1.06 (0.54), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.80 (0.41), residues: 240 Details of bonding type rmsd hydrogen bonds : bond 0.02991 ( 8) hydrogen bonds : angle 8.42896 ( 24) covalent geometry : bond 0.00256 ( 1720) covalent geometry : angle 0.68134 ( 2300) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.340 Fit side-chains REVERT: G 32 ILE cc_start: 0.9191 (mt) cc_final: 0.8789 (mp) REVERT: J 32 ILE cc_start: 0.8991 (mt) cc_final: 0.8760 (mp) REVERT: N 32 ILE cc_start: 0.8762 (mt) cc_final: 0.8433 (mp) REVERT: O 32 ILE cc_start: 0.8937 (mt) cc_final: 0.8698 (mp) outliers start: 2 outliers final: 1 residues processed: 48 average time/residue: 0.2564 time to fit residues: 15.3352 Evaluate side-chains 48 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 34 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.158359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.129861 restraints weight = 9194.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.136699 restraints weight = 4665.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.141681 restraints weight = 2787.702| |-----------------------------------------------------------------------------| r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1720 Z= 0.108 Angle : 0.672 6.044 2300 Z= 0.321 Chirality : 0.066 0.146 340 Planarity : 0.002 0.007 260 Dihedral : 5.408 15.393 260 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.50 % Allowed : 26.88 % Favored : 70.62 % 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: -1.09 (0.54), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.82 (0.41), residues: 240 Details of bonding type rmsd hydrogen bonds : bond 0.03070 ( 8) hydrogen bonds : angle 8.01464 ( 24) covalent geometry : bond 0.00231 ( 1720) covalent geometry : angle 0.67176 ( 2300) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.296 Fit side-chains REVERT: G 32 ILE cc_start: 0.9164 (mt) cc_final: 0.8708 (mp) REVERT: J 32 ILE cc_start: 0.8953 (mt) cc_final: 0.8718 (mp) REVERT: K 32 ILE cc_start: 0.9002 (mt) cc_final: 0.8645 (mp) REVERT: M 34 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7201 (tt) REVERT: N 32 ILE cc_start: 0.8720 (mt) cc_final: 0.8414 (mp) REVERT: O 32 ILE cc_start: 0.8915 (mt) cc_final: 0.8646 (mp) REVERT: Q 34 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7619 (tt) outliers start: 4 outliers final: 0 residues processed: 52 average time/residue: 0.1840 time to fit residues: 12.2333 Evaluate side-chains 48 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain Q residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.175830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.140123 restraints weight = 9399.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.148025 restraints weight = 4413.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.153494 restraints weight = 2489.815| |-----------------------------------------------------------------------------| r_work (final): 0.4368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1720 Z= 0.139 Angle : 0.671 6.114 2300 Z= 0.330 Chirality : 0.064 0.148 340 Planarity : 0.002 0.006 260 Dihedral : 5.550 15.585 260 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.50 % Allowed : 26.88 % Favored : 70.62 % 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: -1.41 (0.53), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.41), residues: 240 Details of bonding type rmsd hydrogen bonds : bond 0.02922 ( 8) hydrogen bonds : angle 8.20146 ( 24) covalent geometry : bond 0.00271 ( 1720) covalent geometry : angle 0.67136 ( 2300) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.653 Fit side-chains REVERT: G 32 ILE cc_start: 0.9195 (mt) cc_final: 0.8795 (mp) REVERT: J 32 ILE cc_start: 0.8950 (mt) cc_final: 0.8700 (mp) REVERT: M 34 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7321 (tt) REVERT: O 32 ILE cc_start: 0.8955 (mt) cc_final: 0.8665 (mp) REVERT: Q 34 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7696 (tt) outliers start: 4 outliers final: 2 residues processed: 44 average time/residue: 0.3201 time to fit residues: 18.4899 Evaluate side-chains 45 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 19 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.241412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.151202 restraints weight = 10671.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.158478 restraints weight = 5203.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.163380 restraints weight = 3132.691| |-----------------------------------------------------------------------------| r_work (final): 0.4531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 1720 Z= 0.117 Angle : 0.651 6.012 2300 Z= 0.316 Chirality : 0.065 0.144 340 Planarity : 0.002 0.006 260 Dihedral : 5.297 14.816 260 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.88 % Allowed : 27.50 % Favored : 70.62 % 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: -1.46 (0.53), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.41), residues: 240 Details of bonding type rmsd hydrogen bonds : bond 0.03017 ( 8) hydrogen bonds : angle 7.91692 ( 24) covalent geometry : bond 0.00238 ( 1720) covalent geometry : angle 0.65096 ( 2300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2518.95 seconds wall clock time: 45 minutes 10.67 seconds (2710.67 seconds total)