Starting phenix.real_space_refine on Tue Feb 3 16:15:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hx4_52457/02_2026/9hx4_52457.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hx4_52457/02_2026/9hx4_52457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hx4_52457/02_2026/9hx4_52457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hx4_52457/02_2026/9hx4_52457.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hx4_52457/02_2026/9hx4_52457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hx4_52457/02_2026/9hx4_52457.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 3040 2.51 5 N 800 2.21 5 O 990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4840 Number of models: 1 Model: "" Number of chains: 10 Chain: "F" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 484 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "E" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 484 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "B" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 484 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "A" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 484 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "C" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 484 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "D" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 484 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "G" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 484 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "H" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 484 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "I" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 484 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "J" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 484 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Time building chain proxies: 1.20, per 1000 atoms: 0.25 Number of scatterers: 4840 At special positions: 0 Unit cell: (104.96, 98.56, 47.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 990 8.00 N 800 7.00 C 3040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 203.1 milliseconds 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1180 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 23 removed outlier: 6.839A pdb=" N VAL F 22 " --> pdb=" O SER D 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 28 through 35 removed outlier: 6.457A pdb=" N THR B 29 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N TRP D 32 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N MET B 31 " --> pdb=" O TRP D 32 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N TYR D 34 " --> pdb=" O MET B 31 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ASP B 33 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYR F 34 " --> pdb=" O ASP D 33 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N PHE D 35 " --> pdb=" O TYR F 34 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR F 29 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N TRP H 32 " --> pdb=" O THR F 29 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N MET F 31 " --> pdb=" O TRP H 32 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N TYR H 34 " --> pdb=" O MET F 31 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ASP F 33 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR H 29 " --> pdb=" O VAL J 30 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N TRP J 32 " --> pdb=" O THR H 29 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N MET H 31 " --> pdb=" O TRP J 32 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N TYR J 34 " --> pdb=" O MET H 31 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ASP H 33 " --> pdb=" O TYR J 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 48 removed outlier: 7.108A pdb=" N VAL B 46 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL F 46 " --> pdb=" O GLU H 47 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL H 46 " --> pdb=" O GLU J 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 73 removed outlier: 6.570A pdb=" N GLU B 68 " --> pdb=" O VAL D 69 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N THR D 71 " --> pdb=" O GLU B 68 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN B 70 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ALA D 73 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N TYR B 72 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLU F 68 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N THR H 71 " --> pdb=" O GLU F 68 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN F 70 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ALA H 73 " --> pdb=" O ASN F 70 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N TYR F 72 " --> pdb=" O ALA H 73 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU H 68 " --> pdb=" O VAL J 69 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N THR J 71 " --> pdb=" O GLU H 68 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN H 70 " --> pdb=" O THR J 71 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ALA J 73 " --> pdb=" O ASN H 70 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N TYR H 72 " --> pdb=" O ALA J 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 26 through 35 removed outlier: 6.799A pdb=" N TYR A 34 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N PHE C 35 " --> pdb=" O TYR A 34 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TYR C 34 " --> pdb=" O ASP E 33 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N PHE E 35 " --> pdb=" O TYR C 34 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLN E 26 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N THR G 29 " --> pdb=" O GLN E 26 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA E 28 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N MET G 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL E 30 " --> pdb=" O MET G 31 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ASP G 33 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N TRP E 32 " --> pdb=" O ASP G 33 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N PHE G 35 " --> pdb=" O TRP E 32 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N TYR E 34 " --> pdb=" O PHE G 35 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLN G 26 " --> pdb=" O VAL I 27 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR I 29 " --> pdb=" O GLN G 26 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA G 28 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N MET I 31 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL G 30 " --> pdb=" O MET I 31 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ASP I 33 " --> pdb=" O VAL G 30 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N TRP G 32 " --> pdb=" O ASP I 33 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N PHE I 35 " --> pdb=" O TRP G 32 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N TYR G 34 " --> pdb=" O PHE I 35 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 46 through 48 removed outlier: 6.058A pdb=" N GLU A 47 " --> pdb=" O HIS C 48 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL E 46 " --> pdb=" O GLU C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 56 through 57 removed outlier: 6.167A pdb=" N GLN A 56 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLN E 56 " --> pdb=" O GLN G 57 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLN G 56 " --> pdb=" O GLN I 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 68 through 73 removed outlier: 6.646A pdb=" N GLU E 68 " --> pdb=" O VAL C 69 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N THR C 71 " --> pdb=" O GLU E 68 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN E 70 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ALA C 73 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR E 72 " --> pdb=" O ALA C 73 " (cutoff:3.500A) 49 hydrogen bonds defined for protein. 147 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: 0.44 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1630 1.34 - 1.46: 876 1.46 - 1.57: 2374 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 4900 Sorted by residual: bond pdb=" CA ALA J 60 " pdb=" C ALA J 60 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.17e-02 7.31e+03 4.65e-01 bond pdb=" CA ALA D 60 " pdb=" C ALA D 60 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.17e-02 7.31e+03 4.61e-01 bond pdb=" CA ALA F 60 " pdb=" C ALA F 60 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.17e-02 7.31e+03 4.38e-01 bond pdb=" CA ALA B 60 " pdb=" C ALA B 60 " ideal model delta sigma weight residual 1.530 1.523 0.008 1.17e-02 7.31e+03 4.15e-01 bond pdb=" CA ALA H 60 " pdb=" C ALA H 60 " ideal model delta sigma weight residual 1.530 1.523 0.007 1.17e-02 7.31e+03 4.01e-01 ... (remaining 4895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.85: 6047 0.85 - 1.69: 502 1.69 - 2.54: 51 2.54 - 3.38: 10 3.38 - 4.23: 10 Bond angle restraints: 6620 Sorted by residual: angle pdb=" N SER D 36 " pdb=" CA SER D 36 " pdb=" C SER D 36 " ideal model delta sigma weight residual 107.49 111.72 -4.23 1.74e+00 3.30e-01 5.90e+00 angle pdb=" N SER B 36 " pdb=" CA SER B 36 " pdb=" C SER B 36 " ideal model delta sigma weight residual 107.49 111.71 -4.22 1.74e+00 3.30e-01 5.89e+00 angle pdb=" N SER H 36 " pdb=" CA SER H 36 " pdb=" C SER H 36 " ideal model delta sigma weight residual 107.49 111.70 -4.21 1.74e+00 3.30e-01 5.87e+00 angle pdb=" N SER G 36 " pdb=" CA SER G 36 " pdb=" C SER G 36 " ideal model delta sigma weight residual 107.49 111.68 -4.19 1.74e+00 3.30e-01 5.79e+00 angle pdb=" N SER C 36 " pdb=" CA SER C 36 " pdb=" C SER C 36 " ideal model delta sigma weight residual 107.49 111.67 -4.18 1.74e+00 3.30e-01 5.78e+00 ... (remaining 6615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.81: 2610 14.81 - 29.62: 266 29.62 - 44.43: 64 44.43 - 59.24: 10 59.24 - 74.05: 10 Dihedral angle restraints: 2960 sinusoidal: 1160 harmonic: 1800 Sorted by residual: dihedral pdb=" CB MET F 31 " pdb=" CG MET F 31 " pdb=" SD MET F 31 " pdb=" CE MET F 31 " ideal model delta sinusoidal sigma weight residual -60.00 -108.12 48.12 3 1.50e+01 4.44e-03 8.59e+00 dihedral pdb=" CB MET H 31 " pdb=" CG MET H 31 " pdb=" SD MET H 31 " pdb=" CE MET H 31 " ideal model delta sinusoidal sigma weight residual -60.00 -108.12 48.12 3 1.50e+01 4.44e-03 8.59e+00 dihedral pdb=" CB MET B 31 " pdb=" CG MET B 31 " pdb=" SD MET B 31 " pdb=" CE MET B 31 " ideal model delta sinusoidal sigma weight residual -60.00 -108.11 48.11 3 1.50e+01 4.44e-03 8.59e+00 ... (remaining 2957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 360 0.024 - 0.048: 273 0.048 - 0.072: 67 0.072 - 0.096: 10 0.096 - 0.120: 50 Chirality restraints: 760 Sorted by residual: chirality pdb=" CA VAL C 22 " pdb=" N VAL C 22 " pdb=" C VAL C 22 " pdb=" CB VAL C 22 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.59e-01 chirality pdb=" CA VAL I 22 " pdb=" N VAL I 22 " pdb=" C VAL I 22 " pdb=" CB VAL I 22 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.58e-01 chirality pdb=" CA VAL B 22 " pdb=" N VAL B 22 " pdb=" C VAL B 22 " pdb=" CB VAL B 22 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.51e-01 ... (remaining 757 not shown) Planarity restraints: 860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER J 36 " -0.003 2.00e-02 2.50e+03 6.27e-03 3.94e-01 pdb=" C SER J 36 " 0.011 2.00e-02 2.50e+03 pdb=" O SER J 36 " -0.004 2.00e-02 2.50e+03 pdb=" N GLN J 37 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 36 " -0.003 2.00e-02 2.50e+03 6.20e-03 3.85e-01 pdb=" C SER H 36 " 0.011 2.00e-02 2.50e+03 pdb=" O SER H 36 " -0.004 2.00e-02 2.50e+03 pdb=" N GLN H 37 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 36 " -0.003 2.00e-02 2.50e+03 6.17e-03 3.81e-01 pdb=" C SER E 36 " 0.011 2.00e-02 2.50e+03 pdb=" O SER E 36 " -0.004 2.00e-02 2.50e+03 pdb=" N GLN E 37 " -0.004 2.00e-02 2.50e+03 ... (remaining 857 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 366 2.73 - 3.27: 5054 3.27 - 3.82: 8330 3.82 - 4.36: 10002 4.36 - 4.90: 20074 Nonbonded interactions: 43826 Sorted by model distance: nonbonded pdb=" OG SER I 36 " pdb=" OG SER I 39 " model vdw 2.188 3.040 nonbonded pdb=" OG SER G 36 " pdb=" OG SER G 39 " model vdw 2.188 3.040 nonbonded pdb=" OG SER E 36 " pdb=" OG SER E 39 " model vdw 2.189 3.040 nonbonded pdb=" OG SER C 36 " pdb=" OG SER C 39 " model vdw 2.189 3.040 nonbonded pdb=" OG SER A 36 " pdb=" OG SER A 39 " model vdw 2.189 3.040 ... (remaining 43821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 5.230 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 4900 Z= 0.105 Angle : 0.495 4.226 6620 Z= 0.321 Chirality : 0.041 0.120 760 Planarity : 0.001 0.006 860 Dihedral : 13.306 74.050 1780 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.27), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.20), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.000 TYR H 34 PHE 0.002 0.000 PHE A 35 TRP 0.001 0.000 TRP G 32 HIS 0.001 0.000 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00182 ( 4900) covalent geometry : angle 0.49516 ( 6620) hydrogen bonds : bond 0.12684 ( 49) hydrogen bonds : angle 7.73671 ( 147) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.148 Fit side-chains REVERT: F 55 THR cc_start: 0.7678 (t) cc_final: 0.7412 (m) REVERT: E 44 GLU cc_start: 0.8159 (mp0) cc_final: 0.7403 (mp0) REVERT: E 66 LEU cc_start: 0.7364 (mt) cc_final: 0.7121 (mp) REVERT: E 70 ASN cc_start: 0.8787 (m-40) cc_final: 0.8570 (m-40) REVERT: B 63 GLN cc_start: 0.9180 (mt0) cc_final: 0.8899 (mt0) REVERT: A 21 GLU cc_start: 0.6998 (tp30) cc_final: 0.6655 (tp30) REVERT: A 50 GLN cc_start: 0.8808 (mt0) cc_final: 0.8506 (mt0) REVERT: A 51 LYS cc_start: 0.8318 (mttt) cc_final: 0.7695 (mttp) REVERT: A 57 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8219 (mt0) REVERT: A 70 ASN cc_start: 0.8678 (m-40) cc_final: 0.8383 (m-40) REVERT: A 78 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8160 (mtmm) REVERT: C 78 LYS cc_start: 0.8527 (mtpt) cc_final: 0.8200 (mtmm) REVERT: C 80 LEU cc_start: 0.8115 (mp) cc_final: 0.7668 (mt) REVERT: G 38 LEU cc_start: 0.8226 (tp) cc_final: 0.7986 (tp) REVERT: G 70 ASN cc_start: 0.8859 (m-40) cc_final: 0.8638 (m-40) REVERT: G 78 LYS cc_start: 0.8615 (mtpt) cc_final: 0.8172 (mtmt) REVERT: H 26 GLN cc_start: 0.8154 (mt0) cc_final: 0.7792 (mt0) REVERT: H 57 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7324 (mm-40) REVERT: H 78 LYS cc_start: 0.8242 (mtpt) cc_final: 0.7849 (mtpt) REVERT: I 50 GLN cc_start: 0.8312 (mt0) cc_final: 0.7866 (mt0) REVERT: I 78 LYS cc_start: 0.8400 (mtpt) cc_final: 0.8113 (mtpp) REVERT: J 41 ASN cc_start: 0.8781 (m-40) cc_final: 0.8566 (m110) REVERT: J 57 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7836 (mm-40) REVERT: J 78 LYS cc_start: 0.8262 (mtpt) cc_final: 0.8028 (mtpt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.0576 time to fit residues: 10.9189 Evaluate side-chains 123 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.2980 chunk 24 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 0.1980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 26 GLN F 41 ASN F 63 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN B 41 ASN B 63 GLN A 37 GLN A 41 ASN A 63 GLN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN C 77 GLN D 41 ASN ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN H 41 ASN H 50 GLN H 63 GLN H 77 GLN ** I 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN J 50 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.122463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.108644 restraints weight = 6862.043| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.25 r_work: 0.3631 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4900 Z= 0.173 Angle : 0.595 6.229 6620 Z= 0.318 Chirality : 0.045 0.132 760 Planarity : 0.002 0.011 860 Dihedral : 4.720 15.939 620 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.21 % Allowed : 6.98 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.26), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.20), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR E 72 PHE 0.006 0.001 PHE D 35 TRP 0.005 0.001 TRP A 32 HIS 0.001 0.001 HIS G 48 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 4900) covalent geometry : angle 0.59455 ( 6620) hydrogen bonds : bond 0.01487 ( 49) hydrogen bonds : angle 4.13430 ( 147) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 59 ASN cc_start: 0.8649 (m-40) cc_final: 0.8264 (m-40) REVERT: F 78 LYS cc_start: 0.8633 (mttm) cc_final: 0.8293 (mttp) REVERT: E 38 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8936 (mp) REVERT: E 41 ASN cc_start: 0.9140 (m-40) cc_final: 0.8850 (m110) REVERT: E 44 GLU cc_start: 0.8205 (mp0) cc_final: 0.7401 (mp0) REVERT: E 63 GLN cc_start: 0.8707 (mt0) cc_final: 0.8373 (mt0) REVERT: E 70 ASN cc_start: 0.9084 (m-40) cc_final: 0.8858 (m-40) REVERT: E 72 TYR cc_start: 0.8071 (m-80) cc_final: 0.7803 (m-80) REVERT: B 44 GLU cc_start: 0.8930 (mp0) cc_final: 0.8251 (mp0) REVERT: B 47 GLU cc_start: 0.8246 (mt-10) cc_final: 0.8013 (mt-10) REVERT: B 57 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7836 (mm-40) REVERT: B 75 ASP cc_start: 0.8638 (p0) cc_final: 0.8278 (p0) REVERT: B 78 LYS cc_start: 0.8870 (mtpt) cc_final: 0.8394 (mttt) REVERT: C 78 LYS cc_start: 0.8683 (mtpt) cc_final: 0.8295 (mtmm) REVERT: D 33 ASP cc_start: 0.8469 (t0) cc_final: 0.8236 (t0) REVERT: D 57 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7166 (mm-40) REVERT: D 75 ASP cc_start: 0.8352 (p0) cc_final: 0.8112 (p0) REVERT: D 78 LYS cc_start: 0.8876 (mttp) cc_final: 0.8627 (mttm) REVERT: G 50 GLN cc_start: 0.8644 (mt0) cc_final: 0.8331 (mt0) REVERT: G 51 LYS cc_start: 0.8436 (mttt) cc_final: 0.7867 (mtpp) REVERT: G 63 GLN cc_start: 0.8621 (mt0) cc_final: 0.8285 (mt0) REVERT: G 78 LYS cc_start: 0.8852 (mtpt) cc_final: 0.8485 (ttmt) REVERT: H 26 GLN cc_start: 0.8646 (mt0) cc_final: 0.8364 (mt0) REVERT: H 44 GLU cc_start: 0.8719 (mp0) cc_final: 0.8167 (mp0) REVERT: H 78 LYS cc_start: 0.8608 (mtpt) cc_final: 0.8254 (mtpt) REVERT: I 51 LYS cc_start: 0.8692 (mttt) cc_final: 0.8175 (mttp) REVERT: I 78 LYS cc_start: 0.8768 (mtpt) cc_final: 0.8272 (mttp) REVERT: J 26 GLN cc_start: 0.8494 (mt0) cc_final: 0.8280 (mt0) REVERT: J 33 ASP cc_start: 0.8619 (t0) cc_final: 0.8150 (t0) REVERT: J 38 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8319 (tp) REVERT: J 40 ASN cc_start: 0.8813 (m-40) cc_final: 0.8373 (m-40) REVERT: J 47 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7994 (mt-10) outliers start: 17 outliers final: 10 residues processed: 150 average time/residue: 0.0496 time to fit residues: 9.7573 Evaluate side-chains 140 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 48 HIS Chi-restraints excluded: chain J residue 38 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 13 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 41 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 GLN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN H 63 GLN I 50 GLN J 37 GLN J 41 ASN ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.122096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.108102 restraints weight = 6798.091| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.32 r_work: 0.3633 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4900 Z= 0.148 Angle : 0.554 5.744 6620 Z= 0.294 Chirality : 0.044 0.126 760 Planarity : 0.002 0.012 860 Dihedral : 4.612 17.086 620 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.64 % Allowed : 12.26 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.27), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.21), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR J 34 PHE 0.007 0.001 PHE A 35 TRP 0.003 0.001 TRP A 32 HIS 0.001 0.000 HIS D 48 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 4900) covalent geometry : angle 0.55409 ( 6620) hydrogen bonds : bond 0.01458 ( 49) hydrogen bonds : angle 4.04203 ( 147) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 59 ASN cc_start: 0.8739 (m-40) cc_final: 0.8295 (m-40) REVERT: F 75 ASP cc_start: 0.7376 (p0) cc_final: 0.6905 (p0) REVERT: E 44 GLU cc_start: 0.8291 (mp0) cc_final: 0.7297 (mp0) REVERT: E 70 ASN cc_start: 0.9066 (m-40) cc_final: 0.8865 (m-40) REVERT: E 72 TYR cc_start: 0.8119 (m-80) cc_final: 0.7827 (m-80) REVERT: B 39 SER cc_start: 0.7806 (m) cc_final: 0.7157 (m) REVERT: B 41 ASN cc_start: 0.8725 (m-40) cc_final: 0.8512 (m110) REVERT: B 44 GLU cc_start: 0.9002 (mp0) cc_final: 0.8163 (mp0) REVERT: B 47 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8215 (mt-10) REVERT: B 75 ASP cc_start: 0.8589 (p0) cc_final: 0.8146 (p0) REVERT: B 78 LYS cc_start: 0.8756 (mtpt) cc_final: 0.8204 (mttt) REVERT: C 78 LYS cc_start: 0.8673 (mtpt) cc_final: 0.8244 (mtmm) REVERT: D 33 ASP cc_start: 0.8690 (t0) cc_final: 0.8446 (t0) REVERT: D 75 ASP cc_start: 0.8460 (p0) cc_final: 0.8134 (p0) REVERT: D 78 LYS cc_start: 0.8877 (mttt) cc_final: 0.8670 (mttp) REVERT: G 50 GLN cc_start: 0.8647 (mt0) cc_final: 0.8348 (mt0) REVERT: G 51 LYS cc_start: 0.8396 (mttt) cc_final: 0.7708 (mttp) REVERT: G 63 GLN cc_start: 0.8619 (mt0) cc_final: 0.8343 (mt0) REVERT: G 78 LYS cc_start: 0.8839 (mtpt) cc_final: 0.8338 (mtmt) REVERT: H 26 GLN cc_start: 0.8622 (mt0) cc_final: 0.8334 (mt0) REVERT: H 41 ASN cc_start: 0.9087 (m-40) cc_final: 0.8868 (m110) REVERT: H 44 GLU cc_start: 0.8815 (mp0) cc_final: 0.8111 (mp0) REVERT: H 59 ASN cc_start: 0.8818 (m-40) cc_final: 0.8516 (m-40) REVERT: H 78 LYS cc_start: 0.8538 (mtpt) cc_final: 0.8217 (mtpt) REVERT: I 51 LYS cc_start: 0.8645 (mttt) cc_final: 0.8117 (mttp) REVERT: I 78 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8282 (mttp) REVERT: J 26 GLN cc_start: 0.8432 (mt0) cc_final: 0.8070 (mt0) REVERT: J 33 ASP cc_start: 0.8741 (t0) cc_final: 0.8260 (t0) REVERT: J 40 ASN cc_start: 0.8938 (m-40) cc_final: 0.8365 (m-40) REVERT: J 44 GLU cc_start: 0.8666 (mp0) cc_final: 0.8337 (mp0) REVERT: J 47 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8029 (mt-10) REVERT: J 65 LYS cc_start: 0.8520 (mttt) cc_final: 0.6234 (mmtt) outliers start: 14 outliers final: 11 residues processed: 139 average time/residue: 0.0610 time to fit residues: 10.9471 Evaluate side-chains 133 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 76 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 15 optimal weight: 0.0170 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 overall best weight: 3.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 ASN ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.114923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.100995 restraints weight = 6959.355| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.24 r_work: 0.3528 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4900 Z= 0.228 Angle : 0.612 5.927 6620 Z= 0.326 Chirality : 0.046 0.122 760 Planarity : 0.002 0.009 860 Dihedral : 4.940 17.367 620 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.58 % Allowed : 14.72 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.27), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.20), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR J 34 PHE 0.008 0.001 PHE C 62 TRP 0.003 0.001 TRP J 32 HIS 0.002 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 4900) covalent geometry : angle 0.61175 ( 6620) hydrogen bonds : bond 0.01764 ( 49) hydrogen bonds : angle 4.03111 ( 147) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 59 ASN cc_start: 0.8846 (m-40) cc_final: 0.8493 (m110) REVERT: F 75 ASP cc_start: 0.7662 (p0) cc_final: 0.7153 (p0) REVERT: E 44 GLU cc_start: 0.8466 (mp0) cc_final: 0.7507 (mp0) REVERT: E 72 TYR cc_start: 0.8126 (m-80) cc_final: 0.7865 (m-80) REVERT: B 44 GLU cc_start: 0.8956 (mp0) cc_final: 0.8203 (mp0) REVERT: B 57 GLN cc_start: 0.8544 (mt0) cc_final: 0.8321 (mt0) REVERT: B 75 ASP cc_start: 0.8640 (p0) cc_final: 0.8137 (p0) REVERT: B 78 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8203 (mttt) REVERT: A 33 ASP cc_start: 0.9019 (t0) cc_final: 0.8722 (t0) REVERT: A 44 GLU cc_start: 0.8727 (mp0) cc_final: 0.8383 (mp0) REVERT: A 51 LYS cc_start: 0.8481 (mttt) cc_final: 0.7943 (mttp) REVERT: C 78 LYS cc_start: 0.8853 (mtpt) cc_final: 0.8273 (mtmm) REVERT: D 33 ASP cc_start: 0.8690 (t0) cc_final: 0.8481 (t0) REVERT: D 34 TYR cc_start: 0.8756 (t80) cc_final: 0.8503 (t80) REVERT: D 75 ASP cc_start: 0.8513 (p0) cc_final: 0.8048 (p0) REVERT: D 78 LYS cc_start: 0.8839 (mttt) cc_final: 0.8590 (mttp) REVERT: G 51 LYS cc_start: 0.8354 (mttt) cc_final: 0.7779 (mtpp) REVERT: G 63 GLN cc_start: 0.8615 (mt0) cc_final: 0.8316 (mt0) REVERT: H 26 GLN cc_start: 0.8702 (mt0) cc_final: 0.8449 (mt0) REVERT: H 44 GLU cc_start: 0.8910 (mp0) cc_final: 0.8205 (mp0) REVERT: H 57 GLN cc_start: 0.8296 (mm-40) cc_final: 0.7193 (mm-40) REVERT: H 63 GLN cc_start: 0.9231 (mt0) cc_final: 0.9001 (mt0) REVERT: H 78 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8230 (mtpt) REVERT: I 51 LYS cc_start: 0.8666 (mttt) cc_final: 0.8025 (mttp) REVERT: I 78 LYS cc_start: 0.8788 (mtpt) cc_final: 0.8237 (mttp) REVERT: J 26 GLN cc_start: 0.8460 (mt0) cc_final: 0.8140 (mt0) REVERT: J 33 ASP cc_start: 0.8821 (t0) cc_final: 0.8273 (t0) REVERT: J 40 ASN cc_start: 0.8801 (m-40) cc_final: 0.8389 (m-40) REVERT: J 44 GLU cc_start: 0.8830 (mp0) cc_final: 0.8499 (mp0) REVERT: J 47 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7857 (mt-10) REVERT: J 57 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8012 (mm-40) REVERT: J 65 LYS cc_start: 0.8615 (mttt) cc_final: 0.6480 (mmtt) outliers start: 19 outliers final: 16 residues processed: 147 average time/residue: 0.0739 time to fit residues: 13.9062 Evaluate side-chains 142 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain J residue 76 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 5 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 15 optimal weight: 0.1980 chunk 40 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 0.0670 chunk 38 optimal weight: 7.9990 overall best weight: 2.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 GLN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 ASN ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.119004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.105319 restraints weight = 6979.879| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.27 r_work: 0.3604 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4900 Z= 0.155 Angle : 0.557 8.410 6620 Z= 0.293 Chirality : 0.044 0.125 760 Planarity : 0.002 0.009 860 Dihedral : 4.668 18.731 620 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.64 % Allowed : 17.92 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.27), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.21), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR J 34 PHE 0.008 0.001 PHE C 62 TRP 0.003 0.001 TRP A 32 HIS 0.002 0.000 HIS D 48 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 4900) covalent geometry : angle 0.55683 ( 6620) hydrogen bonds : bond 0.01449 ( 49) hydrogen bonds : angle 3.99088 ( 147) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 59 ASN cc_start: 0.8771 (m-40) cc_final: 0.8409 (m110) REVERT: F 75 ASP cc_start: 0.7562 (p0) cc_final: 0.6938 (p0) REVERT: F 77 GLN cc_start: 0.8917 (mt0) cc_final: 0.8564 (mp10) REVERT: E 44 GLU cc_start: 0.8494 (mp0) cc_final: 0.7501 (mp0) REVERT: E 72 TYR cc_start: 0.8224 (m-80) cc_final: 0.7846 (m-80) REVERT: B 44 GLU cc_start: 0.8983 (mp0) cc_final: 0.8213 (mp0) REVERT: B 75 ASP cc_start: 0.8596 (p0) cc_final: 0.8089 (p0) REVERT: B 78 LYS cc_start: 0.8749 (mtpt) cc_final: 0.8207 (mttt) REVERT: A 33 ASP cc_start: 0.9104 (t0) cc_final: 0.8730 (t0) REVERT: A 44 GLU cc_start: 0.8771 (mp0) cc_final: 0.8513 (mp0) REVERT: C 31 MET cc_start: 0.9226 (mtm) cc_final: 0.8902 (mtm) REVERT: C 78 LYS cc_start: 0.8891 (mtpt) cc_final: 0.8317 (mtmm) REVERT: D 33 ASP cc_start: 0.8701 (t0) cc_final: 0.8493 (t0) REVERT: D 75 ASP cc_start: 0.8392 (p0) cc_final: 0.7990 (p0) REVERT: G 51 LYS cc_start: 0.8315 (mttt) cc_final: 0.7767 (mtpp) REVERT: G 63 GLN cc_start: 0.8565 (mt0) cc_final: 0.8271 (mt0) REVERT: H 26 GLN cc_start: 0.8676 (mt0) cc_final: 0.8411 (mt0) REVERT: H 41 ASN cc_start: 0.9163 (m-40) cc_final: 0.8939 (m110) REVERT: H 44 GLU cc_start: 0.8914 (mp0) cc_final: 0.8168 (mp0) REVERT: H 78 LYS cc_start: 0.8619 (mtpt) cc_final: 0.8191 (mtpp) REVERT: I 51 LYS cc_start: 0.8634 (mttt) cc_final: 0.8037 (mttp) REVERT: I 78 LYS cc_start: 0.8793 (mtpt) cc_final: 0.8239 (mttp) REVERT: J 26 GLN cc_start: 0.8422 (mt0) cc_final: 0.8024 (mt0) REVERT: J 33 ASP cc_start: 0.8893 (t0) cc_final: 0.8337 (t0) REVERT: J 40 ASN cc_start: 0.8721 (m-40) cc_final: 0.8511 (m-40) REVERT: J 44 GLU cc_start: 0.8793 (mp0) cc_final: 0.8495 (mp0) REVERT: J 65 LYS cc_start: 0.8478 (mttt) cc_final: 0.6437 (mmtt) outliers start: 14 outliers final: 12 residues processed: 138 average time/residue: 0.0596 time to fit residues: 10.6227 Evaluate side-chains 135 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 76 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.107357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.093978 restraints weight = 7456.936| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.24 r_work: 0.3410 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.050 4900 Z= 0.384 Angle : 0.720 8.045 6620 Z= 0.385 Chirality : 0.050 0.141 760 Planarity : 0.003 0.020 860 Dihedral : 5.492 19.246 620 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 5.47 % Allowed : 16.42 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.75 (0.26), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.19), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.023 0.003 TYR J 34 PHE 0.014 0.002 PHE C 62 TRP 0.006 0.001 TRP D 32 HIS 0.003 0.001 HIS J 48 Details of bonding type rmsd covalent geometry : bond 0.00876 ( 4900) covalent geometry : angle 0.71997 ( 6620) hydrogen bonds : bond 0.02037 ( 49) hydrogen bonds : angle 4.19480 ( 147) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: F 38 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8802 (tt) REVERT: F 59 ASN cc_start: 0.8948 (m-40) cc_final: 0.8670 (m110) REVERT: F 78 LYS cc_start: 0.8776 (mttm) cc_final: 0.8323 (mttp) REVERT: E 44 GLU cc_start: 0.8519 (mp0) cc_final: 0.7684 (mp0) REVERT: E 51 LYS cc_start: 0.8135 (mttt) cc_final: 0.7792 (mttp) REVERT: E 55 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8441 (m) REVERT: E 72 TYR cc_start: 0.8133 (m-80) cc_final: 0.7774 (m-80) REVERT: B 37 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.8922 (tt0) REVERT: B 44 GLU cc_start: 0.9079 (mp0) cc_final: 0.8278 (mp0) REVERT: B 59 ASN cc_start: 0.8856 (m-40) cc_final: 0.8645 (m-40) REVERT: B 63 GLN cc_start: 0.9239 (mt0) cc_final: 0.8844 (mt0) REVERT: B 65 LYS cc_start: 0.8913 (mttt) cc_final: 0.8587 (mttt) REVERT: B 75 ASP cc_start: 0.8599 (p0) cc_final: 0.8025 (p0) REVERT: B 78 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8024 (mttt) REVERT: A 33 ASP cc_start: 0.9057 (t0) cc_final: 0.8747 (t0) REVERT: A 44 GLU cc_start: 0.8804 (mp0) cc_final: 0.8415 (mp0) REVERT: A 51 LYS cc_start: 0.8569 (mttt) cc_final: 0.8038 (mttp) REVERT: C 51 LYS cc_start: 0.8483 (mttt) cc_final: 0.7764 (mttp) REVERT: C 77 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.8276 (mt0) REVERT: C 78 LYS cc_start: 0.8929 (mtpt) cc_final: 0.8574 (ttmt) REVERT: D 33 ASP cc_start: 0.8719 (t0) cc_final: 0.8509 (t0) REVERT: G 51 LYS cc_start: 0.8329 (mttt) cc_final: 0.7795 (mtpp) REVERT: G 56 GLN cc_start: 0.9006 (mt0) cc_final: 0.8782 (mt0) REVERT: G 57 GLN cc_start: 0.8735 (mt0) cc_final: 0.8368 (mt0) REVERT: H 26 GLN cc_start: 0.8720 (mt0) cc_final: 0.8443 (mt0) REVERT: H 44 GLU cc_start: 0.9149 (mp0) cc_final: 0.8420 (mp0) REVERT: H 57 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8246 (mt0) REVERT: H 78 LYS cc_start: 0.8625 (mtpt) cc_final: 0.8006 (mttt) REVERT: I 51 LYS cc_start: 0.8660 (mttt) cc_final: 0.8161 (mttp) REVERT: I 78 LYS cc_start: 0.8797 (mtpt) cc_final: 0.8396 (mttt) REVERT: J 26 GLN cc_start: 0.8527 (mt0) cc_final: 0.8205 (mt0) REVERT: J 37 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8654 (tt0) REVERT: J 44 GLU cc_start: 0.8866 (mp0) cc_final: 0.8446 (mp0) REVERT: J 78 LYS cc_start: 0.8849 (mtpt) cc_final: 0.8058 (mttt) outliers start: 29 outliers final: 21 residues processed: 154 average time/residue: 0.0647 time to fit residues: 12.8255 Evaluate side-chains 150 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 76 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 GLN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 GLN ** J 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.110692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.097341 restraints weight = 7070.167| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.17 r_work: 0.3466 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 4900 Z= 0.280 Angle : 0.651 8.848 6620 Z= 0.347 Chirality : 0.048 0.131 760 Planarity : 0.002 0.017 860 Dihedral : 5.283 17.564 620 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.28 % Allowed : 17.17 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.71 (0.26), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.20), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.003 TYR J 34 PHE 0.011 0.002 PHE C 62 TRP 0.003 0.001 TRP J 32 HIS 0.002 0.001 HIS J 48 Details of bonding type rmsd covalent geometry : bond 0.00637 ( 4900) covalent geometry : angle 0.65113 ( 6620) hydrogen bonds : bond 0.01767 ( 49) hydrogen bonds : angle 4.18078 ( 147) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 38 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8725 (tt) REVERT: F 59 ASN cc_start: 0.8904 (m-40) cc_final: 0.8617 (m110) REVERT: E 44 GLU cc_start: 0.8630 (mp0) cc_final: 0.7796 (mp0) REVERT: E 51 LYS cc_start: 0.8181 (mttt) cc_final: 0.7811 (mttp) REVERT: E 72 TYR cc_start: 0.8139 (m-80) cc_final: 0.7814 (m-80) REVERT: B 44 GLU cc_start: 0.9073 (mp0) cc_final: 0.8258 (mp0) REVERT: B 63 GLN cc_start: 0.9186 (mt0) cc_final: 0.8672 (mt0) REVERT: B 65 LYS cc_start: 0.8917 (mttt) cc_final: 0.8382 (mttt) REVERT: B 75 ASP cc_start: 0.8660 (p0) cc_final: 0.8063 (p0) REVERT: B 78 LYS cc_start: 0.8634 (mtpt) cc_final: 0.7950 (mttt) REVERT: A 33 ASP cc_start: 0.9010 (t0) cc_final: 0.8719 (t0) REVERT: A 44 GLU cc_start: 0.8843 (mp0) cc_final: 0.8433 (mp0) REVERT: A 51 LYS cc_start: 0.8512 (mttt) cc_final: 0.7965 (mttp) REVERT: C 31 MET cc_start: 0.9177 (mtm) cc_final: 0.8861 (mtm) REVERT: C 51 LYS cc_start: 0.8488 (mttt) cc_final: 0.7762 (mttp) REVERT: C 78 LYS cc_start: 0.8964 (mtpt) cc_final: 0.8588 (ttmt) REVERT: D 33 ASP cc_start: 0.8688 (t0) cc_final: 0.8485 (t0) REVERT: G 51 LYS cc_start: 0.8347 (mttt) cc_final: 0.7795 (mtpp) REVERT: G 63 GLN cc_start: 0.8669 (mt0) cc_final: 0.8390 (mt0) REVERT: H 26 GLN cc_start: 0.8605 (mt0) cc_final: 0.8318 (mt0) REVERT: H 38 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8830 (mp) REVERT: H 44 GLU cc_start: 0.9132 (mp0) cc_final: 0.8371 (mp0) REVERT: H 57 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8181 (mt0) REVERT: H 78 LYS cc_start: 0.8633 (mtpt) cc_final: 0.7984 (mttt) REVERT: I 51 LYS cc_start: 0.8681 (mttt) cc_final: 0.8179 (mttp) REVERT: J 26 GLN cc_start: 0.8453 (mt0) cc_final: 0.8120 (mt0) REVERT: J 37 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8536 (tt0) REVERT: J 44 GLU cc_start: 0.8911 (mp0) cc_final: 0.8489 (mp0) outliers start: 28 outliers final: 24 residues processed: 148 average time/residue: 0.0597 time to fit residues: 11.4314 Evaluate side-chains 152 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain J residue 37 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 12 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.115469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.102033 restraints weight = 6972.914| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.15 r_work: 0.3553 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4900 Z= 0.164 Angle : 0.584 8.327 6620 Z= 0.307 Chirality : 0.045 0.142 760 Planarity : 0.002 0.012 860 Dihedral : 4.823 15.666 620 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.91 % Allowed : 17.55 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.27), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.20), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR J 34 PHE 0.008 0.001 PHE C 62 TRP 0.002 0.001 TRP F 32 HIS 0.002 0.001 HIS D 48 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 4900) covalent geometry : angle 0.58385 ( 6620) hydrogen bonds : bond 0.01460 ( 49) hydrogen bonds : angle 4.04481 ( 147) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 59 ASN cc_start: 0.8888 (m-40) cc_final: 0.8572 (m110) REVERT: E 44 GLU cc_start: 0.8631 (mp0) cc_final: 0.7794 (mp0) REVERT: E 55 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8528 (m) REVERT: E 72 TYR cc_start: 0.8217 (m-80) cc_final: 0.7839 (m-80) REVERT: B 44 GLU cc_start: 0.9052 (mp0) cc_final: 0.8223 (mp0) REVERT: B 63 GLN cc_start: 0.9140 (mt0) cc_final: 0.8712 (mt0) REVERT: B 75 ASP cc_start: 0.8599 (p0) cc_final: 0.7990 (p0) REVERT: B 78 LYS cc_start: 0.8683 (mtpt) cc_final: 0.7997 (mttt) REVERT: A 33 ASP cc_start: 0.9020 (t0) cc_final: 0.8732 (t0) REVERT: A 44 GLU cc_start: 0.8841 (mp0) cc_final: 0.8450 (mp0) REVERT: A 51 LYS cc_start: 0.8565 (mttt) cc_final: 0.8044 (mttp) REVERT: C 31 MET cc_start: 0.9164 (mtm) cc_final: 0.8831 (mtm) REVERT: C 77 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8227 (mt0) REVERT: C 78 LYS cc_start: 0.8967 (mtpt) cc_final: 0.8352 (mtmm) REVERT: D 38 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8810 (mp) REVERT: D 44 GLU cc_start: 0.8956 (mp0) cc_final: 0.8253 (mp0) REVERT: D 57 GLN cc_start: 0.8262 (mt0) cc_final: 0.7963 (mt0) REVERT: G 38 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9107 (mp) REVERT: G 51 LYS cc_start: 0.8442 (mttt) cc_final: 0.7924 (mtpp) REVERT: G 63 GLN cc_start: 0.8604 (mt0) cc_final: 0.8323 (mt0) REVERT: H 26 GLN cc_start: 0.8592 (mt0) cc_final: 0.8302 (mt0) REVERT: H 38 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8729 (mp) REVERT: H 44 GLU cc_start: 0.9042 (mp0) cc_final: 0.8273 (mp0) REVERT: H 78 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8112 (mttt) REVERT: I 51 LYS cc_start: 0.8679 (mttt) cc_final: 0.8173 (mttp) REVERT: J 26 GLN cc_start: 0.8346 (mt0) cc_final: 0.7997 (mt0) REVERT: J 37 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: J 44 GLU cc_start: 0.8819 (mp0) cc_final: 0.8431 (mp0) REVERT: J 57 GLN cc_start: 0.8634 (mt0) cc_final: 0.8072 (mt0) REVERT: J 65 LYS cc_start: 0.8571 (mttt) cc_final: 0.6353 (mmtt) REVERT: J 78 LYS cc_start: 0.8885 (mtpt) cc_final: 0.7995 (mttt) outliers start: 26 outliers final: 18 residues processed: 152 average time/residue: 0.0621 time to fit residues: 12.4656 Evaluate side-chains 148 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 76 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 10 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 21 optimal weight: 0.0170 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 ASN ** J 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.112262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.098825 restraints weight = 6979.924| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.16 r_work: 0.3491 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4900 Z= 0.228 Angle : 0.638 9.101 6620 Z= 0.336 Chirality : 0.046 0.148 760 Planarity : 0.002 0.010 860 Dihedral : 5.046 16.765 620 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.09 % Allowed : 18.30 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.26), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.20), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR J 34 PHE 0.011 0.001 PHE C 62 TRP 0.003 0.001 TRP A 32 HIS 0.002 0.001 HIS J 48 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 4900) covalent geometry : angle 0.63837 ( 6620) hydrogen bonds : bond 0.01560 ( 49) hydrogen bonds : angle 4.09974 ( 147) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: F 59 ASN cc_start: 0.8899 (m-40) cc_final: 0.8573 (m110) REVERT: F 78 LYS cc_start: 0.8814 (mttm) cc_final: 0.8142 (mttt) REVERT: E 44 GLU cc_start: 0.8607 (mp0) cc_final: 0.7780 (mp0) REVERT: E 51 LYS cc_start: 0.8278 (mttt) cc_final: 0.7930 (mttp) REVERT: E 55 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8442 (m) REVERT: E 72 TYR cc_start: 0.8192 (m-80) cc_final: 0.7804 (m-80) REVERT: B 44 GLU cc_start: 0.9080 (mp0) cc_final: 0.8222 (mp0) REVERT: B 63 GLN cc_start: 0.9169 (mt0) cc_final: 0.8608 (mt0) REVERT: B 65 LYS cc_start: 0.8800 (mttt) cc_final: 0.8394 (mttt) REVERT: B 75 ASP cc_start: 0.8598 (p0) cc_final: 0.8034 (p0) REVERT: B 78 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8036 (mttt) REVERT: A 33 ASP cc_start: 0.9091 (t0) cc_final: 0.8725 (t0) REVERT: A 44 GLU cc_start: 0.8874 (mp0) cc_final: 0.8472 (mp0) REVERT: A 51 LYS cc_start: 0.8533 (mttt) cc_final: 0.7996 (mttp) REVERT: C 31 MET cc_start: 0.9197 (mtm) cc_final: 0.8850 (mtm) REVERT: C 51 LYS cc_start: 0.8445 (mttt) cc_final: 0.7800 (mttp) REVERT: C 77 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8324 (mt0) REVERT: C 78 LYS cc_start: 0.8955 (mtpt) cc_final: 0.8346 (mtmm) REVERT: G 51 LYS cc_start: 0.8375 (mttt) cc_final: 0.7865 (mtpp) REVERT: G 63 GLN cc_start: 0.8649 (mt0) cc_final: 0.8379 (mt0) REVERT: H 26 GLN cc_start: 0.8587 (mt0) cc_final: 0.8291 (mt0) REVERT: H 38 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8794 (mp) REVERT: H 44 GLU cc_start: 0.9091 (mp0) cc_final: 0.8360 (mp0) REVERT: H 78 LYS cc_start: 0.8653 (mtpt) cc_final: 0.8049 (mttt) REVERT: I 51 LYS cc_start: 0.8669 (mttt) cc_final: 0.8153 (mttp) REVERT: J 33 ASP cc_start: 0.8793 (t0) cc_final: 0.7915 (t0) REVERT: J 37 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8442 (tt0) REVERT: J 57 GLN cc_start: 0.8697 (mt0) cc_final: 0.8268 (mt0) REVERT: J 78 LYS cc_start: 0.8875 (mtpt) cc_final: 0.7976 (mttt) outliers start: 27 outliers final: 18 residues processed: 148 average time/residue: 0.0553 time to fit residues: 10.4771 Evaluate side-chains 146 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 76 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 38 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 51 optimal weight: 0.0970 chunk 22 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.112463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.098951 restraints weight = 7025.228| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.14 r_work: 0.3503 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4900 Z= 0.210 Angle : 0.633 9.050 6620 Z= 0.331 Chirality : 0.046 0.147 760 Planarity : 0.002 0.013 860 Dihedral : 5.021 16.435 620 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.15 % Allowed : 19.25 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.27), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.20), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR H 34 PHE 0.011 0.001 PHE C 62 TRP 0.004 0.001 TRP A 32 HIS 0.002 0.001 HIS D 48 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 4900) covalent geometry : angle 0.63331 ( 6620) hydrogen bonds : bond 0.01531 ( 49) hydrogen bonds : angle 4.12278 ( 147) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: F 59 ASN cc_start: 0.8886 (m-40) cc_final: 0.8567 (m110) REVERT: F 78 LYS cc_start: 0.8730 (mttm) cc_final: 0.8435 (mttm) REVERT: E 44 GLU cc_start: 0.8623 (mp0) cc_final: 0.7806 (mp0) REVERT: E 55 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8450 (m) REVERT: E 72 TYR cc_start: 0.8222 (m-80) cc_final: 0.7840 (m-80) REVERT: B 44 GLU cc_start: 0.9071 (mp0) cc_final: 0.8246 (mp0) REVERT: B 63 GLN cc_start: 0.9149 (mt0) cc_final: 0.8577 (mt0) REVERT: B 65 LYS cc_start: 0.8783 (mttt) cc_final: 0.8378 (mttt) REVERT: B 75 ASP cc_start: 0.8581 (p0) cc_final: 0.8025 (p0) REVERT: B 78 LYS cc_start: 0.8742 (mtpt) cc_final: 0.8069 (mttt) REVERT: A 33 ASP cc_start: 0.9105 (t0) cc_final: 0.8755 (t0) REVERT: A 44 GLU cc_start: 0.8879 (mp0) cc_final: 0.8482 (mp0) REVERT: A 51 LYS cc_start: 0.8557 (mttt) cc_final: 0.8002 (mttp) REVERT: C 31 MET cc_start: 0.9192 (mtm) cc_final: 0.8847 (mtm) REVERT: C 77 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8271 (mt0) REVERT: C 78 LYS cc_start: 0.8982 (mtpt) cc_final: 0.8378 (mtmm) REVERT: D 44 GLU cc_start: 0.8991 (mp0) cc_final: 0.8304 (mp0) REVERT: G 51 LYS cc_start: 0.8414 (mttt) cc_final: 0.7911 (mtpp) REVERT: G 63 GLN cc_start: 0.8609 (mt0) cc_final: 0.8311 (mt0) REVERT: H 26 GLN cc_start: 0.8616 (mt0) cc_final: 0.8325 (mt0) REVERT: H 38 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8725 (mp) REVERT: H 44 GLU cc_start: 0.9091 (mp0) cc_final: 0.8349 (mp0) REVERT: H 78 LYS cc_start: 0.8686 (mtpt) cc_final: 0.8067 (mttt) REVERT: I 51 LYS cc_start: 0.8677 (mttt) cc_final: 0.8171 (mttp) REVERT: J 33 ASP cc_start: 0.8637 (t0) cc_final: 0.7997 (t0) REVERT: J 37 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: J 44 GLU cc_start: 0.8706 (mp0) cc_final: 0.8433 (mp0) REVERT: J 57 GLN cc_start: 0.8699 (mt0) cc_final: 0.8422 (mt0) REVERT: J 78 LYS cc_start: 0.8906 (mtpt) cc_final: 0.8006 (mttt) outliers start: 22 outliers final: 17 residues processed: 142 average time/residue: 0.0548 time to fit residues: 10.1370 Evaluate side-chains 143 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 76 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.109996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.096456 restraints weight = 7114.468| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.16 r_work: 0.3460 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 4900 Z= 0.264 Angle : 0.662 9.227 6620 Z= 0.348 Chirality : 0.047 0.155 760 Planarity : 0.002 0.015 860 Dihedral : 5.267 17.581 620 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.72 % Allowed : 18.30 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.71 (0.26), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.20), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.002 TYR J 34 PHE 0.012 0.002 PHE C 62 TRP 0.003 0.001 TRP B 32 HIS 0.002 0.001 HIS J 48 Details of bonding type rmsd covalent geometry : bond 0.00601 ( 4900) covalent geometry : angle 0.66206 ( 6620) hydrogen bonds : bond 0.01639 ( 49) hydrogen bonds : angle 4.17866 ( 147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1080.70 seconds wall clock time: 19 minutes 38.83 seconds (1178.83 seconds total)