Starting phenix.real_space_refine on Mon Apr 8 07:57:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6h_29769/04_2024/8g6h_29769_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6h_29769/04_2024/8g6h_29769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6h_29769/04_2024/8g6h_29769.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6h_29769/04_2024/8g6h_29769.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6h_29769/04_2024/8g6h_29769_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6h_29769/04_2024/8g6h_29769_updated.pdb" } resolution = 3.06 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= 0.002 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 314 5.49 5 S 13 5.16 5 C 7171 2.51 5 N 2423 2.21 5 O 3053 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 133": "OE1" <-> "OE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "K GLU 18": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12974 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 803 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MLY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 742 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MLY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3196 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Chain: "J" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3241 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Chain: "K" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LEU K 73 " occ=0.52 ... (6 atoms not shown) pdb=" CD2 LEU K 73 " occ=0.52 Time building chain proxies: 7.15, per 1000 atoms: 0.55 Number of scatterers: 12974 At special positions: 0 Unit cell: (124.696, 95.048, 133.416, 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 13 16.00 P 314 15.00 O 3053 8.00 N 2423 7.00 C 7171 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 - 3.50 Amino acid : False - 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: 6.62 Conformation dependent library (CDL) restraints added in 1.4 seconds 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 1 sheets defined 60.8% alpha, 1.9% beta 157 base pairs and 282 stacking pairs defined. Time for finding SS restraints: 7.16 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 64 through 77 removed outlier: 4.013A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.539A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.654A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 35 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.575A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 88 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 102 through 120 Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 86 through 114 removed outlier: 3.510A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 28 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.584A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.955A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 34 Processing helix chain 'K' and resid 57 through 59 No H-bonds generated for 'chain 'K' and resid 57 through 59' Processing sheet with id= A, first strand: chain 'K' and resid 12 through 16 360 hydrogen bonds defined for protein. 1077 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 405 hydrogen bonds 810 hydrogen bond angles 0 basepair planarities 157 basepair parallelities 282 stacking parallelities Total time for adding SS restraints: 4.73 Time building geometry restraints manager: 6.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2532 1.33 - 1.45: 4475 1.45 - 1.57: 6185 1.57 - 1.69: 626 1.69 - 1.81: 24 Bond restraints: 13842 Sorted by residual: bond pdb=" P DA J 16 " pdb=" OP2 DA J 16 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.45e+00 bond pdb=" P DG J 27 " pdb=" OP2 DG J 27 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.36e+00 bond pdb=" P DG J 27 " pdb=" OP1 DG J 27 " ideal model delta sigma weight residual 1.480 1.513 -0.033 2.00e-02 2.50e+03 2.70e+00 bond pdb=" P DA J 16 " pdb=" OP1 DA J 16 " ideal model delta sigma weight residual 1.480 1.512 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" CB GLN K 31 " pdb=" CG GLN K 31 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.55e+00 ... (remaining 13837 not shown) Histogram of bond angle deviations from ideal: 98.25 - 105.10: 1280 105.10 - 111.94: 7631 111.94 - 118.78: 3494 118.78 - 125.62: 6598 125.62 - 132.47: 1047 Bond angle restraints: 20050 Sorted by residual: angle pdb=" C3' DA J 26 " pdb=" O3' DA J 26 " pdb=" P DG J 27 " ideal model delta sigma weight residual 120.20 113.74 6.46 1.50e+00 4.44e-01 1.86e+01 angle pdb=" O3' DG J 27 " pdb=" P DA J 28 " pdb=" O5' DA J 28 " ideal model delta sigma weight residual 104.00 98.25 5.75 1.50e+00 4.44e-01 1.47e+01 angle pdb=" O3' DA J 16 " pdb=" P DA J 17 " pdb=" O5' DA J 17 " ideal model delta sigma weight residual 104.00 98.58 5.42 1.50e+00 4.44e-01 1.31e+01 angle pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DA J 16 " ideal model delta sigma weight residual 120.20 114.95 5.25 1.50e+00 4.44e-01 1.22e+01 angle pdb=" N ASP B 24 " pdb=" CA ASP B 24 " pdb=" CB ASP B 24 " ideal model delta sigma weight residual 113.65 109.16 4.49 1.47e+00 4.63e-01 9.35e+00 ... (remaining 20045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 5957 35.81 - 71.61: 1534 71.61 - 107.42: 11 107.42 - 143.23: 3 143.23 - 179.03: 1 Dihedral angle restraints: 7506 sinusoidal: 5116 harmonic: 2390 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 40.97 179.03 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC I 4 " pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " pdb=" P DC I 5 " ideal model delta sinusoidal sigma weight residual 220.00 88.60 131.40 1 3.50e+01 8.16e-04 1.30e+01 dihedral pdb=" C4' DC J 34 " pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " pdb=" P DT J 35 " ideal model delta sinusoidal sigma weight residual 220.00 89.63 130.37 1 3.50e+01 8.16e-04 1.29e+01 ... (remaining 7503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2237 0.088 - 0.176: 52 0.176 - 0.264: 0 0.264 - 0.352: 0 0.352 - 0.440: 2 Chirality restraints: 2291 Sorted by residual: chirality pdb=" P DG J 27 " pdb=" OP1 DG J 27 " pdb=" OP2 DG J 27 " pdb=" O5' DG J 27 " both_signs ideal model delta sigma weight residual True 2.35 -2.79 -0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" P DA J 16 " pdb=" OP1 DA J 16 " pdb=" OP2 DA J 16 " pdb=" O5' DA J 16 " both_signs ideal model delta sigma weight residual True 2.35 -2.77 -0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 2288 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 24 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C ASP B 24 " 0.033 2.00e-02 2.50e+03 pdb=" O ASP B 24 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN B 25 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.025 2.00e-02 2.50e+03 1.05e-02 3.33e+00 pdb=" N9 DG I 47 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " -0.024 2.00e-02 2.50e+03 9.95e-03 2.97e+00 pdb=" N9 DG I 26 " 0.022 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " 0.002 2.00e-02 2.50e+03 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2202 2.78 - 3.31: 10640 3.31 - 3.84: 24309 3.84 - 4.37: 29494 4.37 - 4.90: 42179 Nonbonded interactions: 108824 Sorted by model distance: nonbonded pdb=" N GLU C 91 " pdb=" OE1 GLU C 91 " model vdw 2.254 2.520 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH1 ARG A 131 " model vdw 2.263 2.520 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.274 2.440 nonbonded pdb=" O GLN K 62 " pdb=" OG SER K 65 " model vdw 2.283 2.440 nonbonded pdb=" O GLU K 16 " pdb=" NZ LYS K 29 " model vdw 2.291 2.520 ... (remaining 108819 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } 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=0.52 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 7.170 Check model and map are aligned: 0.210 Set scattering table: 0.100 Process input model: 42.510 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 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 : 0.003 0.037 13842 Z= 0.174 Angle : 0.562 8.726 20050 Z= 0.343 Chirality : 0.036 0.440 2291 Planarity : 0.004 0.037 1450 Dihedral : 28.192 179.033 5962 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 18.90 % Favored : 81.10 % 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: 2.68 (0.30), residues: 800 helix: 2.65 (0.22), residues: 535 sheet: 1.95 (0.98), residues: 25 loop : -0.30 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS K 68 PHE 0.009 0.001 PHE F 61 TYR 0.012 0.001 TYR F 51 ARG 0.002 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.008 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.3563 time to fit residues: 57.9443 Evaluate side-chains 123 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.0470 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 overall best weight: 1.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.0451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13842 Z= 0.230 Angle : 0.522 6.110 20050 Z= 0.319 Chirality : 0.033 0.126 2291 Planarity : 0.004 0.037 1450 Dihedral : 30.126 178.969 4342 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.60 % Allowed : 18.02 % Favored : 80.38 % 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: 2.88 (0.30), residues: 800 helix: 2.85 (0.22), residues: 537 sheet: 1.70 (1.09), residues: 19 loop : -0.31 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS K 68 PHE 0.009 0.001 PHE F 61 TYR 0.007 0.001 TYR F 51 ARG 0.002 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.044 Fit side-chains REVERT: B 93 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7486 (mp10) REVERT: C 64 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7947 (tt0) outliers start: 11 outliers final: 6 residues processed: 127 average time/residue: 0.3676 time to fit residues: 61.2339 Evaluate side-chains 130 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 106 optimal weight: 0.0020 chunk 87 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 overall best weight: 1.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.0477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13842 Z= 0.213 Angle : 0.523 6.127 20050 Z= 0.320 Chirality : 0.033 0.149 2291 Planarity : 0.004 0.036 1450 Dihedral : 30.134 178.945 4342 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.89 % Allowed : 18.17 % Favored : 79.94 % 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: 2.89 (0.30), residues: 800 helix: 2.86 (0.22), residues: 537 sheet: 1.67 (1.11), residues: 19 loop : -0.28 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.009 0.001 PHE F 61 TYR 0.008 0.001 TYR F 51 ARG 0.002 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 1.051 Fit side-chains REVERT: B 93 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7500 (mp10) REVERT: C 64 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7939 (tt0) outliers start: 13 outliers final: 11 residues processed: 125 average time/residue: 0.3405 time to fit residues: 56.1630 Evaluate side-chains 134 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.0550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13842 Z= 0.229 Angle : 0.520 6.193 20050 Z= 0.319 Chirality : 0.033 0.126 2291 Planarity : 0.004 0.037 1450 Dihedral : 30.134 179.076 4342 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.89 % Allowed : 18.60 % Favored : 79.51 % 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: 2.89 (0.30), residues: 800 helix: 2.86 (0.22), residues: 537 sheet: 1.82 (1.14), residues: 19 loop : -0.32 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.009 0.001 PHE F 61 TYR 0.007 0.001 TYR F 51 ARG 0.002 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 1.001 Fit side-chains REVERT: B 93 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7551 (mp10) REVERT: C 64 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7932 (tt0) REVERT: G 36 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8435 (mtpp) REVERT: G 73 ASN cc_start: 0.8150 (t0) cc_final: 0.7556 (t0) outliers start: 13 outliers final: 10 residues processed: 127 average time/residue: 0.3641 time to fit residues: 61.3307 Evaluate side-chains 135 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 0.0570 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.0605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13842 Z= 0.278 Angle : 0.535 7.172 20050 Z= 0.325 Chirality : 0.034 0.127 2291 Planarity : 0.004 0.038 1450 Dihedral : 30.186 178.073 4342 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.33 % Allowed : 18.46 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.79 (0.30), residues: 800 helix: 2.80 (0.22), residues: 537 sheet: 1.80 (1.13), residues: 19 loop : -0.39 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 39 PHE 0.009 0.002 PHE F 61 TYR 0.008 0.001 TYR F 51 ARG 0.002 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 0.976 Fit side-chains REVERT: B 93 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.7573 (mp10) REVERT: C 64 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: G 36 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8446 (mtpp) REVERT: G 73 ASN cc_start: 0.8177 (t0) cc_final: 0.7637 (t0) outliers start: 16 outliers final: 12 residues processed: 129 average time/residue: 0.3670 time to fit residues: 62.4872 Evaluate side-chains 139 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 0.2980 chunk 104 optimal weight: 0.0170 chunk 86 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.0050 overall best weight: 0.3632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.0609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13842 Z= 0.159 Angle : 0.528 7.702 20050 Z= 0.322 Chirality : 0.032 0.129 2291 Planarity : 0.004 0.036 1450 Dihedral : 30.219 178.559 4342 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.18 % Allowed : 19.04 % Favored : 78.78 % 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: 2.97 (0.30), residues: 800 helix: 2.93 (0.22), residues: 537 sheet: 1.43 (1.21), residues: 20 loop : -0.26 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE F 61 TYR 0.010 0.001 TYR F 51 ARG 0.002 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 1.016 Fit side-chains REVERT: B 93 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.7587 (mp10) REVERT: C 64 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7896 (tt0) REVERT: G 36 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8447 (mtpp) REVERT: G 73 ASN cc_start: 0.8105 (t0) cc_final: 0.7612 (t0) REVERT: K 1 MET cc_start: 0.6272 (tmm) cc_final: 0.5747 (tmm) outliers start: 15 outliers final: 11 residues processed: 127 average time/residue: 0.3628 time to fit residues: 60.4337 Evaluate side-chains 137 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 0.0020 chunk 65 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.0617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13842 Z= 0.177 Angle : 0.517 7.897 20050 Z= 0.317 Chirality : 0.032 0.126 2291 Planarity : 0.003 0.034 1450 Dihedral : 30.204 179.665 4342 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.33 % Allowed : 18.90 % Favored : 78.78 % 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: 2.96 (0.30), residues: 800 helix: 2.92 (0.22), residues: 537 sheet: 1.48 (1.22), residues: 20 loop : -0.26 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE F 61 TYR 0.009 0.001 TYR F 51 ARG 0.001 0.000 ARG H 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 1.021 Fit side-chains REVERT: B 93 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.7617 (mp10) REVERT: C 64 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7915 (tt0) REVERT: E 131 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8909 (mtp85) REVERT: G 36 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8453 (mtpp) REVERT: G 73 ASN cc_start: 0.8105 (t0) cc_final: 0.7595 (t0) REVERT: K 1 MET cc_start: 0.6061 (tmm) cc_final: 0.5714 (tmm) outliers start: 16 outliers final: 11 residues processed: 129 average time/residue: 0.3693 time to fit residues: 62.2102 Evaluate side-chains 138 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.0658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13842 Z= 0.174 Angle : 0.516 8.315 20050 Z= 0.315 Chirality : 0.032 0.126 2291 Planarity : 0.003 0.034 1450 Dihedral : 30.200 179.921 4342 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.03 % Allowed : 19.19 % Favored : 78.78 % 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: 2.97 (0.30), residues: 800 helix: 2.92 (0.22), residues: 537 sheet: 1.14 (1.22), residues: 21 loop : -0.22 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE F 61 TYR 0.008 0.001 TYR F 51 ARG 0.001 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 1.032 Fit side-chains REVERT: B 93 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.7619 (mp10) REVERT: C 64 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7913 (tt0) REVERT: E 131 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8908 (mtp85) REVERT: G 36 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8452 (mtpp) REVERT: G 73 ASN cc_start: 0.8088 (t0) cc_final: 0.7525 (t0) REVERT: K 1 MET cc_start: 0.5946 (tmm) cc_final: 0.5439 (tmm) outliers start: 14 outliers final: 10 residues processed: 128 average time/residue: 0.3528 time to fit residues: 59.6376 Evaluate side-chains 137 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 58 optimal weight: 0.0050 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 13842 Z= 0.416 Angle : 0.589 8.449 20050 Z= 0.353 Chirality : 0.038 0.142 2291 Planarity : 0.004 0.037 1450 Dihedral : 30.292 175.839 4342 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.47 % Allowed : 18.90 % Favored : 78.63 % 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: 2.52 (0.30), residues: 800 helix: 2.59 (0.22), residues: 537 sheet: 1.02 (1.19), residues: 21 loop : -0.43 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 39 PHE 0.012 0.002 PHE H 67 TYR 0.012 0.002 TYR E 54 ARG 0.003 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 1.035 Fit side-chains REVERT: B 93 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7578 (mp10) REVERT: C 64 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7948 (tt0) REVERT: E 131 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8958 (mtp85) REVERT: G 36 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8432 (mtpp) REVERT: G 73 ASN cc_start: 0.8195 (t0) cc_final: 0.7741 (t0) outliers start: 17 outliers final: 10 residues processed: 136 average time/residue: 0.3726 time to fit residues: 65.8184 Evaluate side-chains 141 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 30.0000 chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 71 optimal weight: 20.0000 chunk 107 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.0652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13842 Z= 0.176 Angle : 0.538 9.784 20050 Z= 0.329 Chirality : 0.033 0.130 2291 Planarity : 0.004 0.035 1450 Dihedral : 30.357 178.766 4342 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.89 % Allowed : 19.48 % Favored : 78.63 % 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: 2.77 (0.30), residues: 800 helix: 2.77 (0.22), residues: 537 sheet: 1.51 (1.25), residues: 20 loop : -0.35 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE F 61 TYR 0.011 0.001 TYR F 51 ARG 0.002 0.000 ARG G 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 1.030 Fit side-chains REVERT: B 93 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7643 (mp10) REVERT: C 64 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: E 131 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8905 (mtp85) REVERT: G 36 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8436 (mtpp) REVERT: G 73 ASN cc_start: 0.8133 (t0) cc_final: 0.7701 (t0) outliers start: 13 outliers final: 9 residues processed: 131 average time/residue: 0.3541 time to fit residues: 60.7355 Evaluate side-chains 138 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.118141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.084575 restraints weight = 21381.204| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.15 r_work: 0.2879 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.0783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 13842 Z= 0.260 Angle : 0.534 7.595 20050 Z= 0.324 Chirality : 0.034 0.126 2291 Planarity : 0.004 0.036 1450 Dihedral : 30.247 178.456 4342 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.89 % Allowed : 19.19 % Favored : 78.92 % 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: 2.79 (0.30), residues: 800 helix: 2.83 (0.22), residues: 534 sheet: 1.06 (1.21), residues: 21 loop : -0.37 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.009 0.002 PHE F 61 TYR 0.008 0.001 TYR F 51 ARG 0.002 0.000 ARG B 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2571.99 seconds wall clock time: 47 minutes 22.60 seconds (2842.60 seconds total)