Starting phenix.real_space_refine on Tue Apr 7 23:16:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zqc_74564/04_2026/9zqc_74564.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zqc_74564/04_2026/9zqc_74564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zqc_74564/04_2026/9zqc_74564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zqc_74564/04_2026/9zqc_74564.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zqc_74564/04_2026/9zqc_74564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zqc_74564/04_2026/9zqc_74564.map" } resolution = 2.37 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= 0.012 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: 6 Type Number sf(0) Gaussians P 306 5.49 5 S 40 5.16 5 C 9810 2.51 5 N 3125 2.21 5 O 3843 1.98 5 H 14545 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31669 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1730 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "B" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1730 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "C" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1605 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "D" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1605 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "E" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1700 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "F" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1696 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "G" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1372 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "H" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1413 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "I" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3569 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "J" Number of atoms: 3583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 3583 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 222} Chain breaks: 1 Chain: "K" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 1489 Classifications: {'DNA': 47} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 46} Chain: "L" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 3345 Classifications: {'DNA': 106} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 105} Chain: "M" Number of atoms: 4874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 4874 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "P" Number of atoms: 1958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1958 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Time building chain proxies: 5.44, per 1000 atoms: 0.17 Number of scatterers: 31669 At special positions: 0 Unit cell: (136.62, 135.792, 120.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 306 15.00 O 3843 8.00 N 3125 7.00 C 9810 6.00 H 14545 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS I 47 " - pdb=" SG CYS I 112 " distance=2.04 Simple disulfide: pdb=" SG CYS I 176 " - pdb=" SG CYS I 250 " distance=2.03 Simple disulfide: pdb=" SG CYS J 47 " - pdb=" SG CYS J 112 " distance=2.03 Simple disulfide: pdb=" SG CYS J 176 " - pdb=" SG CYS J 250 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 554.5 milliseconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2554 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 24 sheets defined 44.4% alpha, 23.2% beta 152 base pairs and 272 stacking pairs defined. Time for finding SS restraints: 5.97 Creating SS restraints... Processing helix chain 'A' and resid 16 through 22 Processing helix chain 'A' and resid 26 through 37 Processing helix chain 'A' and resid 45 through 73 removed outlier: 4.224A pdb=" N VAL A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 89 Processing helix chain 'A' and resid 90 through 97 Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'B' and resid 16 through 22 Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 45 through 73 removed outlier: 4.257A pdb=" N VAL B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 90 through 97 Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'C' and resid 36 through 48 Processing helix chain 'C' and resid 54 through 83 Processing helix chain 'C' and resid 89 through 101 Processing helix chain 'C' and resid 103 through 123 removed outlier: 3.683A pdb=" N LYS C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 54 through 83 Processing helix chain 'D' and resid 89 through 101 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.753A pdb=" N LYS D 107 " --> pdb=" O GLY D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 133 Processing helix chain 'F' and resid 45 through 58 Processing helix chain 'F' and resid 64 through 80 removed outlier: 4.075A pdb=" N ASP F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE F 79 " --> pdb=" O ILE F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 115 Processing helix chain 'F' and resid 121 through 132 Processing helix chain 'G' and resid 27 through 31 Processing helix chain 'G' and resid 32 through 43 Processing helix chain 'G' and resid 51 through 78 removed outlier: 3.694A pdb=" N GLU G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP G 70 " --> pdb=" O ASN G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 94 Processing helix chain 'H' and resid 26 through 31 removed outlier: 3.513A pdb=" N GLN H 29 " --> pdb=" O ASP H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 43 Processing helix chain 'H' and resid 51 through 78 removed outlier: 3.691A pdb=" N GLU H 55 " --> pdb=" O LEU H 51 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP H 70 " --> pdb=" O ASN H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 95 Processing helix chain 'I' and resid 103 through 107 Processing helix chain 'I' and resid 182 through 184 No H-bonds generated for 'chain 'I' and resid 182 through 184' Processing helix chain 'I' and resid 216 through 219 Processing helix chain 'I' and resid 241 through 245 Processing helix chain 'J' and resid 103 through 107 Processing helix chain 'J' and resid 182 through 184 No H-bonds generated for 'chain 'J' and resid 182 through 184' Processing helix chain 'J' and resid 241 through 245 Processing helix chain 'P' and resid 168 through 185 removed outlier: 3.518A pdb=" N ALA P 172 " --> pdb=" O ASN P 168 " (cutoff:3.500A) Processing helix chain 'P' and resid 187 through 191 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 7.226A pdb=" N ARG A 42 " --> pdb=" O ILE C 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 78 Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.911A pdb=" N THR A 101 " --> pdb=" O TYR G 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 42 through 43 removed outlier: 7.152A pdb=" N ARG B 42 " --> pdb=" O ILE D 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.976A pdb=" N THR B 101 " --> pdb=" O TYR H 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.876A pdb=" N ARG E 84 " --> pdb=" O VAL G 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'F' and resid 84 through 85 removed outlier: 6.885A pdb=" N ARG F 84 " --> pdb=" O VAL H 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 119 through 120 Processing sheet with id=AB2, first strand: chain 'I' and resid 28 through 31 Processing sheet with id=AB3, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.776A pdb=" N MET I 35 " --> pdb=" O GLU I 129 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LYS I 131 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA I 37 " --> pdb=" O LYS I 131 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE I 72 " --> pdb=" O TRP I 59 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLN I 61 " --> pdb=" O THR I 70 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N THR I 70 " --> pdb=" O GLN I 61 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.776A pdb=" N MET I 35 " --> pdb=" O GLU I 129 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LYS I 131 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA I 37 " --> pdb=" O LYS I 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 157 through 160 Processing sheet with id=AB6, first strand: chain 'I' and resid 164 through 166 removed outlier: 6.471A pdb=" N ILE I 188 " --> pdb=" O TYR I 204 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR I 204 " --> pdb=" O ILE I 188 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP I 190 " --> pdb=" O ILE I 202 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 164 through 166 removed outlier: 3.831A pdb=" N TYR I 263 " --> pdb=" O ARG I 252 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 28 through 31 removed outlier: 5.914A pdb=" N GLN J 93 " --> pdb=" O ALA J 49 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N GLN J 51 " --> pdb=" O SER J 91 " (cutoff:3.500A) removed outlier: 10.168A pdb=" N SER J 91 " --> pdb=" O GLN J 51 " (cutoff:3.500A) removed outlier: 11.832A pdb=" N ILE J 53 " --> pdb=" O SER J 89 " (cutoff:3.500A) removed outlier: 11.662A pdb=" N SER J 89 " --> pdb=" O ILE J 53 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 34 through 38 removed outlier: 6.747A pdb=" N MET J 35 " --> pdb=" O GLU J 129 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LYS J 131 " --> pdb=" O MET J 35 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ALA J 37 " --> pdb=" O LYS J 131 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TRP J 59 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 34 through 38 removed outlier: 6.747A pdb=" N MET J 35 " --> pdb=" O GLU J 129 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LYS J 131 " --> pdb=" O MET J 35 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ALA J 37 " --> pdb=" O LYS J 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 157 through 160 Processing sheet with id=AC3, first strand: chain 'J' and resid 164 through 166 removed outlier: 6.546A pdb=" N ILE J 188 " --> pdb=" O TYR J 204 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR J 204 " --> pdb=" O ILE J 188 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP J 190 " --> pdb=" O ILE J 202 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 164 through 166 removed outlier: 3.897A pdb=" N TYR J 263 " --> pdb=" O ARG J 252 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 106 through 107 Processing sheet with id=AC6, first strand: chain 'P' and resid 106 through 107 611 hydrogen bonds defined for protein. 1659 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 390 hydrogen bonds 780 hydrogen bond angles 0 basepair planarities 152 basepair parallelities 272 stacking parallelities Total time for adding SS restraints: 7.96 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14542 1.03 - 1.23: 222 1.23 - 1.43: 8144 1.43 - 1.62: 9640 1.62 - 1.82: 69 Bond restraints: 32617 Sorted by residual: bond pdb=" C3' DG M 97 " pdb=" O3' DG M 97 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.54e+00 bond pdb=" CB GLN P 205 " pdb=" CG GLN P 205 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CB GLU P 192 " pdb=" CG GLU P 192 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.27e+00 bond pdb=" C3' DG L 50 " pdb=" O3' DG L 50 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.25e+00 bond pdb=" CB LYS F 38 " pdb=" CG LYS F 38 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 ... (remaining 32612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 58289 2.12 - 4.23: 716 4.23 - 6.35: 12 6.35 - 8.46: 2 8.46 - 10.58: 6 Bond angle restraints: 59025 Sorted by residual: angle pdb=" CB LYS F 38 " pdb=" CG LYS F 38 " pdb=" CD LYS F 38 " ideal model delta sigma weight residual 111.30 120.77 -9.47 2.30e+00 1.89e-01 1.70e+01 angle pdb=" OP1 DC K 4 " pdb=" P DC K 4 " pdb=" OP2 DC K 4 " ideal model delta sigma weight residual 120.00 109.42 10.58 3.00e+00 1.11e-01 1.24e+01 angle pdb=" CB MET I 24 " pdb=" CG MET I 24 " pdb=" SD MET I 24 " ideal model delta sigma weight residual 112.70 123.26 -10.56 3.00e+00 1.11e-01 1.24e+01 angle pdb=" OP1 DA M 4 " pdb=" P DA M 4 " pdb=" OP2 DA M 4 " ideal model delta sigma weight residual 120.00 109.49 10.51 3.00e+00 1.11e-01 1.23e+01 angle pdb=" O3' DC K 3 " pdb=" P DC K 4 " pdb=" OP1 DC K 4 " ideal model delta sigma weight residual 108.00 117.66 -9.66 3.00e+00 1.11e-01 1.04e+01 ... (remaining 59020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.93: 12097 32.93 - 65.85: 1954 65.85 - 98.78: 42 98.78 - 131.71: 0 131.71 - 164.64: 3 Dihedral angle restraints: 14096 sinusoidal: 9523 harmonic: 4573 Sorted by residual: dihedral pdb=" CA SER I 118 " pdb=" C SER I 118 " pdb=" N PRO I 119 " pdb=" CA PRO I 119 " ideal model delta harmonic sigma weight residual -180.00 -147.20 -32.80 0 5.00e+00 4.00e-02 4.30e+01 dihedral pdb=" C4' DG L 84 " pdb=" C3' DG L 84 " pdb=" O3' DG L 84 " pdb=" P DT L 85 " ideal model delta sinusoidal sigma weight residual 220.00 55.36 164.64 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DG M 97 " pdb=" C3' DG M 97 " pdb=" O3' DG M 97 " pdb=" P DG M 98 " ideal model delta sinusoidal sigma weight residual 220.00 63.26 156.74 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 14093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2641 0.082 - 0.163: 228 0.163 - 0.245: 1 0.245 - 0.326: 0 0.326 - 0.407: 2 Chirality restraints: 2872 Sorted by residual: chirality pdb=" P DC K 4 " pdb=" OP1 DC K 4 " pdb=" OP2 DC K 4 " pdb=" O5' DC K 4 " both_signs ideal model delta sigma weight residual True 2.35 -2.75 -0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" P DA M 4 " pdb=" OP1 DA M 4 " pdb=" OP2 DA M 4 " pdb=" O5' DA M 4 " both_signs ideal model delta sigma weight residual True 2.35 -2.74 -0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CA ILE I 72 " pdb=" N ILE I 72 " pdb=" C ILE I 72 " pdb=" CB ILE I 72 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.73e-01 ... (remaining 2869 not shown) Planarity restraints: 3738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER I 118 " -0.089 5.00e-02 4.00e+02 1.34e-01 2.87e+01 pdb=" N PRO I 119 " 0.231 5.00e-02 4.00e+02 pdb=" CA PRO I 119 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO I 119 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 30 " -0.222 9.50e-02 1.11e+02 7.42e-02 6.69e+00 pdb=" NE ARG D 30 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG D 30 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG D 30 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 30 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG D 30 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG D 30 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D 30 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG D 30 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 42 " 0.178 9.50e-02 1.11e+02 5.95e-02 4.23e+00 pdb=" NE ARG J 42 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG J 42 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG J 42 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG J 42 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG J 42 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG J 42 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG J 42 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG J 42 " 0.000 2.00e-02 2.50e+03 ... (remaining 3735 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.36: 9996 2.36 - 2.92: 65473 2.92 - 3.48: 80289 3.48 - 4.04: 120901 4.04 - 4.60: 168799 Nonbonded interactions: 445458 Sorted by model distance: nonbonded pdb=" HG2 ARG J 42 " pdb="HH11 ARG J 42 " model vdw 1.803 2.270 nonbonded pdb=" HG SER A 18 " pdb=" H VAL A 27 " model vdw 1.804 2.100 nonbonded pdb=" HZ2 TRP J 201 " pdb=" HD2 TYR J 204 " model vdw 1.807 2.100 nonbonded pdb=" HZ2 TRP I 201 " pdb=" HD2 TYR I 204 " model vdw 1.820 2.100 nonbonded pdb="HH22 ARG A 20 " pdb=" HE3 LYS C 124 " model vdw 1.836 2.270 ... (remaining 445453 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' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 37 through 135) selection = (chain 'F' and (resid 37 through 113 or (resid 114 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 115 through 135)) } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 22 through 104) } ncs_group { reference = chain 'I' selection = (chain 'J' and resid 23 through 274) } 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: 4.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.170 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 34.330 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.070 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:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 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 : 0.004 0.043 18076 Z= 0.183 Angle : 0.605 10.579 25713 Z= 0.355 Chirality : 0.043 0.407 2872 Planarity : 0.006 0.134 2191 Dihedral : 25.453 164.635 7542 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.01 % Favored : 97.91 % Rotamer: Outliers : 0.86 % Allowed : 14.85 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: 1.74 (0.24), residues: 1342 helix: 2.45 (0.22), residues: 558 sheet: 0.13 (0.34), residues: 244 loop : 0.37 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 30 TYR 0.015 0.001 TYR I 73 PHE 0.010 0.001 PHE P 126 TRP 0.006 0.001 TRP J 190 HIS 0.002 0.001 HIS P 106 Details of bonding type rmsd covalent geometry : bond 0.00398 (18072) covalent geometry : angle 0.60486 (25705) SS BOND : bond 0.00270 ( 4) SS BOND : angle 0.45702 ( 8) hydrogen bonds : bond 0.11709 ( 977) hydrogen bonds : angle 5.40112 ( 2439) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 174 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.9026 (tt0) cc_final: 0.8661 (tt0) REVERT: A 73 ASN cc_start: 0.8823 (t0) cc_final: 0.8135 (t0) REVERT: E 60 GLU cc_start: 0.8798 (pm20) cc_final: 0.8461 (pm20) REVERT: F 60 GLU cc_start: 0.8947 (pm20) cc_final: 0.8649 (pm20) REVERT: H 97 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8118 (mtp-110) REVERT: I 74 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.8385 (t80) outliers start: 10 outliers final: 6 residues processed: 181 average time/residue: 1.8134 time to fit residues: 354.3293 Evaluate side-chains 172 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain I residue 47 CYS Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 227 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 GLN C 94 GLN E 126 GLN P 144 ASN P 205 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.091522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.065516 restraints weight = 85521.925| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.73 r_work: 0.3002 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.0677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 18076 Z= 0.284 Angle : 0.608 7.489 25713 Z= 0.363 Chirality : 0.046 0.168 2872 Planarity : 0.005 0.136 2191 Dihedral : 28.343 165.200 4871 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.38 % Favored : 97.54 % Rotamer: Outliers : 1.72 % Allowed : 14.76 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: 1.73 (0.23), residues: 1342 helix: 2.44 (0.22), residues: 564 sheet: 0.41 (0.34), residues: 253 loop : 0.16 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 30 TYR 0.021 0.001 TYR I 73 PHE 0.012 0.001 PHE P 180 TRP 0.006 0.001 TRP I 190 HIS 0.004 0.001 HIS H 77 Details of bonding type rmsd covalent geometry : bond 0.00621 (18072) covalent geometry : angle 0.60801 (25705) SS BOND : bond 0.00676 ( 4) SS BOND : angle 0.79458 ( 8) hydrogen bonds : bond 0.04949 ( 977) hydrogen bonds : angle 3.92429 ( 2439) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8722 (t0) cc_final: 0.8088 (t0) REVERT: B 41 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8338 (tt0) REVERT: B 90 ASP cc_start: 0.9061 (t0) cc_final: 0.8834 (t0) REVERT: D 30 ARG cc_start: 0.7853 (mmm160) cc_final: 0.7547 (mmm-85) REVERT: E 60 GLU cc_start: 0.8610 (pm20) cc_final: 0.8245 (pm20) REVERT: F 57 LYS cc_start: 0.9297 (ttmm) cc_final: 0.9048 (ttpp) REVERT: F 60 GLU cc_start: 0.8686 (pm20) cc_final: 0.8316 (pm20) REVERT: I 227 ASP cc_start: 0.8504 (t70) cc_final: 0.8297 (t0) REVERT: P 159 GLN cc_start: 0.7695 (mp-120) cc_final: 0.7197 (mt0) outliers start: 20 outliers final: 8 residues processed: 179 average time/residue: 1.7492 time to fit residues: 338.6553 Evaluate side-chains 172 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 47 CYS Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain P residue 137 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 128 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 GLN ** P 205 GLN ** 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 = 0.3628 r_free = 0.3628 target = 0.093217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.067131 restraints weight = 84815.109| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.73 r_work: 0.3042 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18076 Z= 0.184 Angle : 0.577 6.823 25713 Z= 0.347 Chirality : 0.041 0.169 2872 Planarity : 0.005 0.133 2191 Dihedral : 28.307 165.091 4860 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.38 % Favored : 97.54 % Rotamer: Outliers : 1.46 % Allowed : 15.11 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: 1.94 (0.23), residues: 1342 helix: 2.61 (0.22), residues: 564 sheet: 0.64 (0.33), residues: 253 loop : 0.20 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 42 TYR 0.016 0.001 TYR I 73 PHE 0.017 0.001 PHE P 180 TRP 0.006 0.001 TRP I 190 HIS 0.003 0.001 HIS H 77 Details of bonding type rmsd covalent geometry : bond 0.00401 (18072) covalent geometry : angle 0.57723 (25705) SS BOND : bond 0.00556 ( 4) SS BOND : angle 0.73891 ( 8) hydrogen bonds : bond 0.03655 ( 977) hydrogen bonds : angle 3.62489 ( 2439) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8665 (t0) cc_final: 0.8455 (t0) REVERT: E 60 GLU cc_start: 0.8612 (pm20) cc_final: 0.8321 (pm20) REVERT: F 57 LYS cc_start: 0.9293 (ttmm) cc_final: 0.9047 (ttpp) REVERT: F 60 GLU cc_start: 0.8634 (pm20) cc_final: 0.8265 (pm20) REVERT: H 97 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8355 (mtp-110) REVERT: I 159 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7990 (mm-40) REVERT: I 227 ASP cc_start: 0.8432 (t70) cc_final: 0.8198 (t0) outliers start: 17 outliers final: 10 residues processed: 188 average time/residue: 1.8079 time to fit residues: 366.9967 Evaluate side-chains 177 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 47 CYS Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 145 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 93 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 GLN P 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.092568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.066683 restraints weight = 84945.147| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.72 r_work: 0.2722 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18076 Z= 0.215 Angle : 0.584 7.045 25713 Z= 0.350 Chirality : 0.043 0.168 2872 Planarity : 0.005 0.130 2191 Dihedral : 28.284 164.922 4860 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.46 % Favored : 97.47 % Rotamer: Outliers : 1.97 % Allowed : 15.28 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: 1.93 (0.23), residues: 1342 helix: 2.61 (0.22), residues: 564 sheet: 0.71 (0.34), residues: 248 loop : 0.14 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 42 TYR 0.018 0.001 TYR I 73 PHE 0.009 0.001 PHE F 68 TRP 0.005 0.001 TRP I 190 HIS 0.003 0.001 HIS H 77 Details of bonding type rmsd covalent geometry : bond 0.00468 (18072) covalent geometry : angle 0.58439 (25705) SS BOND : bond 0.00552 ( 4) SS BOND : angle 0.76197 ( 8) hydrogen bonds : bond 0.04066 ( 977) hydrogen bonds : angle 3.49811 ( 2439) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8674 (t0) cc_final: 0.8451 (t0) REVERT: A 91 GLU cc_start: 0.9019 (tp30) cc_final: 0.8533 (tp30) REVERT: B 74 LYS cc_start: 0.9262 (mppt) cc_final: 0.9038 (mmmm) REVERT: E 60 GLU cc_start: 0.8632 (pm20) cc_final: 0.8339 (pm20) REVERT: F 57 LYS cc_start: 0.9307 (ttmm) cc_final: 0.9054 (ttpp) REVERT: F 60 GLU cc_start: 0.8670 (pm20) cc_final: 0.8306 (pm20) REVERT: H 97 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8340 (mtp-110) REVERT: I 159 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7950 (mm-40) REVERT: I 227 ASP cc_start: 0.8433 (t70) cc_final: 0.8164 (t0) REVERT: P 126 PHE cc_start: 0.8864 (m-80) cc_final: 0.8584 (m-80) REVERT: P 135 GLN cc_start: 0.8373 (mt0) cc_final: 0.8135 (mt0) REVERT: P 159 GLN cc_start: 0.7770 (mp-120) cc_final: 0.7320 (mt0) REVERT: P 165 CYS cc_start: 0.5492 (OUTLIER) cc_final: 0.5288 (p) outliers start: 23 outliers final: 8 residues processed: 189 average time/residue: 1.7389 time to fit residues: 355.7577 Evaluate side-chains 178 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 168 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 145 PHE Chi-restraints excluded: chain P residue 165 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 88 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 125 GLN ** P 205 GLN ** 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 = 0.3555 r_free = 0.3555 target = 0.089364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.063306 restraints weight = 82715.091| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.72 r_work: 0.2818 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18076 Z= 0.209 Angle : 0.581 7.683 25713 Z= 0.348 Chirality : 0.042 0.165 2872 Planarity : 0.005 0.130 2191 Dihedral : 28.281 165.098 4859 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.38 % Favored : 97.54 % Rotamer: Outliers : 1.72 % Allowed : 15.79 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: 1.96 (0.23), residues: 1342 helix: 2.65 (0.22), residues: 564 sheet: 0.73 (0.34), residues: 248 loop : 0.15 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 42 TYR 0.017 0.001 TYR I 73 PHE 0.009 0.001 PHE F 68 TRP 0.005 0.001 TRP I 190 HIS 0.003 0.001 HIS H 77 Details of bonding type rmsd covalent geometry : bond 0.00456 (18072) covalent geometry : angle 0.58081 (25705) SS BOND : bond 0.00364 ( 4) SS BOND : angle 0.86456 ( 8) hydrogen bonds : bond 0.03828 ( 977) hydrogen bonds : angle 3.41905 ( 2439) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8703 (t0) cc_final: 0.8469 (t0) REVERT: A 91 GLU cc_start: 0.9018 (tp30) cc_final: 0.8513 (tp30) REVERT: B 74 LYS cc_start: 0.9254 (mppt) cc_final: 0.9046 (mmmm) REVERT: E 60 GLU cc_start: 0.8628 (pm20) cc_final: 0.8336 (pm20) REVERT: E 126 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8383 (mp10) REVERT: F 60 GLU cc_start: 0.8640 (pm20) cc_final: 0.8282 (pm20) REVERT: H 97 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8345 (mtp-110) REVERT: I 159 GLN cc_start: 0.8327 (mm-40) cc_final: 0.7962 (mm-40) REVERT: I 227 ASP cc_start: 0.8431 (t70) cc_final: 0.8170 (t0) REVERT: P 165 CYS cc_start: 0.5294 (OUTLIER) cc_final: 0.5037 (p) outliers start: 20 outliers final: 8 residues processed: 188 average time/residue: 1.7741 time to fit residues: 360.7275 Evaluate side-chains 177 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain E residue 126 GLN Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 145 PHE Chi-restraints excluded: chain P residue 165 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 119 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 153 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.089321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.063214 restraints weight = 82646.461| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.74 r_work: 0.2818 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18076 Z= 0.212 Angle : 0.583 8.303 25713 Z= 0.349 Chirality : 0.043 0.167 2872 Planarity : 0.005 0.124 2191 Dihedral : 28.275 165.097 4859 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.31 % Favored : 97.62 % Rotamer: Outliers : 1.80 % Allowed : 15.62 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: 2.00 (0.23), residues: 1342 helix: 2.65 (0.22), residues: 564 sheet: 0.76 (0.34), residues: 255 loop : 0.21 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 42 TYR 0.017 0.001 TYR I 73 PHE 0.009 0.001 PHE F 68 TRP 0.005 0.001 TRP I 190 HIS 0.003 0.001 HIS H 77 Details of bonding type rmsd covalent geometry : bond 0.00462 (18072) covalent geometry : angle 0.58293 (25705) SS BOND : bond 0.00449 ( 4) SS BOND : angle 0.92440 ( 8) hydrogen bonds : bond 0.03862 ( 977) hydrogen bonds : angle 3.37662 ( 2439) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8726 (t0) cc_final: 0.8492 (t0) REVERT: A 91 GLU cc_start: 0.9002 (tp30) cc_final: 0.8528 (tp30) REVERT: B 74 LYS cc_start: 0.9259 (mppt) cc_final: 0.9055 (mmmm) REVERT: E 60 GLU cc_start: 0.8604 (pm20) cc_final: 0.8315 (pm20) REVERT: F 38 LYS cc_start: 0.8769 (tppp) cc_final: 0.7562 (pttm) REVERT: F 60 GLU cc_start: 0.8639 (pm20) cc_final: 0.8271 (pm20) REVERT: H 97 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8263 (mtp-110) REVERT: I 159 GLN cc_start: 0.8333 (mm-40) cc_final: 0.7959 (mm-40) REVERT: I 227 ASP cc_start: 0.8441 (t70) cc_final: 0.8170 (t0) REVERT: P 159 GLN cc_start: 0.7675 (mp-120) cc_final: 0.7196 (mt0) REVERT: P 165 CYS cc_start: 0.5230 (OUTLIER) cc_final: 0.4971 (p) outliers start: 21 outliers final: 10 residues processed: 185 average time/residue: 1.7808 time to fit residues: 356.4675 Evaluate side-chains 179 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 145 PHE Chi-restraints excluded: chain P residue 165 CYS Chi-restraints excluded: chain P residue 184 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 68 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 154 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 159 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 205 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.088220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.062094 restraints weight = 82702.842| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.73 r_work: 0.2790 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 18076 Z= 0.271 Angle : 0.598 8.872 25713 Z= 0.357 Chirality : 0.045 0.169 2872 Planarity : 0.005 0.125 2191 Dihedral : 28.327 166.132 4859 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.38 % Favored : 97.54 % Rotamer: Outliers : 2.15 % Allowed : 15.19 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: 1.93 (0.23), residues: 1342 helix: 2.54 (0.22), residues: 564 sheet: 0.81 (0.34), residues: 255 loop : 0.17 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 42 TYR 0.021 0.001 TYR I 73 PHE 0.008 0.001 PHE F 68 TRP 0.005 0.001 TRP P 148 HIS 0.004 0.001 HIS H 77 Details of bonding type rmsd covalent geometry : bond 0.00594 (18072) covalent geometry : angle 0.59824 (25705) SS BOND : bond 0.00475 ( 4) SS BOND : angle 0.98593 ( 8) hydrogen bonds : bond 0.04507 ( 977) hydrogen bonds : angle 3.42289 ( 2439) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8770 (t0) cc_final: 0.8496 (t0) REVERT: A 91 GLU cc_start: 0.9035 (tp30) cc_final: 0.8500 (tp30) REVERT: B 74 LYS cc_start: 0.9261 (mppt) cc_final: 0.9058 (mmmm) REVERT: E 60 GLU cc_start: 0.8622 (pm20) cc_final: 0.8293 (pm20) REVERT: F 38 LYS cc_start: 0.8823 (tppp) cc_final: 0.7714 (pttm) REVERT: F 57 LYS cc_start: 0.9315 (ttmm) cc_final: 0.9053 (ttpp) REVERT: F 60 GLU cc_start: 0.8656 (pm20) cc_final: 0.8301 (pm20) REVERT: H 97 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8343 (mtp-110) REVERT: I 159 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8028 (mm-40) REVERT: I 227 ASP cc_start: 0.8408 (t70) cc_final: 0.8136 (t0) outliers start: 25 outliers final: 11 residues processed: 187 average time/residue: 1.7628 time to fit residues: 356.4574 Evaluate side-chains 176 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 145 PHE Chi-restraints excluded: chain P residue 184 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 18 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 151 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 27 ASN ** P 205 GLN ** 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 = 0.3552 r_free = 0.3552 target = 0.089183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.063111 restraints weight = 82483.522| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.71 r_work: 0.2812 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18076 Z= 0.181 Angle : 0.587 9.929 25713 Z= 0.351 Chirality : 0.041 0.175 2872 Planarity : 0.006 0.129 2191 Dihedral : 28.342 165.885 4859 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.46 % Favored : 97.47 % Rotamer: Outliers : 1.80 % Allowed : 15.36 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: 2.00 (0.23), residues: 1342 helix: 2.62 (0.22), residues: 564 sheet: 0.88 (0.34), residues: 247 loop : 0.17 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.000 ARG D 30 TYR 0.017 0.001 TYR I 73 PHE 0.009 0.001 PHE F 68 TRP 0.007 0.001 TRP I 190 HIS 0.003 0.001 HIS H 77 Details of bonding type rmsd covalent geometry : bond 0.00399 (18072) covalent geometry : angle 0.58698 (25705) SS BOND : bond 0.00388 ( 4) SS BOND : angle 0.90171 ( 8) hydrogen bonds : bond 0.03839 ( 977) hydrogen bonds : angle 3.38990 ( 2439) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8746 (t0) cc_final: 0.8464 (t0) REVERT: A 91 GLU cc_start: 0.9016 (tp30) cc_final: 0.8492 (tp30) REVERT: B 74 LYS cc_start: 0.9256 (mppt) cc_final: 0.9054 (mmmm) REVERT: E 60 GLU cc_start: 0.8616 (pm20) cc_final: 0.8332 (pm20) REVERT: F 38 LYS cc_start: 0.8808 (tppp) cc_final: 0.7719 (pttm) REVERT: F 57 LYS cc_start: 0.9311 (ttmm) cc_final: 0.9053 (ttpp) REVERT: F 60 GLU cc_start: 0.8639 (pm20) cc_final: 0.8286 (pm20) REVERT: H 97 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8230 (mtp-110) REVERT: I 159 GLN cc_start: 0.8332 (mm-40) cc_final: 0.7981 (mm-40) REVERT: I 227 ASP cc_start: 0.8423 (t70) cc_final: 0.8147 (t0) outliers start: 21 outliers final: 10 residues processed: 180 average time/residue: 1.7953 time to fit residues: 349.2615 Evaluate side-chains 177 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 145 PHE Chi-restraints excluded: chain P residue 184 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 83 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 160 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 149 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.089295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.063248 restraints weight = 82600.438| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.72 r_work: 0.2820 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18076 Z= 0.197 Angle : 0.586 9.248 25713 Z= 0.349 Chirality : 0.042 0.167 2872 Planarity : 0.005 0.125 2191 Dihedral : 28.296 165.400 4859 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.38 % Favored : 97.54 % Rotamer: Outliers : 1.29 % Allowed : 15.88 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: 2.05 (0.23), residues: 1342 helix: 2.66 (0.22), residues: 564 sheet: 0.96 (0.34), residues: 247 loop : 0.17 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 30 TYR 0.016 0.001 TYR I 73 PHE 0.009 0.001 PHE F 68 TRP 0.007 0.001 TRP J 190 HIS 0.003 0.001 HIS H 77 Details of bonding type rmsd covalent geometry : bond 0.00432 (18072) covalent geometry : angle 0.58572 (25705) SS BOND : bond 0.00367 ( 4) SS BOND : angle 0.77465 ( 8) hydrogen bonds : bond 0.03737 ( 977) hydrogen bonds : angle 3.33842 ( 2439) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8749 (t0) cc_final: 0.8465 (t0) REVERT: A 91 GLU cc_start: 0.9032 (tp30) cc_final: 0.8503 (tp30) REVERT: E 60 GLU cc_start: 0.8602 (pm20) cc_final: 0.8317 (pm20) REVERT: F 38 LYS cc_start: 0.8832 (tppp) cc_final: 0.7780 (pttm) REVERT: F 57 LYS cc_start: 0.9309 (ttmm) cc_final: 0.9057 (ttpp) REVERT: F 60 GLU cc_start: 0.8642 (pm20) cc_final: 0.8278 (pm20) REVERT: H 97 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8241 (mtp-110) REVERT: I 159 GLN cc_start: 0.8339 (mm-40) cc_final: 0.7983 (mm-40) REVERT: I 227 ASP cc_start: 0.8421 (t70) cc_final: 0.8144 (t0) REVERT: P 118 MET cc_start: 0.8619 (tpp) cc_final: 0.8397 (tpp) outliers start: 15 outliers final: 9 residues processed: 181 average time/residue: 1.8150 time to fit residues: 355.5308 Evaluate side-chains 175 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain P residue 145 PHE Chi-restraints excluded: chain P residue 184 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 48 optimal weight: 0.9980 chunk 98 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.089796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.063924 restraints weight = 82532.737| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.69 r_work: 0.2833 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18076 Z= 0.154 Angle : 0.590 11.957 25713 Z= 0.350 Chirality : 0.040 0.173 2872 Planarity : 0.005 0.124 2191 Dihedral : 28.301 165.226 4859 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.38 % Favored : 97.54 % Rotamer: Outliers : 0.94 % Allowed : 16.74 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: 2.08 (0.23), residues: 1342 helix: 2.68 (0.22), residues: 564 sheet: 0.96 (0.34), residues: 247 loop : 0.20 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 42 TYR 0.014 0.001 TYR I 73 PHE 0.009 0.001 PHE F 68 TRP 0.005 0.001 TRP P 148 HIS 0.003 0.001 HIS P 160 Details of bonding type rmsd covalent geometry : bond 0.00340 (18072) covalent geometry : angle 0.58953 (25705) SS BOND : bond 0.00313 ( 4) SS BOND : angle 0.57895 ( 8) hydrogen bonds : bond 0.03584 ( 977) hydrogen bonds : angle 3.32265 ( 2439) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 169 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8739 (t0) cc_final: 0.8483 (t0) REVERT: A 91 GLU cc_start: 0.9008 (tp30) cc_final: 0.8504 (tp30) REVERT: E 60 GLU cc_start: 0.8607 (pm20) cc_final: 0.8326 (pm20) REVERT: F 38 LYS cc_start: 0.8829 (tppp) cc_final: 0.7779 (pttm) REVERT: F 57 LYS cc_start: 0.9302 (ttmm) cc_final: 0.9051 (ttpp) REVERT: F 60 GLU cc_start: 0.8647 (pm20) cc_final: 0.8294 (pm20) REVERT: H 97 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8239 (mtp-110) REVERT: I 159 GLN cc_start: 0.8330 (mm-40) cc_final: 0.7982 (mm-40) REVERT: I 227 ASP cc_start: 0.8416 (t70) cc_final: 0.8138 (t0) REVERT: P 118 MET cc_start: 0.8644 (tpp) cc_final: 0.8418 (tpp) outliers start: 11 outliers final: 9 residues processed: 178 average time/residue: 1.7992 time to fit residues: 346.7859 Evaluate side-chains 179 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain P residue 145 PHE Chi-restraints excluded: chain P residue 184 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.089929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.063980 restraints weight = 82560.531| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.69 r_work: 0.2838 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18076 Z= 0.172 Angle : 0.581 9.686 25713 Z= 0.346 Chirality : 0.041 0.165 2872 Planarity : 0.006 0.129 2191 Dihedral : 28.224 164.601 4859 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.31 % Favored : 97.62 % Rotamer: Outliers : 0.77 % Allowed : 17.00 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: 2.15 (0.23), residues: 1342 helix: 2.74 (0.22), residues: 564 sheet: 1.00 (0.34), residues: 247 loop : 0.24 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG D 30 TYR 0.015 0.001 TYR I 73 PHE 0.008 0.001 PHE F 68 TRP 0.006 0.001 TRP P 148 HIS 0.004 0.001 HIS P 160 Details of bonding type rmsd covalent geometry : bond 0.00379 (18072) covalent geometry : angle 0.58148 (25705) SS BOND : bond 0.00361 ( 4) SS BOND : angle 0.61707 ( 8) hydrogen bonds : bond 0.03414 ( 977) hydrogen bonds : angle 3.26048 ( 2439) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15595.91 seconds wall clock time: 263 minutes 17.25 seconds (15797.25 seconds total)