Starting phenix.real_space_refine on Sat Jul 4 08:46:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k63_22687/07_2026/7k63_22687.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k63_22687/07_2026/7k63_22687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k63_22687/07_2026/7k63_22687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k63_22687/07_2026/7k63_22687.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k63_22687/07_2026/7k63_22687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k63_22687/07_2026/7k63_22687.map" } resolution = 3.03 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2242 atoms to isotropic. 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 394 5.49 5 S 32 5.16 5 C 10288 2.51 5 N 3355 2.21 5 O 4261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18330 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 4015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 4015 Classifications: {'DNA': 197} Link IDs: {'rna3p': 196} Chain: "J" Number of atoms: 4062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 4062 Classifications: {'DNA': 197} Link IDs: {'rna3p': 196} Chain: "M" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "N" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "U" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 607 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Time building chain proxies: 2.98, per 1000 atoms: 0.16 Number of scatterers: 18330 At special positions: 0 Unit cell: (131.62, 123.643, 196.766, 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 32 16.00 P 394 15.00 O 4261 8.00 N 3355 7.00 C 10288 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: 1.41 Conformation dependent library (CDL) restraints added in 466.1 milliseconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2410 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 23 sheets defined 48.8% alpha, 20.6% beta 197 base pairs and 334 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.559A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.950A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.156A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.602A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.567A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.255A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.540A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.899A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 102 Processing helix chain 'M' and resid 177 through 179 No H-bonds generated for 'chain 'M' and resid 177 through 179' Processing helix chain 'M' and resid 211 through 214 removed outlier: 3.709A pdb=" N LYS M 214 " --> pdb=" O GLU M 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 211 through 214' Processing helix chain 'M' and resid 236 through 240 Processing helix chain 'N' and resid 98 through 102 removed outlier: 3.514A pdb=" N THR N 102 " --> pdb=" O SER N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 179 No H-bonds generated for 'chain 'N' and resid 177 through 179' Processing helix chain 'N' and resid 211 through 214 removed outlier: 3.717A pdb=" N LYS N 214 " --> pdb=" O GLU N 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 211 through 214' Processing helix chain 'N' and resid 236 through 240 Processing helix chain 'U' and resid 45 through 59 removed outlier: 3.800A pdb=" N ARG U 56 " --> pdb=" O VAL U 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 74 Processing helix chain 'U' and resid 83 through 98 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.869A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.067A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.486A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.632A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.996A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 23 through 25 removed outlier: 3.699A pdb=" N ASP M 89 " --> pdb=" O SER M 86 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER M 91 " --> pdb=" O SER M 84 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 29 through 32 removed outlier: 3.849A pdb=" N GLU M 124 " --> pdb=" O MET M 30 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA M 32 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP M 54 " --> pdb=" O LEU M 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 29 through 32 removed outlier: 3.849A pdb=" N GLU M 124 " --> pdb=" O MET M 30 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA M 32 " --> pdb=" O GLU M 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 152 through 155 Processing sheet with id=AB6, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.555A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP M 185 " --> pdb=" O ILE M 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 159 through 161 removed outlier: 3.996A pdb=" N TYR M 258 " --> pdb=" O ARG M 247 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 23 through 25 Processing sheet with id=AB9, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.757A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP N 54 " --> pdb=" O LEU N 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 29 through 32 Processing sheet with id=AC2, first strand: chain 'N' and resid 152 through 155 Processing sheet with id=AC3, first strand: chain 'N' and resid 159 through 161 removed outlier: 6.615A pdb=" N ILE N 183 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TRP N 185 " --> pdb=" O ILE N 197 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 159 through 161 removed outlier: 3.944A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N SER N 249 " --> pdb=" O LEU N 256 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU N 256 " --> pdb=" O SER N 249 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 64 through 65 617 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 510 hydrogen bonds 1020 hydrogen bond angles 0 basepair planarities 197 basepair parallelities 334 stacking parallelities Total time for adding SS restraints: 3.57 Time building geometry restraints manager: 1.92 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: 3676 1.33 - 1.45: 6202 1.45 - 1.57: 8770 1.57 - 1.69: 786 1.69 - 1.81: 52 Bond restraints: 19486 Sorted by residual: bond pdb=" C3' DG J 120 " pdb=" C2' DG J 120 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DC J 175 " pdb=" C2' DC J 175 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DT J 153 " pdb=" C2' DT J 153 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.12e+00 bond pdb=" C3' DT J 32 " pdb=" C2' DT J 32 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.10e+00 bond pdb=" C3' DT J 34 " pdb=" C2' DT J 34 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.93e+00 ... (remaining 19481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 25919 1.42 - 2.85: 1950 2.85 - 4.27: 130 4.27 - 5.69: 19 5.69 - 7.12: 5 Bond angle restraints: 28023 Sorted by residual: angle pdb=" O4' DA J 115 " pdb=" C1' DA J 115 " pdb=" N9 DA J 115 " ideal model delta sigma weight residual 108.00 111.42 -3.42 7.00e-01 2.04e+00 2.39e+01 angle pdb=" O4' DC J 71 " pdb=" C4' DC J 71 " pdb=" C3' DC J 71 " ideal model delta sigma weight residual 106.00 103.17 2.83 6.00e-01 2.78e+00 2.22e+01 angle pdb=" N3 DT J 83 " pdb=" C4 DT J 83 " pdb=" O4 DT J 83 " ideal model delta sigma weight residual 119.90 122.65 -2.75 6.00e-01 2.78e+00 2.10e+01 angle pdb=" N3 DT I 56 " pdb=" C4 DT I 56 " pdb=" O4 DT I 56 " ideal model delta sigma weight residual 119.90 122.65 -2.75 6.00e-01 2.78e+00 2.10e+01 angle pdb=" N3 DT J 19 " pdb=" C4 DT J 19 " pdb=" O4 DT J 19 " ideal model delta sigma weight residual 119.90 122.65 -2.75 6.00e-01 2.78e+00 2.10e+01 ... (remaining 28018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 8763 35.60 - 71.19: 1849 71.19 - 106.79: 24 106.79 - 142.38: 0 142.38 - 177.98: 2 Dihedral angle restraints: 10638 sinusoidal: 6875 harmonic: 3763 Sorted by residual: dihedral pdb=" C4' DT J 153 " pdb=" C3' DT J 153 " pdb=" O3' DT J 153 " pdb=" P DC J 154 " ideal model delta sinusoidal sigma weight residual 220.00 42.02 177.98 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA LEU A 82 " pdb=" C LEU A 82 " pdb=" N ARG A 83 " pdb=" CA ARG A 83 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" C4' DG J 119 " pdb=" C3' DG J 119 " pdb=" O3' DG J 119 " pdb=" P DG J 120 " ideal model delta sinusoidal sigma weight residual 220.00 70.16 149.84 1 3.50e+01 8.16e-04 1.46e+01 ... (remaining 10635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1699 0.031 - 0.063: 954 0.063 - 0.094: 323 0.094 - 0.125: 158 0.125 - 0.156: 20 Chirality restraints: 3154 Sorted by residual: chirality pdb=" C3' DT J 153 " pdb=" C4' DT J 153 " pdb=" O3' DT J 153 " pdb=" C2' DT J 153 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CB THR M 102 " pdb=" CA THR M 102 " pdb=" OG1 THR M 102 " pdb=" CG2 THR M 102 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.07e-01 chirality pdb=" CA ILE N 67 " pdb=" N ILE N 67 " pdb=" C ILE N 67 " pdb=" CB ILE N 67 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 3151 not shown) Planarity restraints: 2171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET M 169 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO M 170 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO M 170 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO M 170 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO D 103 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO H 103 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " -0.023 5.00e-02 4.00e+02 ... (remaining 2168 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 861 2.71 - 3.25: 16531 3.25 - 3.80: 35102 3.80 - 4.35: 44424 4.35 - 4.90: 64273 Nonbonded interactions: 161191 Sorted by model distance: nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.158 3.040 nonbonded pdb=" OE1 GLU C 92 " pdb=" NH1 ARG M 251 " model vdw 2.204 3.120 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.205 3.120 nonbonded pdb=" OE1 GLN M 184 " pdb=" NE1 TRP M 196 " model vdw 2.236 3.120 nonbonded pdb=" OE1 GLU D 71 " pdb=" NZ LYS F 91 " model vdw 2.251 3.120 ... (remaining 161186 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' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.860 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 0.006 0.041 19486 Z= 0.503 Angle : 0.759 7.116 28023 Z= 0.645 Chirality : 0.046 0.156 3154 Planarity : 0.004 0.057 2171 Dihedral : 26.716 177.979 8228 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.09 % Allowed : 0.00 % Favored : 99.91 % 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: 0.98 (0.23), residues: 1272 helix: 1.53 (0.21), residues: 592 sheet: 0.23 (0.33), residues: 238 loop : -0.18 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 33 TYR 0.022 0.002 TYR G 50 PHE 0.013 0.002 PHE C 25 TRP 0.019 0.002 TRP M 196 HIS 0.005 0.001 HIS M 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.50 (19486) covalent geometry : angle 0.75855 / 0.65 (28023) hydrogen bonds : bond 0.09742 / 6.33 ( 1103) hydrogen bonds : angle 4.53669 / 3.34 ( 2712) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7366 (mm-30) REVERT: C 71 ARG cc_start: 0.8219 (ttp-170) cc_final: 0.7953 (ttm-80) REVERT: D 59 MET cc_start: 0.8102 (tpt) cc_final: 0.7660 (tpt) REVERT: D 86 ARG cc_start: 0.8279 (mtp85) cc_final: 0.8036 (mmt-90) REVERT: E 60 LEU cc_start: 0.8527 (mt) cc_final: 0.8224 (mt) REVERT: F 55 ARG cc_start: 0.8681 (mtt90) cc_final: 0.8464 (mtm-85) REVERT: F 79 LYS cc_start: 0.8084 (mttp) cc_final: 0.7858 (mttp) REVERT: F 85 ASP cc_start: 0.7515 (m-30) cc_final: 0.7300 (m-30) REVERT: G 73 ASN cc_start: 0.7897 (t0) cc_final: 0.7286 (t0) REVERT: H 83 TYR cc_start: 0.8482 (m-10) cc_final: 0.8188 (m-10) REVERT: M 68 TYR cc_start: 0.8352 (p90) cc_final: 0.8068 (p90) REVERT: M 155 GLN cc_start: 0.7442 (tt0) cc_final: 0.7188 (tt0) REVERT: U 70 TYR cc_start: 0.8753 (t80) cc_final: 0.8436 (t80) outliers start: 1 outliers final: 0 residues processed: 280 average time/residue: 0.1645 time to fit residues: 64.4625 Evaluate side-chains 237 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 50.0000 chunk 149 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 68 GLN E 125 GLN F 25 ASN F 27 GLN G 24 GLN N 95 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.151375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.106694 restraints weight = 26328.042| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.32 r_work: 0.3191 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 19486 Z= 0.240 Angle : 0.680 6.190 28023 Z= 0.388 Chirality : 0.048 0.248 3154 Planarity : 0.005 0.055 2171 Dihedral : 30.326 178.638 5718 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.72 % Allowed : 6.26 % Favored : 92.02 % 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: 0.96 (0.23), residues: 1272 helix: 1.63 (0.21), residues: 592 sheet: 0.28 (0.34), residues: 226 loop : -0.43 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG U 56 TYR 0.022 0.002 TYR G 50 PHE 0.014 0.002 PHE C 25 TRP 0.015 0.002 TRP N 185 HIS 0.008 0.001 HIS M 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.24 (19486) covalent geometry : angle 0.68007 / 0.39 (28023) hydrogen bonds : bond 0.04903 / 3.23 ( 1103) hydrogen bonds : angle 3.82215 / 2.80 ( 2712) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 250 time to evaluate : 0.533 Fit side-chains REVERT: B 26 ILE cc_start: 0.8522 (tp) cc_final: 0.8181 (tp) REVERT: C 64 GLU cc_start: 0.8192 (tt0) cc_final: 0.7914 (tt0) REVERT: C 71 ARG cc_start: 0.8523 (ttp-170) cc_final: 0.8290 (ttm-80) REVERT: D 59 MET cc_start: 0.8801 (tpt) cc_final: 0.8194 (tpt) REVERT: D 72 ARG cc_start: 0.8701 (mtp180) cc_final: 0.8468 (mtm180) REVERT: F 85 ASP cc_start: 0.7949 (m-30) cc_final: 0.7683 (m-30) REVERT: G 73 ASN cc_start: 0.8091 (t0) cc_final: 0.7479 (t0) REVERT: H 83 TYR cc_start: 0.8686 (m-10) cc_final: 0.8280 (m-10) REVERT: M 68 TYR cc_start: 0.8860 (p90) cc_final: 0.8628 (p90) REVERT: M 155 GLN cc_start: 0.7961 (tt0) cc_final: 0.7606 (tt0) REVERT: N 23 MET cc_start: 0.7807 (mmm) cc_final: 0.7487 (mmm) REVERT: N 38 VAL cc_start: 0.8163 (t) cc_final: 0.7663 (t) REVERT: N 223 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7646 (mttm) outliers start: 19 outliers final: 16 residues processed: 257 average time/residue: 0.1610 time to fit residues: 58.2352 Evaluate side-chains 243 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 226 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain N residue 191 ARG Chi-restraints excluded: chain N residue 223 LYS Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain U residue 69 ILE Chi-restraints excluded: chain U residue 86 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 47 optimal weight: 0.6980 chunk 102 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 92 optimal weight: 50.0000 chunk 6 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 68 GLN E 125 GLN M 110 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.153237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108666 restraints weight = 26516.587| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.30 r_work: 0.3227 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19486 Z= 0.146 Angle : 0.616 6.465 28023 Z= 0.357 Chirality : 0.044 0.253 3154 Planarity : 0.004 0.047 2171 Dihedral : 30.326 176.495 5718 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.27 % Allowed : 8.70 % Favored : 89.03 % 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: 1.22 (0.23), residues: 1272 helix: 1.98 (0.21), residues: 592 sheet: 0.32 (0.34), residues: 214 loop : -0.45 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 129 TYR 0.022 0.002 TYR U 90 PHE 0.008 0.001 PHE C 25 TRP 0.008 0.002 TRP M 185 HIS 0.004 0.001 HIS M 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (19486) covalent geometry : angle 0.61580 / 0.36 (28023) hydrogen bonds : bond 0.04070 / 2.66 ( 1103) hydrogen bonds : angle 3.52964 / 2.59 ( 2712) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 245 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: B 26 ILE cc_start: 0.8385 (tp) cc_final: 0.8038 (tp) REVERT: C 64 GLU cc_start: 0.8134 (tt0) cc_final: 0.7871 (tt0) REVERT: C 71 ARG cc_start: 0.8510 (ttp-110) cc_final: 0.8243 (ttp-110) REVERT: D 72 ARG cc_start: 0.8700 (mtp180) cc_final: 0.8494 (mtm180) REVERT: D 86 ARG cc_start: 0.8700 (mtp85) cc_final: 0.8486 (mmt-90) REVERT: G 73 ASN cc_start: 0.8060 (t0) cc_final: 0.7456 (t0) REVERT: H 83 TYR cc_start: 0.8793 (m-10) cc_final: 0.8423 (m-10) REVERT: M 30 MET cc_start: 0.7606 (ptp) cc_final: 0.7160 (mtp) REVERT: M 68 TYR cc_start: 0.8788 (p90) cc_final: 0.8569 (p90) REVERT: M 155 GLN cc_start: 0.8005 (tt0) cc_final: 0.7784 (tt0) REVERT: M 211 GLU cc_start: 0.6885 (pm20) cc_final: 0.6662 (pm20) REVERT: U 83 ASN cc_start: 0.8203 (p0) cc_final: 0.7924 (p0) outliers start: 25 outliers final: 21 residues processed: 255 average time/residue: 0.1643 time to fit residues: 58.5989 Evaluate side-chains 253 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 191 ARG Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 86 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 63 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 127 optimal weight: 0.5980 chunk 85 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 156 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 104 GLN D 47 GLN E 125 GLN F 75 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.152914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.108405 restraints weight = 26453.765| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.29 r_work: 0.3221 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19486 Z= 0.159 Angle : 0.607 7.493 28023 Z= 0.350 Chirality : 0.044 0.239 3154 Planarity : 0.004 0.046 2171 Dihedral : 30.379 176.555 5718 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.45 % Allowed : 9.70 % Favored : 87.85 % 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: 1.29 (0.23), residues: 1272 helix: 2.10 (0.21), residues: 592 sheet: 0.33 (0.35), residues: 214 loop : -0.48 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 56 TYR 0.026 0.002 TYR U 90 PHE 0.009 0.001 PHE C 25 TRP 0.008 0.001 TRP M 185 HIS 0.004 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 (19486) covalent geometry : angle 0.60674 / 0.35 (28023) hydrogen bonds : bond 0.04092 / 2.67 ( 1103) hydrogen bonds : angle 3.39285 / 2.48 ( 2712) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 240 time to evaluate : 0.497 Fit side-chains REVERT: C 64 GLU cc_start: 0.8125 (tt0) cc_final: 0.7898 (tt0) REVERT: C 71 ARG cc_start: 0.8498 (ttp-110) cc_final: 0.8223 (ttp-110) REVERT: G 73 ASN cc_start: 0.8040 (t0) cc_final: 0.7437 (t0) REVERT: M 155 GLN cc_start: 0.8076 (tt0) cc_final: 0.7797 (tt0) REVERT: M 211 GLU cc_start: 0.6834 (pm20) cc_final: 0.6574 (pm20) REVERT: N 152 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8251 (mt0) outliers start: 27 outliers final: 24 residues processed: 251 average time/residue: 0.1737 time to fit residues: 61.2667 Evaluate side-chains 251 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 191 ARG Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 86 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 145 optimal weight: 0.4980 chunk 17 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 104 optimal weight: 10.9990 chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 23 optimal weight: 0.0870 chunk 148 optimal weight: 0.5980 chunk 81 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 47 GLN E 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.154196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.109829 restraints weight = 26400.121| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.31 r_work: 0.3242 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 19486 Z= 0.129 Angle : 0.592 7.988 28023 Z= 0.342 Chirality : 0.043 0.239 3154 Planarity : 0.004 0.047 2171 Dihedral : 30.359 175.462 5718 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.18 % Allowed : 11.24 % Favored : 86.58 % 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: 1.45 (0.23), residues: 1272 helix: 2.29 (0.21), residues: 592 sheet: 0.38 (0.35), residues: 214 loop : -0.49 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 129 TYR 0.018 0.001 TYR U 70 PHE 0.007 0.001 PHE A 67 TRP 0.008 0.001 TRP M 185 HIS 0.002 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.13 (19486) covalent geometry : angle 0.59172 / 0.34 (28023) hydrogen bonds : bond 0.03789 / 2.47 ( 1103) hydrogen bonds : angle 3.29779 / 2.42 ( 2712) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 238 time to evaluate : 0.476 Fit side-chains REVERT: C 64 GLU cc_start: 0.8120 (tt0) cc_final: 0.7878 (tt0) REVERT: C 73 ASN cc_start: 0.7994 (t0) cc_final: 0.7747 (t0) REVERT: D 59 MET cc_start: 0.8423 (tpt) cc_final: 0.7912 (tpt) REVERT: F 79 LYS cc_start: 0.8243 (mttp) cc_final: 0.7978 (mttp) REVERT: G 73 ASN cc_start: 0.8038 (t0) cc_final: 0.7432 (t0) REVERT: M 155 GLN cc_start: 0.8073 (tt0) cc_final: 0.7806 (tt0) REVERT: M 211 GLU cc_start: 0.6821 (pm20) cc_final: 0.6564 (pm20) REVERT: N 98 GLU cc_start: 0.7775 (mp0) cc_final: 0.7181 (mp0) REVERT: N 101 ASP cc_start: 0.7580 (m-30) cc_final: 0.6873 (m-30) REVERT: N 152 GLN cc_start: 0.8422 (mm-40) cc_final: 0.8214 (mt0) REVERT: U 83 ASN cc_start: 0.8101 (p0) cc_final: 0.7852 (p0) outliers start: 24 outliers final: 22 residues processed: 249 average time/residue: 0.1754 time to fit residues: 61.6945 Evaluate side-chains 252 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 191 ARG Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain U residue 107 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 78 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS C 104 GLN D 47 GLN E 68 GLN E 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 103 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.150924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.105717 restraints weight = 26250.879| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.32 r_work: 0.3181 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 19486 Z= 0.235 Angle : 0.641 8.711 28023 Z= 0.363 Chirality : 0.046 0.234 3154 Planarity : 0.004 0.048 2171 Dihedral : 30.505 176.113 5718 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.99 % Allowed : 11.42 % Favored : 85.58 % 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: 1.15 (0.23), residues: 1272 helix: 2.00 (0.21), residues: 592 sheet: 0.25 (0.35), residues: 214 loop : -0.57 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 37 TYR 0.019 0.002 TYR U 70 PHE 0.013 0.002 PHE C 25 TRP 0.013 0.002 TRP N 185 HIS 0.004 0.001 HIS M 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.23 (19486) covalent geometry : angle 0.64081 / 0.36 (28023) hydrogen bonds : bond 0.04632 / 3.05 ( 1103) hydrogen bonds : angle 3.42289 / 2.50 ( 2712) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 0.503 Fit side-chains REVERT: C 64 GLU cc_start: 0.8229 (tt0) cc_final: 0.8022 (tt0) REVERT: C 73 ASN cc_start: 0.8149 (t0) cc_final: 0.7923 (t0) REVERT: G 73 ASN cc_start: 0.8068 (t0) cc_final: 0.7472 (t0) REVERT: N 152 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8235 (mt0) REVERT: U 114 LYS cc_start: 0.7989 (ttpt) cc_final: 0.7475 (ttpp) outliers start: 33 outliers final: 27 residues processed: 253 average time/residue: 0.1666 time to fit residues: 59.7166 Evaluate side-chains 260 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 233 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 191 ARG Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain U residue 107 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 7 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 114 optimal weight: 0.0870 chunk 139 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN C 104 GLN D 47 GLN D 49 HIS E 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 ASN N 110 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.153017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.108115 restraints weight = 26353.590| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.32 r_work: 0.3217 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19486 Z= 0.141 Angle : 0.611 8.272 28023 Z= 0.348 Chirality : 0.043 0.237 3154 Planarity : 0.004 0.049 2171 Dihedral : 30.489 173.735 5718 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.27 % Allowed : 12.87 % Favored : 84.86 % 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: 1.33 (0.23), residues: 1272 helix: 2.20 (0.21), residues: 592 sheet: 0.28 (0.35), residues: 214 loop : -0.53 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 33 TYR 0.015 0.002 TYR B 88 PHE 0.008 0.001 PHE G 25 TRP 0.010 0.001 TRP M 185 HIS 0.004 0.001 HIS M 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (19486) covalent geometry : angle 0.61139 / 0.35 (28023) hydrogen bonds : bond 0.03930 / 2.56 ( 1103) hydrogen bonds : angle 3.33008 / 2.44 ( 2712) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 232 time to evaluate : 0.386 Fit side-chains REVERT: C 64 GLU cc_start: 0.8159 (tt0) cc_final: 0.7931 (tt0) REVERT: C 73 ASN cc_start: 0.8068 (t0) cc_final: 0.7830 (t0) REVERT: D 59 MET cc_start: 0.8462 (tpt) cc_final: 0.7905 (tpt) REVERT: G 73 ASN cc_start: 0.8033 (t0) cc_final: 0.7436 (t0) REVERT: M 195 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8438 (tt0) REVERT: M 212 LYS cc_start: 0.8445 (mtpp) cc_final: 0.8213 (mtpt) REVERT: N 152 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8209 (mt0) REVERT: U 83 ASN cc_start: 0.8270 (p0) cc_final: 0.8051 (p0) REVERT: U 114 LYS cc_start: 0.7972 (ttpt) cc_final: 0.7609 (ttpp) outliers start: 25 outliers final: 21 residues processed: 243 average time/residue: 0.1664 time to fit residues: 57.3371 Evaluate side-chains 251 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 229 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 191 ARG Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain U residue 107 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 102 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 109 optimal weight: 50.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN C 104 GLN D 47 GLN E 125 GLN F 27 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.152962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.107921 restraints weight = 26341.258| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.30 r_work: 0.3216 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19486 Z= 0.153 Angle : 0.607 8.768 28023 Z= 0.347 Chirality : 0.043 0.233 3154 Planarity : 0.004 0.048 2171 Dihedral : 30.449 173.834 5718 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.27 % Allowed : 12.87 % Favored : 84.86 % 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: 1.38 (0.23), residues: 1272 helix: 2.26 (0.21), residues: 592 sheet: 0.31 (0.35), residues: 214 loop : -0.53 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 56 TYR 0.028 0.002 TYR U 70 PHE 0.008 0.001 PHE G 25 TRP 0.009 0.001 TRP M 185 HIS 0.003 0.001 HIS M 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (19486) covalent geometry : angle 0.60712 / 0.35 (28023) hydrogen bonds : bond 0.03969 / 2.60 ( 1103) hydrogen bonds : angle 3.30264 / 2.42 ( 2712) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 0.456 Fit side-chains REVERT: A 79 LYS cc_start: 0.8442 (ttpp) cc_final: 0.8140 (ttpt) REVERT: C 64 GLU cc_start: 0.8172 (tt0) cc_final: 0.7934 (tt0) REVERT: C 73 ASN cc_start: 0.8086 (t0) cc_final: 0.7858 (t0) REVERT: G 73 ASN cc_start: 0.8034 (t0) cc_final: 0.7451 (t0) REVERT: M 195 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8421 (tt0) REVERT: M 212 LYS cc_start: 0.8412 (mtpp) cc_final: 0.8203 (mtpt) REVERT: N 152 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8212 (mt0) REVERT: N 216 LYS cc_start: 0.8462 (tppt) cc_final: 0.8180 (tptm) REVERT: U 114 LYS cc_start: 0.8014 (ttpt) cc_final: 0.7663 (ttpp) outliers start: 25 outliers final: 22 residues processed: 248 average time/residue: 0.1643 time to fit residues: 57.8034 Evaluate side-chains 256 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 191 ARG Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain U residue 107 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 122 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 45 optimal weight: 0.0370 chunk 128 optimal weight: 2.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 47 GLN E 125 GLN F 27 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.153982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.109299 restraints weight = 26313.831| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.29 r_work: 0.3237 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 19486 Z= 0.133 Angle : 0.598 8.296 28023 Z= 0.344 Chirality : 0.043 0.233 3154 Planarity : 0.004 0.052 2171 Dihedral : 30.407 173.418 5718 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.99 % Allowed : 13.24 % Favored : 84.77 % 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: 1.48 (0.23), residues: 1272 helix: 2.36 (0.21), residues: 592 sheet: 0.24 (0.35), residues: 220 loop : -0.46 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 56 TYR 0.025 0.002 TYR U 70 PHE 0.007 0.001 PHE G 25 TRP 0.007 0.001 TRP M 185 HIS 0.003 0.001 HIS M 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 (19486) covalent geometry : angle 0.59838 / 0.34 (28023) hydrogen bonds : bond 0.03800 / 2.47 ( 1103) hydrogen bonds : angle 3.25016 / 2.39 ( 2712) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 238 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8418 (ttpp) cc_final: 0.8110 (ttpt) REVERT: C 64 GLU cc_start: 0.8133 (tt0) cc_final: 0.7910 (tt0) REVERT: C 73 ASN cc_start: 0.8125 (t0) cc_final: 0.7888 (t0) REVERT: D 59 MET cc_start: 0.8402 (tpt) cc_final: 0.7888 (tpt) REVERT: G 73 ASN cc_start: 0.8071 (t0) cc_final: 0.7480 (t0) REVERT: M 30 MET cc_start: 0.7725 (ptm) cc_final: 0.7097 (mtp) REVERT: M 195 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8409 (tt0) REVERT: N 216 LYS cc_start: 0.8401 (tppt) cc_final: 0.8076 (tptm) REVERT: N 236 THR cc_start: 0.7834 (OUTLIER) cc_final: 0.7524 (m) REVERT: U 114 LYS cc_start: 0.8007 (ttpt) cc_final: 0.7663 (ttpp) outliers start: 22 outliers final: 20 residues processed: 249 average time/residue: 0.1644 time to fit residues: 58.1163 Evaluate side-chains 252 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 191 ARG Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain N residue 264 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 137 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 73 optimal weight: 50.0000 chunk 128 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 145 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 0.0020 chunk 108 optimal weight: 30.0000 chunk 44 optimal weight: 0.7980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN D 47 GLN E 125 GLN F 27 GLN N 95 ASN N 152 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.155007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.110347 restraints weight = 26350.366| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.32 r_work: 0.3255 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 19486 Z= 0.128 Angle : 0.586 8.745 28023 Z= 0.339 Chirality : 0.042 0.234 3154 Planarity : 0.004 0.049 2171 Dihedral : 30.318 173.242 5718 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.09 % Allowed : 13.78 % Favored : 84.13 % 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: 1.63 (0.23), residues: 1272 helix: 2.50 (0.21), residues: 592 sheet: 0.33 (0.35), residues: 210 loop : -0.40 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 129 TYR 0.022 0.001 TYR U 70 PHE 0.006 0.001 PHE G 25 TRP 0.007 0.001 TRP M 185 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.13 (19486) covalent geometry : angle 0.58601 / 0.34 (28023) hydrogen bonds : bond 0.03681 / 2.41 ( 1103) hydrogen bonds : angle 3.18469 / 2.33 ( 2712) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 238 time to evaluate : 0.538 Fit side-chains REVERT: A 79 LYS cc_start: 0.8396 (ttpp) cc_final: 0.8092 (ttpt) REVERT: C 15 LYS cc_start: 0.8241 (mtpp) cc_final: 0.7882 (mtpp) REVERT: C 64 GLU cc_start: 0.8100 (tt0) cc_final: 0.7864 (tt0) REVERT: C 73 ASN cc_start: 0.8120 (t0) cc_final: 0.7886 (t0) REVERT: D 59 MET cc_start: 0.8356 (tpt) cc_final: 0.7849 (tpt) REVERT: F 85 ASP cc_start: 0.7495 (m-30) cc_final: 0.7243 (m-30) REVERT: G 73 ASN cc_start: 0.8073 (t0) cc_final: 0.7513 (t0) REVERT: M 30 MET cc_start: 0.7707 (ptm) cc_final: 0.7106 (mtp) REVERT: M 98 GLU cc_start: 0.7146 (mp0) cc_final: 0.6513 (mp0) REVERT: N 216 LYS cc_start: 0.8415 (tppt) cc_final: 0.8113 (tptm) REVERT: N 236 THR cc_start: 0.7796 (OUTLIER) cc_final: 0.7503 (m) REVERT: U 114 LYS cc_start: 0.7992 (ttpt) cc_final: 0.7668 (ttpp) outliers start: 23 outliers final: 22 residues processed: 250 average time/residue: 0.1639 time to fit residues: 57.3473 Evaluate side-chains 255 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 232 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 191 ARG Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain U residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 127 optimal weight: 2.9990 chunk 123 optimal weight: 0.0980 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 84 GLN C 104 GLN D 47 GLN E 125 GLN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.155017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.110418 restraints weight = 26438.991| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.31 r_work: 0.3255 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.217 19486 Z= 0.187 Angle : 0.744 59.151 28023 Z= 0.441 Chirality : 0.042 0.235 3154 Planarity : 0.004 0.049 2171 Dihedral : 30.316 173.228 5718 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.27 % Allowed : 14.23 % Favored : 83.50 % 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: 1.62 (0.23), residues: 1272 helix: 2.48 (0.21), residues: 592 sheet: 0.34 (0.35), residues: 210 loop : -0.40 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 129 TYR 0.018 0.001 TYR U 70 PHE 0.006 0.001 PHE G 25 TRP 0.007 0.001 TRP M 185 HIS 0.002 0.001 HIS M 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.19 (19486) covalent geometry : angle 0.74399 / 0.44 (28023) hydrogen bonds : bond 0.03715 / 2.44 ( 1103) hydrogen bonds : angle 3.19167 / 2.34 ( 2712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5465.30 seconds wall clock time: 93 minutes 45.52 seconds (5625.52 seconds total)