Starting phenix.real_space_refine on Fri Nov 15 06:07:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crb_16807/11_2024/8crb_16807.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crb_16807/11_2024/8crb_16807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crb_16807/11_2024/8crb_16807.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crb_16807/11_2024/8crb_16807.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crb_16807/11_2024/8crb_16807.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crb_16807/11_2024/8crb_16807.cif" } resolution = 4.6 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= 0.000 sd= 0.001 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 13 5.16 5 C 2743 2.51 5 N 738 2.21 5 O 885 1.98 5 H 4286 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8665 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3320 Classifications: {'peptide': 227} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Chain: "B" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3187 Classifications: {'peptide': 216} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 198} Chain: "C" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2158 Classifications: {'peptide': 139} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131} Time building chain proxies: 4.67, per 1000 atoms: 0.54 Number of scatterers: 8665 At special positions: 0 Unit cell: (73.1, 81.6, 113.9, 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 O 885 8.00 N 738 7.00 C 2743 6.00 H 4286 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: 2.36 Conformation dependent library (CDL) restraints added in 896.8 milliseconds 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1064 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 11 sheets defined 21.8% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.666A pdb=" N ASP A 90 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 removed outlier: 4.321A pdb=" N SER A 146 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 80 through 84 Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'C' and resid 129 through 158 removed outlier: 3.584A pdb=" N ALA C 154 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 189 through 198 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 236 through 264 Proline residue: C 250 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.546A pdb=" N THR A 121 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.546A pdb=" N THR A 121 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 116 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 137 removed outlier: 3.518A pdb=" N SER A 134 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR A 190 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 168 Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.715A pdb=" N ASP B 86 " --> pdb=" O GLN B 39 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN B 39 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AA8, first strand: chain 'B' and resid 118 through 122 removed outlier: 6.162A pdb=" N TYR B 176 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 118 through 122 removed outlier: 6.162A pdb=" N TYR B 176 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AB2, first strand: chain 'C' and resid 162 through 163 198 hydrogen bonds defined for protein. 501 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: 2.84 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.11: 4275 1.11 - 1.29: 732 1.29 - 1.46: 1380 1.46 - 1.64: 2361 1.64 - 1.81: 15 Bond restraints: 8763 Sorted by residual: bond pdb=" N SER A 49 " pdb=" H SER A 49 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N ASN A 74 " pdb=" H ASN A 74 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N GLY B 69 " pdb=" H GLY B 69 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N ASN B 174 " pdb=" H ASN B 174 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CD1 PHE A 160 " pdb=" HD1 PHE A 160 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 8758 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 13930 3.08 - 6.15: 1519 6.15 - 9.23: 352 9.23 - 12.31: 8 12.31 - 15.39: 5 Bond angle restraints: 15814 Sorted by residual: angle pdb=" N PRO B 7 " pdb=" CA PRO B 7 " pdb=" C PRO B 7 " ideal model delta sigma weight residual 110.70 121.25 -10.55 1.22e+00 6.72e-01 7.48e+01 angle pdb=" C LYS B 46 " pdb=" N VAL B 47 " pdb=" CA VAL B 47 " ideal model delta sigma weight residual 120.50 128.86 -8.36 1.34e+00 5.57e-01 3.89e+01 angle pdb=" CA PHE A 114 " pdb=" CB PHE A 114 " pdb=" CG PHE A 114 " ideal model delta sigma weight residual 113.80 119.77 -5.97 1.00e+00 1.00e+00 3.57e+01 angle pdb=" CA PHE A 27 " pdb=" CB PHE A 27 " pdb=" CG PHE A 27 " ideal model delta sigma weight residual 113.80 119.39 -5.59 1.00e+00 1.00e+00 3.13e+01 angle pdb=" C GLY B 102 " pdb=" N PRO B 103 " pdb=" CA PRO B 103 " ideal model delta sigma weight residual 119.87 125.68 -5.81 1.04e+00 9.25e-01 3.12e+01 ... (remaining 15809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 3783 17.77 - 35.55: 282 35.55 - 53.32: 102 53.32 - 71.10: 30 71.10 - 88.87: 8 Dihedral angle restraints: 4205 sinusoidal: 2281 harmonic: 1924 Sorted by residual: dihedral pdb=" CA PRO B 7 " pdb=" C PRO B 7 " pdb=" N PRO B 8 " pdb=" CA PRO B 8 " ideal model delta harmonic sigma weight residual -180.00 -150.74 -29.26 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA SER B 2 " pdb=" C SER B 2 " pdb=" N VAL B 3 " pdb=" CA VAL B 3 " ideal model delta harmonic sigma weight residual -180.00 -150.96 -29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ASN C 234 " pdb=" C ASN C 234 " pdb=" N ASN C 235 " pdb=" CA ASN C 235 " ideal model delta harmonic sigma weight residual -180.00 -151.13 -28.87 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 4202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 384 0.083 - 0.165: 226 0.165 - 0.248: 59 0.248 - 0.330: 11 0.330 - 0.412: 2 Chirality restraints: 682 Sorted by residual: chirality pdb=" CA ASN B 174 " pdb=" N ASN B 174 " pdb=" C ASN B 174 " pdb=" CB ASN B 174 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CA TYR A 108 " pdb=" N TYR A 108 " pdb=" C TYR A 108 " pdb=" CB TYR A 108 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CA ASN A 218 " pdb=" N ASN A 218 " pdb=" C ASN A 218 " pdb=" CB ASN A 218 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 679 not shown) Planarity restraints: 1332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 37 " 0.307 2.00e-02 2.50e+03 1.40e-01 5.87e+02 pdb=" CG TYR B 37 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 37 " -0.086 2.00e-02 2.50e+03 pdb=" CD2 TYR B 37 " -0.094 2.00e-02 2.50e+03 pdb=" CE1 TYR B 37 " -0.082 2.00e-02 2.50e+03 pdb=" CE2 TYR B 37 " -0.074 2.00e-02 2.50e+03 pdb=" CZ TYR B 37 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 37 " 0.306 2.00e-02 2.50e+03 pdb=" HD1 TYR B 37 " -0.047 2.00e-02 2.50e+03 pdb=" HD2 TYR B 37 " -0.073 2.00e-02 2.50e+03 pdb=" HE1 TYR B 37 " -0.077 2.00e-02 2.50e+03 pdb=" HE2 TYR B 37 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 117 " 0.179 2.00e-02 2.50e+03 1.18e-01 5.53e+02 pdb=" CG TRP A 117 " 0.094 2.00e-02 2.50e+03 pdb=" CD1 TRP A 117 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 TRP A 117 " -0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP A 117 " -0.092 2.00e-02 2.50e+03 pdb=" CE2 TRP A 117 " -0.078 2.00e-02 2.50e+03 pdb=" CE3 TRP A 117 " -0.133 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 117 " -0.037 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 117 " -0.028 2.00e-02 2.50e+03 pdb=" CH2 TRP A 117 " 0.078 2.00e-02 2.50e+03 pdb=" HD1 TRP A 117 " 0.101 2.00e-02 2.50e+03 pdb=" HE1 TRP A 117 " -0.153 2.00e-02 2.50e+03 pdb=" HE3 TRP A 117 " -0.188 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 117 " -0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 117 " 0.005 2.00e-02 2.50e+03 pdb=" HH2 TRP A 117 " 0.254 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 36 " -0.175 2.00e-02 2.50e+03 7.09e-02 2.01e+02 pdb=" CG TRP A 36 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP A 36 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 36 " 0.050 2.00e-02 2.50e+03 pdb=" NE1 TRP A 36 " 0.069 2.00e-02 2.50e+03 pdb=" CE2 TRP A 36 " 0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP A 36 " 0.069 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 36 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 36 " 0.026 2.00e-02 2.50e+03 pdb=" CH2 TRP A 36 " -0.037 2.00e-02 2.50e+03 pdb=" HD1 TRP A 36 " -0.047 2.00e-02 2.50e+03 pdb=" HE1 TRP A 36 " 0.106 2.00e-02 2.50e+03 pdb=" HE3 TRP A 36 " 0.079 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 36 " -0.076 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 36 " 0.021 2.00e-02 2.50e+03 pdb=" HH2 TRP A 36 " -0.090 2.00e-02 2.50e+03 ... (remaining 1329 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 639 2.19 - 2.79: 15350 2.79 - 3.39: 23731 3.39 - 4.00: 29777 4.00 - 4.60: 43550 Nonbonded interactions: 113047 Sorted by model distance: nonbonded pdb=" OD1 ASP A 73 " pdb=" HG SER A 75 " model vdw 1.584 2.450 nonbonded pdb=" H ASP A 73 " pdb=" HG LEU A 79 " model vdw 1.586 2.270 nonbonded pdb=" OD2 ASP C 199 " pdb=" HG SER C 214 " model vdw 1.601 2.450 nonbonded pdb=" OD1 ASP C 173 " pdb=" HG1 THR C 175 " model vdw 1.622 2.450 nonbonded pdb=" HG SER A 54 " pdb=" OD2 ASP C 246 " model vdw 1.625 2.450 ... (remaining 113042 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.300 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: 0.150 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.840 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 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 : 0.013 0.043 4477 Z= 0.858 Angle : 1.985 10.554 6092 Z= 1.299 Chirality : 0.105 0.412 682 Planarity : 0.016 0.162 789 Dihedral : 14.753 88.871 1621 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 1.91 % Allowed : 10.07 % Favored : 88.02 % Rotamer: Outliers : 1.23 % Allowed : 5.33 % Favored : 93.44 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 11.11 % 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: -2.65 (0.30), residues: 576 helix: -1.56 (0.40), residues: 109 sheet: -1.03 (0.52), residues: 98 loop : -2.13 (0.28), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.144 0.030 TRP A 117 HIS 0.013 0.007 HIS A 214 PHE 0.079 0.017 PHE A 114 TYR 0.279 0.029 TYR B 37 ARG 0.004 0.001 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 PHE cc_start: 0.0319 (p90) cc_final: -0.0730 (p90) REVERT: A 67 ARG cc_start: 0.7665 (mtt180) cc_final: 0.7382 (mpp80) REVERT: A 117 TRP cc_start: 0.7366 (m100) cc_final: 0.7067 (m100) REVERT: A 225 VAL cc_start: 0.7751 (t) cc_final: 0.7332 (t) REVERT: B 67 LYS cc_start: 0.7176 (pttt) cc_final: 0.6547 (ptpp) REVERT: B 159 VAL cc_start: 0.6504 (m) cc_final: 0.6280 (t) REVERT: B 180 SER cc_start: 0.8146 (p) cc_final: 0.7789 (t) REVERT: C 139 THR cc_start: 0.8712 (m) cc_final: 0.8502 (p) REVERT: C 143 LYS cc_start: 0.8901 (tttt) cc_final: 0.8693 (tttt) REVERT: C 153 ASN cc_start: 0.8141 (m-40) cc_final: 0.7856 (m-40) outliers start: 6 outliers final: 3 residues processed: 150 average time/residue: 0.4939 time to fit residues: 87.1334 Evaluate side-chains 105 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN B 174 ASN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4477 Z= 0.332 Angle : 0.880 7.567 6092 Z= 0.489 Chirality : 0.047 0.181 682 Planarity : 0.007 0.078 789 Dihedral : 8.621 36.704 630 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.46 % Favored : 88.02 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -2.67 (0.31), residues: 576 helix: -0.32 (0.46), residues: 107 sheet: -1.40 (0.39), residues: 150 loop : -2.56 (0.30), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 47 HIS 0.003 0.002 HIS B 201 PHE 0.021 0.003 PHE A 29 TYR 0.035 0.003 TYR B 37 ARG 0.005 0.001 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 THR cc_start: 0.7177 (m) cc_final: 0.6139 (m) REVERT: A 217 SER cc_start: 0.8475 (p) cc_final: 0.8164 (t) REVERT: B 67 LYS cc_start: 0.7125 (pttt) cc_final: 0.6447 (ptpp) REVERT: B 84 GLU cc_start: 0.7441 (tp30) cc_final: 0.6951 (tm-30) REVERT: C 139 THR cc_start: 0.8633 (m) cc_final: 0.8423 (p) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.4017 time to fit residues: 59.2612 Evaluate side-chains 92 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN C 234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4477 Z= 0.259 Angle : 0.770 7.593 6092 Z= 0.427 Chirality : 0.045 0.180 682 Planarity : 0.007 0.078 789 Dihedral : 7.725 32.229 630 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.02 % Favored : 86.81 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.78 (0.31), residues: 576 helix: -0.07 (0.46), residues: 107 sheet: -1.49 (0.40), residues: 150 loop : -2.76 (0.30), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 36 HIS 0.004 0.002 HIS A 178 PHE 0.014 0.002 PHE A 114 TYR 0.021 0.002 TYR B 37 ARG 0.003 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.7139 (mmtt) cc_final: 0.5926 (mttt) REVERT: A 115 GLU cc_start: 0.6658 (tm-30) cc_final: 0.6178 (tm-30) REVERT: A 217 SER cc_start: 0.8441 (p) cc_final: 0.8149 (t) REVERT: B 67 LYS cc_start: 0.7076 (pttt) cc_final: 0.6350 (ptpp) REVERT: B 84 GLU cc_start: 0.7293 (tp30) cc_final: 0.7043 (tm-30) REVERT: B 137 VAL cc_start: 0.7680 (t) cc_final: 0.7462 (t) REVERT: B 174 ASN cc_start: 0.7879 (m-40) cc_final: 0.7404 (t0) REVERT: C 217 GLN cc_start: 0.6707 (mt0) cc_final: 0.6483 (mt0) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.3886 time to fit residues: 52.9657 Evaluate side-chains 93 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 24 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 48 optimal weight: 0.0000 chunk 14 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4477 Z= 0.191 Angle : 0.687 7.333 6092 Z= 0.371 Chirality : 0.044 0.164 682 Planarity : 0.006 0.075 789 Dihedral : 6.846 31.811 630 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.94 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.44 (0.32), residues: 576 helix: 0.52 (0.47), residues: 101 sheet: -1.48 (0.40), residues: 156 loop : -2.50 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 36 HIS 0.003 0.001 HIS A 178 PHE 0.031 0.002 PHE A 68 TYR 0.024 0.002 TYR A 60 ARG 0.004 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 THR cc_start: 0.7430 (t) cc_final: 0.7189 (t) REVERT: A 115 GLU cc_start: 0.6432 (tm-30) cc_final: 0.6053 (tm-30) REVERT: A 217 SER cc_start: 0.8308 (p) cc_final: 0.7976 (t) REVERT: B 67 LYS cc_start: 0.6912 (pttt) cc_final: 0.6160 (ptpp) REVERT: B 136 LEU cc_start: 0.7823 (mt) cc_final: 0.7596 (mt) REVERT: B 137 VAL cc_start: 0.7759 (t) cc_final: 0.7522 (t) REVERT: B 174 ASN cc_start: 0.7730 (m-40) cc_final: 0.7501 (t0) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.3793 time to fit residues: 54.6137 Evaluate side-chains 96 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 160 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4477 Z= 0.262 Angle : 0.706 6.736 6092 Z= 0.386 Chirality : 0.044 0.171 682 Planarity : 0.007 0.074 789 Dihedral : 7.041 32.891 630 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.85 % Favored : 86.98 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.71 (0.32), residues: 576 helix: 0.19 (0.46), residues: 107 sheet: -1.67 (0.41), residues: 152 loop : -2.67 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 47 HIS 0.004 0.002 HIS A 178 PHE 0.028 0.003 PHE A 68 TYR 0.023 0.002 TYR B 35 ARG 0.004 0.001 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 LYS cc_start: 0.6930 (pttt) cc_final: 0.6197 (ptpp) REVERT: B 112 GLN cc_start: 0.8682 (tt0) cc_final: 0.8359 (tm-30) REVERT: B 174 ASN cc_start: 0.7902 (m-40) cc_final: 0.7639 (t0) REVERT: B 195 TYR cc_start: 0.7425 (m-80) cc_final: 0.7218 (m-80) REVERT: C 217 GLN cc_start: 0.6828 (mt0) cc_final: 0.6606 (mt0) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.3729 time to fit residues: 48.8180 Evaluate side-chains 91 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.6172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4477 Z= 0.280 Angle : 0.712 6.371 6092 Z= 0.389 Chirality : 0.044 0.168 682 Planarity : 0.007 0.074 789 Dihedral : 7.005 34.034 630 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.37 % Favored : 86.63 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.72 (0.32), residues: 576 helix: 0.38 (0.48), residues: 101 sheet: -1.71 (0.41), residues: 147 loop : -2.67 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 47 HIS 0.005 0.002 HIS A 178 PHE 0.023 0.002 PHE A 68 TYR 0.023 0.002 TYR B 35 ARG 0.002 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.5570 (tmmt) cc_final: 0.5236 (tttp) REVERT: A 115 GLU cc_start: 0.6846 (tm-30) cc_final: 0.6352 (tm-30) REVERT: B 67 LYS cc_start: 0.6894 (pttt) cc_final: 0.6106 (ptpp) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.3721 time to fit residues: 48.8571 Evaluate side-chains 95 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 33 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.6450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4477 Z= 0.177 Angle : 0.629 5.345 6092 Z= 0.340 Chirality : 0.043 0.162 682 Planarity : 0.006 0.074 789 Dihedral : 6.377 29.347 630 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.63 % Favored : 88.02 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.61 (0.33), residues: 576 helix: 0.36 (0.47), residues: 107 sheet: -1.53 (0.41), residues: 149 loop : -2.68 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 92 HIS 0.003 0.001 HIS A 178 PHE 0.023 0.002 PHE A 68 TYR 0.016 0.001 TYR A 60 ARG 0.003 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.6598 (tm-30) cc_final: 0.6215 (tm-30) REVERT: A 217 SER cc_start: 0.8272 (p) cc_final: 0.8029 (t) REVERT: B 67 LYS cc_start: 0.6819 (pttt) cc_final: 0.5969 (ptpp) REVERT: B 137 VAL cc_start: 0.7710 (t) cc_final: 0.7480 (t) REVERT: C 217 GLN cc_start: 0.6837 (mt0) cc_final: 0.6613 (mt0) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.3839 time to fit residues: 53.4664 Evaluate side-chains 96 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 39 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.6651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4477 Z= 0.196 Angle : 0.627 5.287 6092 Z= 0.341 Chirality : 0.043 0.162 682 Planarity : 0.006 0.073 789 Dihedral : 6.195 23.610 630 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.15 % Favored : 87.50 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.57 (0.34), residues: 576 helix: 0.58 (0.49), residues: 104 sheet: -1.66 (0.41), residues: 154 loop : -2.61 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 92 HIS 0.004 0.001 HIS A 178 PHE 0.020 0.002 PHE A 68 TYR 0.014 0.002 TYR B 37 ARG 0.003 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.6751 (tm-30) cc_final: 0.6351 (tm-30) REVERT: B 67 LYS cc_start: 0.6791 (pttt) cc_final: 0.5916 (ptpp) REVERT: C 217 GLN cc_start: 0.6854 (mt0) cc_final: 0.6593 (mt0) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.3938 time to fit residues: 51.4288 Evaluate side-chains 91 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 0.6848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4477 Z= 0.160 Angle : 0.590 5.598 6092 Z= 0.318 Chirality : 0.042 0.157 682 Planarity : 0.006 0.074 789 Dihedral : 5.799 23.054 630 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.76 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.56 (0.33), residues: 576 helix: 0.38 (0.48), residues: 110 sheet: -1.40 (0.42), residues: 145 loop : -2.71 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 36 HIS 0.003 0.001 HIS A 214 PHE 0.018 0.002 PHE A 68 TYR 0.015 0.001 TYR A 159 ARG 0.002 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.6629 (tm-30) cc_final: 0.6319 (tm-30) REVERT: A 217 SER cc_start: 0.8201 (p) cc_final: 0.7889 (t) REVERT: B 67 LYS cc_start: 0.6628 (pttt) cc_final: 0.5668 (ptpp) REVERT: B 137 VAL cc_start: 0.7774 (t) cc_final: 0.7563 (t) REVERT: C 141 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8683 (mt-10) REVERT: C 217 GLN cc_start: 0.6873 (mt0) cc_final: 0.6493 (mt0) REVERT: C 236 PRO cc_start: 0.8141 (Cg_endo) cc_final: 0.7741 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.3734 time to fit residues: 51.6414 Evaluate side-chains 94 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.7045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4477 Z= 0.251 Angle : 0.650 5.468 6092 Z= 0.355 Chirality : 0.043 0.160 682 Planarity : 0.007 0.070 789 Dihedral : 6.166 22.754 630 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.54 % Favored : 86.11 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.61 (0.33), residues: 576 helix: 0.61 (0.49), residues: 104 sheet: -1.58 (0.42), residues: 146 loop : -2.71 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 168 HIS 0.006 0.002 HIS A 178 PHE 0.022 0.002 PHE A 29 TYR 0.015 0.002 TYR B 37 ARG 0.005 0.001 ARG C 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.6814 (tm-30) cc_final: 0.6430 (tm-30) REVERT: B 137 VAL cc_start: 0.7721 (t) cc_final: 0.7518 (t) REVERT: C 217 GLN cc_start: 0.6876 (mt0) cc_final: 0.6529 (mt0) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.4087 time to fit residues: 48.4287 Evaluate side-chains 90 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.126298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.104381 restraints weight = 47468.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.108872 restraints weight = 29001.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.112147 restraints weight = 19862.516| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.7136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4477 Z= 0.280 Angle : 0.685 5.453 6092 Z= 0.375 Chirality : 0.044 0.157 682 Planarity : 0.007 0.068 789 Dihedral : 6.623 23.723 630 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.41 % Favored : 85.07 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.84 (0.33), residues: 576 helix: 0.38 (0.48), residues: 104 sheet: -1.72 (0.41), residues: 149 loop : -2.86 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 36 HIS 0.007 0.002 HIS A 178 PHE 0.021 0.003 PHE A 29 TYR 0.016 0.002 TYR B 37 ARG 0.004 0.001 ARG C 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2615.98 seconds wall clock time: 47 minutes 23.97 seconds (2843.97 seconds total)