Starting phenix.real_space_refine on Fri Sep 11 15:39:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uph_20839/09_2026/6uph_20839.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uph_20839/09_2026/6uph_20839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uph_20839/09_2026/6uph_20839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uph_20839/09_2026/6uph_20839.map" model { file = "/net/cci-nas-00/data/ceres_data/6uph_20839/09_2026/6uph_20839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uph_20839/09_2026/6uph_20839.cif" } resolution = 2.7 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= 0.033 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 238 5.49 5 S 10 5.16 5 C 5969 2.51 5 N 1975 2.21 5 O 2485 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10677 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 766 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "B" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 630 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 744 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "D" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 752 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 794 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "F" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 630 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 762 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "H" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2424 Classifications: {'DNA': 119} Link IDs: {'rna3p': 118} Chain: "J" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2455 Classifications: {'DNA': 119} Link IDs: {'rna3p': 118} Time building chain proxies: 2.81, per 1000 atoms: 0.26 Number of scatterers: 10677 At special positions: 0 Unit cell: (119.709, 105.276, 118.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 238 15.00 O 2485 8.00 N 1975 7.00 C 5969 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: 0.81 Conformation dependent library (CDL) restraints added in 233.3 milliseconds 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 71.6% alpha, 3.3% beta 83 base pairs and 211 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 136 through 146 removed outlier: 3.538A pdb=" N ILE A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 167 removed outlier: 3.715A pdb=" N ASP A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 207 removed outlier: 3.576A pdb=" N ILE A 183 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.546A pdb=" N MET A 218 " --> pdb=" O MET A 214 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 222 " --> pdb=" O MET A 218 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A 223 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.611A pdb=" N ILE B 30 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 43 Processing helix chain 'B' and resid 50 through 77 removed outlier: 3.751A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG B 56 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 77 " --> pdb=" O TYR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.665A pdb=" N VAL B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 88 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 removed outlier: 3.797A pdb=" N ALA C 22 " --> pdb=" O ARG C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 37 removed outlier: 3.576A pdb=" N VAL C 31 " --> pdb=" O PRO C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 74 removed outlier: 3.604A pdb=" N ALA C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.615A pdb=" N LEU C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'D' and resid 42 through 54 removed outlier: 3.780A pdb=" N LYS D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR D 53 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 88 removed outlier: 3.518A pdb=" N LYS D 84 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 107 Processing helix chain 'D' and resid 109 through 127 removed outlier: 3.590A pdb=" N LYS D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL D 123 " --> pdb=" O GLY D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 146 removed outlier: 3.886A pdb=" N ALA E 138 " --> pdb=" O PRO E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 167 removed outlier: 3.512A pdb=" N PHE E 158 " --> pdb=" O SER E 154 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP E 167 " --> pdb=" O LYS E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 208 removed outlier: 3.681A pdb=" N MET E 184 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS E 200 " --> pdb=" O GLY E 196 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA E 208 " --> pdb=" O LEU E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 225 removed outlier: 3.699A pdb=" N MET E 218 " --> pdb=" O MET E 214 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 31 through 41 removed outlier: 3.535A pdb=" N ARG F 37 " --> pdb=" O PRO F 33 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU F 38 " --> pdb=" O ALA F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 77 removed outlier: 4.043A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP F 69 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR F 72 " --> pdb=" O ARG F 68 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA F 77 " --> pdb=" O TYR F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.759A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 23 removed outlier: 3.802A pdb=" N ALA G 22 " --> pdb=" O ARG G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 37 removed outlier: 3.532A pdb=" N VAL G 31 " --> pdb=" O PRO G 27 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG G 33 " --> pdb=" O GLY G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 72 Processing helix chain 'G' and resid 80 through 89 removed outlier: 3.680A pdb=" N LEU G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 removed outlier: 3.556A pdb=" N LEU G 98 " --> pdb=" O LEU G 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 54 removed outlier: 3.742A pdb=" N LYS H 48 " --> pdb=" O SER H 44 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS H 51 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR H 53 " --> pdb=" O VAL H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 89 removed outlier: 3.506A pdb=" N ASN H 72 " --> pdb=" O ASN H 68 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU H 76 " --> pdb=" O ASN H 72 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS H 84 " --> pdb=" O THR H 80 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA H 87 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 Processing helix chain 'H' and resid 108 through 127 removed outlier: 3.684A pdb=" N HIS H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178 removed outlier: 6.839A pdb=" N ARG A 177 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 212 through 213 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.135A pdb=" N ARG C 43 " --> pdb=" O ILE D 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 removed outlier: 6.711A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 177 through 178 removed outlier: 6.708A pdb=" N ARG E 177 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 212 through 213 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.078A pdb=" N ARG G 43 " --> pdb=" O ILE H 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 335 hydrogen bonds defined for protein. 996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 203 hydrogen bonds 398 hydrogen bond angles 0 basepair planarities 83 basepair parallelities 211 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1727 1.33 - 1.45: 3818 1.45 - 1.57: 5306 1.57 - 1.68: 474 1.68 - 1.80: 20 Bond restraints: 11345 Sorted by residual: bond pdb=" C3' DC I 51 " pdb=" C2' DC I 51 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DG J 2 " pdb=" C2' DG J 2 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DC I -21 " pdb=" C2' DC I -21 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DC I -8 " pdb=" C2' DC I -8 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DG I -11 " pdb=" O3' DG I -11 " ideal model delta sigma weight residual 1.435 1.392 0.043 1.30e-02 5.92e+03 1.09e+01 ... (remaining 11340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 15082 1.55 - 3.09: 1202 3.09 - 4.64: 52 4.64 - 6.18: 4 6.18 - 7.73: 2 Bond angle restraints: 16342 Sorted by residual: angle pdb=" O4' DT J 25 " pdb=" C1' DT J 25 " pdb=" N1 DT J 25 " ideal model delta sigma weight residual 108.00 111.20 -3.20 7.00e-01 2.04e+00 2.08e+01 angle pdb=" N3 DT I 1 " pdb=" C4 DT I 1 " pdb=" O4 DT I 1 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT I -17 " pdb=" C4 DT I -17 " pdb=" O4 DT I -17 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT J -29 " pdb=" C4 DT J -29 " pdb=" O4 DT J -29 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT I 30 " pdb=" C4 DT I 30 " pdb=" O4 DT I 30 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 ... (remaining 16337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 5127 34.93 - 69.86: 1057 69.86 - 104.78: 13 104.78 - 139.71: 0 139.71 - 174.64: 2 Dihedral angle restraints: 6199 sinusoidal: 4069 harmonic: 2130 Sorted by residual: dihedral pdb=" CA PRO H 108 " pdb=" C PRO H 108 " pdb=" N GLY H 109 " pdb=" CA GLY H 109 " ideal model delta harmonic sigma weight residual -180.00 -158.17 -21.83 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA PRO D 108 " pdb=" C PRO D 108 " pdb=" N GLY D 109 " pdb=" CA GLY D 109 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 45.36 174.64 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 6196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1035 0.038 - 0.076: 629 0.076 - 0.114: 184 0.114 - 0.152: 25 0.152 - 0.190: 2 Chirality restraints: 1875 Sorted by residual: chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.98e-01 chirality pdb=" C3' DC I 7 " pdb=" C4' DC I 7 " pdb=" O3' DC I 7 " pdb=" C2' DC I 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" C3' DC I -20 " pdb=" C4' DC I -20 " pdb=" O3' DC I -20 " pdb=" C2' DC I -20 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 1872 not shown) Planarity restraints: 1234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 156 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO E 157 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 157 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 157 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 32 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO B 33 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 33 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 33 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 109 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO C 110 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 110 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 110 " 0.025 5.00e-02 4.00e+02 ... (remaining 1231 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1468 2.75 - 3.29: 8276 3.29 - 3.83: 17618 3.83 - 4.36: 25111 4.36 - 4.90: 34893 Nonbonded interactions: 87366 Sorted by model distance: nonbonded pdb=" N4 DC I 51 " pdb=" O6 DG J -51 " model vdw 2.216 3.120 nonbonded pdb=" O6 DG I 11 " pdb=" N4 DC J -11 " model vdw 2.255 3.120 nonbonded pdb=" OH TYR B 99 " pdb=" OD2 ASP H 73 " model vdw 2.274 3.040 nonbonded pdb=" O2 DC I -20 " pdb=" N2 DG J 20 " model vdw 2.274 2.496 nonbonded pdb=" NZ LYS E 215 " pdb=" OE1 GLN E 219 " model vdw 2.321 3.120 ... (remaining 87361 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 'E' and resid 136 through 228) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 17 through 113) } ncs_group { reference = (chain 'D' and resid 38 through 129) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.630 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.580 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 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 : 0.008 0.051 11345 Z= 0.695 Angle : 0.806 7.727 16342 Z= 0.695 Chirality : 0.048 0.190 1875 Planarity : 0.004 0.051 1234 Dihedral : 26.073 174.641 4823 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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: -5.67 (0.19), residues: 716 helix: -3.90 (0.12), residues: 517 sheet: None (None), residues: 0 loop : -2.57 (0.33), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 93 TYR 0.013 0.002 TYR A 145 PHE 0.014 0.002 PHE F 62 TRP 0.004 0.002 TRP E 178 HIS 0.003 0.001 HIS G 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00833 / 0.70 (11345) covalent geometry : angle 0.80566 / 0.69 (16342) hydrogen bonds : bond 0.34023 / 21.92 ( 538) hydrogen bonds : angle 10.11388 / 6.83 ( 1394) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.317 Fit side-chains REVERT: E 155 LYS cc_start: 0.8637 (mttp) cc_final: 0.8278 (mtpt) REVERT: E 174 GLN cc_start: 0.7141 (mm-40) cc_final: 0.6885 (mm110) REVERT: G 16 GLN cc_start: 0.7204 (mt0) cc_final: 0.6986 (pm20) REVERT: H 73 ASP cc_start: 0.8800 (t0) cc_final: 0.8453 (t0) outliers start: 0 outliers final: 1 residues processed: 142 average time/residue: 0.9338 time to fit residues: 138.6045 Evaluate side-chains 130 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 30.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.156144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.129381 restraints weight = 12047.836| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.06 r_work: 0.3461 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11345 Z= 0.187 Angle : 0.746 8.161 16342 Z= 0.433 Chirality : 0.051 0.269 1875 Planarity : 0.005 0.039 1234 Dihedral : 29.474 179.843 3395 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.45 % Allowed : 10.66 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.28), residues: 716 helix: -0.58 (0.22), residues: 512 sheet: None (None), residues: 0 loop : -2.36 (0.31), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 72 TYR 0.014 0.001 TYR E 140 PHE 0.010 0.001 PHE F 62 TRP 0.003 0.001 TRP A 178 HIS 0.005 0.001 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.19 (11345) covalent geometry : angle 0.74635 / 0.43 (16342) hydrogen bonds : bond 0.09640 / 6.11 ( 538) hydrogen bonds : angle 3.59037 / 2.43 ( 1394) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8085 (mtm-85) cc_final: 0.7842 (mtm110) REVERT: C 109 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8545 (mp) REVERT: D 52 GLN cc_start: 0.7964 (tt0) cc_final: 0.7520 (mt0) REVERT: D 53 THR cc_start: 0.8412 (p) cc_final: 0.8192 (t) REVERT: D 76 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: E 184 MET cc_start: 0.8334 (mmp) cc_final: 0.8114 (mmm) REVERT: F 64 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8325 (mt-10) REVERT: F 92 LYS cc_start: 0.8822 (tttp) cc_final: 0.8606 (tttp) REVERT: H 73 ASP cc_start: 0.8905 (t0) cc_final: 0.8499 (t70) REVERT: H 76 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7871 (tm-30) outliers start: 9 outliers final: 1 residues processed: 135 average time/residue: 0.8436 time to fit residues: 119.5684 Evaluate side-chains 130 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain H residue 76 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 76 optimal weight: 30.0000 chunk 45 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 84 optimal weight: 30.0000 chunk 72 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 81 optimal weight: 30.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.153698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.126683 restraints weight = 12105.379| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.07 r_work: 0.3427 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11345 Z= 0.225 Angle : 0.716 7.418 16342 Z= 0.416 Chirality : 0.053 0.298 1875 Planarity : 0.005 0.043 1234 Dihedral : 29.704 176.818 3391 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.42 % Allowed : 12.28 % Favored : 85.30 % 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: -0.46 (0.30), residues: 716 helix: 0.50 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -2.32 (0.32), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 40 TYR 0.012 0.002 TYR A 145 PHE 0.016 0.002 PHE B 62 TRP 0.004 0.001 TRP A 178 HIS 0.003 0.001 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.22 (11345) covalent geometry : angle 0.71576 / 0.42 (16342) hydrogen bonds : bond 0.09533 / 6.09 ( 538) hydrogen bonds : angle 3.33703 / 2.26 ( 1394) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8106 (mtm-85) cc_final: 0.7839 (mtm110) REVERT: A 214 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8599 (mtm) REVERT: C 109 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8580 (mp) REVERT: D 52 GLN cc_start: 0.8025 (tt0) cc_final: 0.7596 (mt0) REVERT: F 64 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8406 (mt-10) REVERT: F 93 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.6878 (ttm-80) REVERT: H 73 ASP cc_start: 0.8955 (t0) cc_final: 0.8637 (t0) REVERT: H 76 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7836 (tm-30) outliers start: 15 outliers final: 5 residues processed: 134 average time/residue: 0.8930 time to fit residues: 125.2866 Evaluate side-chains 137 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 74 optimal weight: 30.0000 chunk 63 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 24 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 82 optimal weight: 30.0000 chunk 51 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.156966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.130201 restraints weight = 12113.408| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.08 r_work: 0.3481 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11345 Z= 0.157 Angle : 0.650 6.844 16342 Z= 0.385 Chirality : 0.048 0.259 1875 Planarity : 0.004 0.043 1234 Dihedral : 29.697 176.695 3391 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.10 % Allowed : 12.76 % Favored : 85.14 % 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: 0.45 (0.31), residues: 716 helix: 1.22 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -2.11 (0.32), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 97 TYR 0.017 0.001 TYR E 140 PHE 0.013 0.001 PHE F 62 TRP 0.003 0.001 TRP E 178 HIS 0.002 0.001 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.16 (11345) covalent geometry : angle 0.65041 / 0.39 (16342) hydrogen bonds : bond 0.07590 / 4.82 ( 538) hydrogen bonds : angle 3.34056 / 2.27 ( 1394) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8097 (mtm-85) cc_final: 0.7825 (mtm110) REVERT: A 214 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8865 (mtt) REVERT: C 109 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8521 (mp) REVERT: D 52 GLN cc_start: 0.7899 (tt0) cc_final: 0.7483 (mt0) REVERT: D 76 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: F 64 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8362 (mt-10) REVERT: F 93 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.6799 (ttm-80) REVERT: H 73 ASP cc_start: 0.8873 (t0) cc_final: 0.8554 (t0) REVERT: H 76 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7863 (tm-30) REVERT: H 81 GLU cc_start: 0.8469 (tp30) cc_final: 0.7814 (tp30) outliers start: 13 outliers final: 5 residues processed: 139 average time/residue: 0.8065 time to fit residues: 117.6858 Evaluate side-chains 138 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 76 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 86 optimal weight: 30.0000 chunk 81 optimal weight: 30.0000 chunk 59 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 overall best weight: 5.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.154424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127572 restraints weight = 11984.231| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.05 r_work: 0.3436 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11345 Z= 0.217 Angle : 0.694 7.353 16342 Z= 0.401 Chirality : 0.052 0.296 1875 Planarity : 0.004 0.042 1234 Dihedral : 29.814 176.864 3391 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.91 % Allowed : 12.76 % Favored : 84.33 % 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: 0.57 (0.31), residues: 716 helix: 1.32 (0.23), residues: 513 sheet: None (None), residues: 0 loop : -2.12 (0.33), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 36 TYR 0.012 0.002 TYR E 140 PHE 0.015 0.002 PHE B 62 TRP 0.003 0.001 TRP A 178 HIS 0.003 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.22 (11345) covalent geometry : angle 0.69355 / 0.40 (16342) hydrogen bonds : bond 0.08636 / 5.51 ( 538) hydrogen bonds : angle 3.16769 / 2.15 ( 1394) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8101 (mtm-85) cc_final: 0.7808 (mtm110) REVERT: A 214 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.8948 (mtt) REVERT: C 109 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8588 (mp) REVERT: D 52 GLN cc_start: 0.7956 (tt0) cc_final: 0.7521 (mt0) REVERT: F 60 LYS cc_start: 0.9029 (tppp) cc_final: 0.8721 (tttp) REVERT: F 64 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8404 (mt-10) REVERT: F 93 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.6778 (ttm-80) REVERT: H 73 ASP cc_start: 0.8954 (t0) cc_final: 0.8636 (t0) REVERT: H 76 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7833 (tm-30) outliers start: 18 outliers final: 7 residues processed: 138 average time/residue: 0.9053 time to fit residues: 131.0664 Evaluate side-chains 140 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 76 optimal weight: 30.0000 chunk 4 optimal weight: 7.9990 chunk 85 optimal weight: 30.0000 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 81 optimal weight: 30.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.154447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.127896 restraints weight = 12096.786| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.06 r_work: 0.3442 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11345 Z= 0.174 Angle : 0.662 7.178 16342 Z= 0.387 Chirality : 0.049 0.284 1875 Planarity : 0.004 0.042 1234 Dihedral : 29.819 177.009 3391 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.26 % Allowed : 14.05 % Favored : 83.68 % 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: 0.71 (0.31), residues: 716 helix: 1.43 (0.23), residues: 513 sheet: None (None), residues: 0 loop : -2.07 (0.33), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 40 TYR 0.013 0.002 TYR E 140 PHE 0.013 0.002 PHE B 62 TRP 0.002 0.001 TRP E 178 HIS 0.003 0.001 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 (11345) covalent geometry : angle 0.66160 / 0.39 (16342) hydrogen bonds : bond 0.08137 / 5.19 ( 538) hydrogen bonds : angle 3.17376 / 2.16 ( 1394) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8108 (mtm-85) cc_final: 0.7815 (mtm110) REVERT: A 214 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.9015 (mtt) REVERT: C 74 ASN cc_start: 0.8422 (m-40) cc_final: 0.8076 (t0) REVERT: C 109 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8571 (mp) REVERT: D 52 GLN cc_start: 0.7937 (tt0) cc_final: 0.7499 (mt0) REVERT: F 60 LYS cc_start: 0.9019 (tppp) cc_final: 0.8717 (tttp) REVERT: F 64 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8382 (mt-10) REVERT: F 93 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.6720 (ttm-80) REVERT: H 73 ASP cc_start: 0.8939 (t0) cc_final: 0.8635 (t0) outliers start: 14 outliers final: 7 residues processed: 132 average time/residue: 0.9035 time to fit residues: 125.4225 Evaluate side-chains 139 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 63 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 68 optimal weight: 50.0000 chunk 22 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 82 optimal weight: 30.0000 chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 87 optimal weight: 30.0000 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.157371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.130705 restraints weight = 12138.808| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.06 r_work: 0.3472 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11345 Z= 0.153 Angle : 0.623 6.575 16342 Z= 0.370 Chirality : 0.047 0.258 1875 Planarity : 0.003 0.037 1234 Dihedral : 29.787 177.636 3391 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.10 % Allowed : 13.89 % Favored : 84.01 % 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: 1.10 (0.31), residues: 716 helix: 1.72 (0.24), residues: 513 sheet: None (None), residues: 0 loop : -1.96 (0.33), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 40 TYR 0.017 0.001 TYR E 140 PHE 0.011 0.001 PHE F 62 TRP 0.002 0.001 TRP E 178 HIS 0.002 0.000 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.15 (11345) covalent geometry : angle 0.62325 / 0.37 (16342) hydrogen bonds : bond 0.07225 / 4.61 ( 538) hydrogen bonds : angle 3.13013 / 2.13 ( 1394) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.294 Fit side-chains REVERT: A 143 ARG cc_start: 0.8099 (mtm-85) cc_final: 0.7812 (mtm110) REVERT: C 74 ASN cc_start: 0.8380 (m-40) cc_final: 0.8038 (t0) REVERT: C 109 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8545 (mp) REVERT: D 76 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7755 (tt0) REVERT: E 174 GLN cc_start: 0.7475 (mm-40) cc_final: 0.6772 (mt0) REVERT: F 60 LYS cc_start: 0.8975 (tppp) cc_final: 0.8662 (tttp) REVERT: F 64 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8371 (mt-10) REVERT: F 93 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.6739 (ttm-80) REVERT: H 73 ASP cc_start: 0.8891 (t0) cc_final: 0.8475 (t0) REVERT: H 76 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7833 (tm-30) outliers start: 13 outliers final: 6 residues processed: 136 average time/residue: 0.8913 time to fit residues: 127.2957 Evaluate side-chains 140 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 76 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 82 optimal weight: 30.0000 chunk 18 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 85 optimal weight: 30.0000 chunk 4 optimal weight: 6.9990 chunk 69 optimal weight: 30.0000 chunk 55 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.155797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.129075 restraints weight = 11992.028| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.06 r_work: 0.3461 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11345 Z= 0.171 Angle : 0.626 6.885 16342 Z= 0.368 Chirality : 0.047 0.279 1875 Planarity : 0.004 0.039 1234 Dihedral : 29.798 178.055 3391 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.10 % Allowed : 14.70 % Favored : 83.20 % 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: 1.21 (0.31), residues: 716 helix: 1.82 (0.23), residues: 513 sheet: None (None), residues: 0 loop : -1.96 (0.33), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 40 TYR 0.015 0.001 TYR E 140 PHE 0.012 0.002 PHE B 62 TRP 0.002 0.001 TRP A 178 HIS 0.003 0.001 HIS H 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.17 (11345) covalent geometry : angle 0.62605 / 0.37 (16342) hydrogen bonds : bond 0.07495 / 4.79 ( 538) hydrogen bonds : angle 2.97796 / 2.02 ( 1394) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8100 (mtm-85) cc_final: 0.7804 (mtm110) REVERT: C 74 ASN cc_start: 0.8295 (m-40) cc_final: 0.7957 (t0) REVERT: C 109 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8572 (mp) REVERT: D 76 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: E 199 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8153 (mt-10) REVERT: F 60 LYS cc_start: 0.9005 (tppp) cc_final: 0.8723 (tttp) REVERT: F 64 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8414 (mt-10) REVERT: F 93 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.6742 (ttm-80) REVERT: G 96 LYS cc_start: 0.8692 (tttp) cc_final: 0.8489 (tttm) REVERT: H 73 ASP cc_start: 0.8954 (t0) cc_final: 0.8643 (t0) REVERT: H 76 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7848 (tm-30) outliers start: 13 outliers final: 5 residues processed: 137 average time/residue: 0.9004 time to fit residues: 129.4605 Evaluate side-chains 141 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 76 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 82 optimal weight: 30.0000 chunk 84 optimal weight: 30.0000 chunk 87 optimal weight: 30.0000 chunk 68 optimal weight: 50.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.155887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.129154 restraints weight = 11995.949| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.07 r_work: 0.3466 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11345 Z= 0.161 Angle : 0.620 6.901 16342 Z= 0.366 Chirality : 0.046 0.276 1875 Planarity : 0.004 0.039 1234 Dihedral : 29.800 178.349 3391 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.26 % Allowed : 15.02 % Favored : 82.71 % 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: 1.24 (0.31), residues: 716 helix: 1.84 (0.23), residues: 513 sheet: None (None), residues: 0 loop : -1.96 (0.33), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 78 TYR 0.014 0.001 TYR E 140 PHE 0.012 0.001 PHE B 62 TRP 0.002 0.001 TRP A 178 HIS 0.002 0.000 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.16 (11345) covalent geometry : angle 0.62007 / 0.37 (16342) hydrogen bonds : bond 0.07456 / 4.77 ( 538) hydrogen bonds : angle 2.97246 / 2.02 ( 1394) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8110 (mtm-85) cc_final: 0.7813 (mtm110) REVERT: C 74 ASN cc_start: 0.8293 (m-40) cc_final: 0.7962 (t0) REVERT: C 109 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8572 (mp) REVERT: D 76 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: D 98 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8514 (mp0) REVERT: E 199 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8121 (mt-10) REVERT: E 225 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8169 (ptt180) REVERT: F 60 LYS cc_start: 0.9013 (tppp) cc_final: 0.8729 (tttp) REVERT: F 64 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8405 (mt-10) REVERT: F 93 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.6826 (ttm-80) REVERT: G 96 LYS cc_start: 0.8699 (tttp) cc_final: 0.8498 (tttm) REVERT: H 73 ASP cc_start: 0.8964 (t0) cc_final: 0.8552 (t0) REVERT: H 76 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7857 (tm-30) outliers start: 14 outliers final: 5 residues processed: 134 average time/residue: 0.8999 time to fit residues: 126.5117 Evaluate side-chains 143 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 225 ARG Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 76 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 8.9990 chunk 80 optimal weight: 30.0000 chunk 28 optimal weight: 0.9980 chunk 79 optimal weight: 50.0000 chunk 30 optimal weight: 6.9990 chunk 89 optimal weight: 40.0000 chunk 71 optimal weight: 30.0000 chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 0.0870 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 overall best weight: 2.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.156183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.129446 restraints weight = 11968.259| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.06 r_work: 0.3465 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11345 Z= 0.149 Angle : 0.613 6.644 16342 Z= 0.363 Chirality : 0.046 0.273 1875 Planarity : 0.004 0.039 1234 Dihedral : 29.805 178.379 3391 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.94 % Allowed : 15.51 % Favored : 82.55 % 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: 1.26 (0.31), residues: 716 helix: 1.86 (0.23), residues: 513 sheet: None (None), residues: 0 loop : -1.96 (0.33), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 93 TYR 0.015 0.001 TYR E 140 PHE 0.012 0.001 PHE B 62 TRP 0.002 0.001 TRP A 178 HIS 0.002 0.001 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.15 (11345) covalent geometry : angle 0.61299 / 0.36 (16342) hydrogen bonds : bond 0.07326 / 4.68 ( 538) hydrogen bonds : angle 2.96880 / 2.02 ( 1394) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8099 (mtm-85) cc_final: 0.7799 (mtm110) REVERT: C 74 ASN cc_start: 0.8285 (m-40) cc_final: 0.7955 (t0) REVERT: C 109 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8570 (mp) REVERT: D 76 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: E 199 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: E 225 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8157 (ptt180) REVERT: F 60 LYS cc_start: 0.9000 (tppp) cc_final: 0.8716 (tttp) REVERT: F 64 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8400 (mt-10) REVERT: F 93 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.6818 (ttm-80) REVERT: G 96 LYS cc_start: 0.8693 (tttp) cc_final: 0.8488 (tttm) REVERT: H 73 ASP cc_start: 0.8956 (t0) cc_final: 0.8644 (t0) REVERT: H 76 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7836 (tm-30) outliers start: 12 outliers final: 5 residues processed: 135 average time/residue: 0.8950 time to fit residues: 126.7978 Evaluate side-chains 142 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 225 ARG Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 76 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 85 optimal weight: 30.0000 chunk 11 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 30.0000 chunk 70 optimal weight: 40.0000 chunk 20 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.156674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.129939 restraints weight = 12204.784| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.06 r_work: 0.3464 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11345 Z= 0.167 Angle : 0.622 6.854 16342 Z= 0.365 Chirality : 0.046 0.276 1875 Planarity : 0.004 0.039 1234 Dihedral : 29.805 178.900 3391 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.10 % Allowed : 15.51 % Favored : 82.39 % 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: 1.28 (0.31), residues: 716 helix: 1.87 (0.23), residues: 513 sheet: None (None), residues: 0 loop : -1.95 (0.33), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 93 TYR 0.015 0.001 TYR E 140 PHE 0.012 0.001 PHE B 62 TRP 0.002 0.001 TRP A 178 HIS 0.002 0.000 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.17 (11345) covalent geometry : angle 0.62191 / 0.37 (16342) hydrogen bonds : bond 0.07430 / 4.76 ( 538) hydrogen bonds : angle 2.94123 / 2.00 ( 1394) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4013.71 seconds wall clock time: 68 minutes 51.67 seconds (4131.67 seconds total)