Starting phenix.real_space_refine on Wed Mar 4 05:32:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r6b_4734/03_2026/6r6b_4734.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r6b_4734/03_2026/6r6b_4734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6r6b_4734/03_2026/6r6b_4734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r6b_4734/03_2026/6r6b_4734.map" model { file = "/net/cci-nas-00/data/ceres_data/6r6b_4734/03_2026/6r6b_4734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r6b_4734/03_2026/6r6b_4734.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 7703 2.51 5 N 1700 2.21 5 O 1939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11416 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1502 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 180} Chain breaks: 1 Chain: "B" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1347 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain breaks: 2 Chain: "C" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1340 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 2 Chain: "D" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1332 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 7, 'TRANS': 160} Chain breaks: 2 Chain: "E" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1348 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 7, 'TRANS': 162} Chain breaks: 2 Chain: "F" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1923 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 9, 'TRANS': 235} Chain: "I" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 656 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "G" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 656 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "H" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 656 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "J" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 656 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Time building chain proxies: 2.48, per 1000 atoms: 0.22 Number of scatterers: 11416 At special positions: 0 Unit cell: (92.886, 92.886, 124.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 1939 8.00 N 1700 7.00 C 7703 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: 0.86 Conformation dependent library (CDL) restraints added in 555.7 milliseconds 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2720 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 0 sheets defined 78.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 Processing helix chain 'A' and resid 26 through 39 removed outlier: 3.610A pdb=" N PHE A 30 " --> pdb=" O CYS A 26 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 78 removed outlier: 3.917A pdb=" N GLY A 54 " --> pdb=" O MET A 50 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Proline residue: A 66 - end of helix removed outlier: 3.812A pdb=" N ALA A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 95 removed outlier: 3.761A pdb=" N ILE A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 removed outlier: 3.561A pdb=" N HIS A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.598A pdb=" N PHE A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 159 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 181 through 196 removed outlier: 4.285A pdb=" N ILE A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Proline residue: A 188 - end of helix removed outlier: 3.909A pdb=" N PHE A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 209 Processing helix chain 'B' and resid 11 through 16 removed outlier: 3.930A pdb=" N LEU B 16 " --> pdb=" O SER B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 25 Processing helix chain 'B' and resid 26 through 32 removed outlier: 3.740A pdb=" N PHE B 30 " --> pdb=" O CYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 41 Processing helix chain 'B' and resid 51 through 73 removed outlier: 3.722A pdb=" N LEU B 57 " --> pdb=" O ASN B 53 " (cutoff:3.500A) Proline residue: B 66 - end of helix removed outlier: 3.883A pdb=" N ALA B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 removed outlier: 4.163A pdb=" N LYS B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N HIS B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.533A pdb=" N ARG B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 174 removed outlier: 3.620A pdb=" N LEU B 159 " --> pdb=" O PHE B 155 " (cutoff:3.500A) Proline residue: B 160 - end of helix removed outlier: 3.565A pdb=" N VAL B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 196 removed outlier: 4.497A pdb=" N ILE B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Proline residue: B 188 - end of helix removed outlier: 3.769A pdb=" N PHE B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 16 through 25 Processing helix chain 'C' and resid 26 through 41 removed outlier: 3.747A pdb=" N PHE C 30 " --> pdb=" O CYS C 26 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 69 Proline residue: C 66 - end of helix Processing helix chain 'C' and resid 99 through 107 removed outlier: 3.717A pdb=" N LYS C 105 " --> pdb=" O GLN C 101 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N HIS C 106 " --> pdb=" O TYR C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 115 removed outlier: 3.712A pdb=" N ARG C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 175 Proline residue: C 160 - end of helix removed outlier: 3.638A pdb=" N VAL C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL C 164 " --> pdb=" O PRO C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.653A pdb=" N VAL C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Proline residue: C 188 - end of helix removed outlier: 3.716A pdb=" N PHE C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 209 removed outlier: 3.530A pdb=" N GLU C 209 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 25 removed outlier: 3.513A pdb=" N THR D 25 " --> pdb=" O VAL D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 32 removed outlier: 3.642A pdb=" N PHE D 30 " --> pdb=" O CYS D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 41 Processing helix chain 'D' and resid 49 through 64 Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.631A pdb=" N ALA D 70 " --> pdb=" O PRO D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 106 removed outlier: 3.538A pdb=" N HIS D 106 " --> pdb=" O TYR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 117 removed outlier: 3.795A pdb=" N ARG D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N PHE D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 175 Proline residue: D 160 - end of helix removed outlier: 3.612A pdb=" N VAL D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 196 removed outlier: 4.592A pdb=" N ILE D 185 " --> pdb=" O SER D 181 " (cutoff:3.500A) Proline residue: D 188 - end of helix removed outlier: 3.973A pdb=" N PHE D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 209 Processing helix chain 'E' and resid 10 through 16 removed outlier: 3.522A pdb=" N PHE E 14 " --> pdb=" O THR E 10 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU E 16 " --> pdb=" O SER E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 25 removed outlier: 4.509A pdb=" N ALA E 23 " --> pdb=" O PHE E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 41 removed outlier: 3.617A pdb=" N PHE E 30 " --> pdb=" O CYS E 26 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 72 removed outlier: 4.173A pdb=" N LEU E 57 " --> pdb=" O ASN E 53 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL E 63 " --> pdb=" O MET E 59 " (cutoff:3.500A) Proline residue: E 66 - end of helix Processing helix chain 'E' and resid 97 through 107 removed outlier: 3.723A pdb=" N HIS E 106 " --> pdb=" O TYR E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 116 removed outlier: 3.518A pdb=" N ARG E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N PHE E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 175 removed outlier: 3.537A pdb=" N LEU E 157 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU E 159 " --> pdb=" O PHE E 155 " (cutoff:3.500A) Proline residue: E 160 - end of helix removed outlier: 3.500A pdb=" N VAL E 164 " --> pdb=" O PRO E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 196 Proline residue: E 188 - end of helix removed outlier: 3.995A pdb=" N PHE E 194 " --> pdb=" O LYS E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 209 removed outlier: 4.141A pdb=" N ALA E 206 " --> pdb=" O ILE E 202 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU E 209 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 29 removed outlier: 3.875A pdb=" N ILE F 15 " --> pdb=" O HIS F 11 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU F 17 " --> pdb=" O PHE F 13 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG F 23 " --> pdb=" O GLY F 19 " (cutoff:3.500A) Proline residue: F 26 - end of helix Processing helix chain 'F' and resid 40 through 56 removed outlier: 4.445A pdb=" N ILE F 45 " --> pdb=" O PRO F 41 " (cutoff:3.500A) Proline residue: F 46 - end of helix removed outlier: 3.750A pdb=" N SER F 53 " --> pdb=" O PHE F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 90 removed outlier: 3.954A pdb=" N PHE F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS F 77 " --> pdb=" O PHE F 73 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU F 83 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N CYS F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU F 89 " --> pdb=" O LEU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 108 removed outlier: 3.748A pdb=" N SER F 101 " --> pdb=" O HIS F 97 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE F 103 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN F 106 " --> pdb=" O ILE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 141 removed outlier: 3.519A pdb=" N ALA F 135 " --> pdb=" O ASN F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 158 removed outlier: 3.531A pdb=" N PHE F 146 " --> pdb=" O GLY F 142 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 206 removed outlier: 3.631A pdb=" N ALA F 182 " --> pdb=" O LEU F 178 " (cutoff:3.500A) Proline residue: F 188 - end of helix removed outlier: 3.711A pdb=" N ILE F 191 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL F 192 " --> pdb=" O PRO F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 230 removed outlier: 3.554A pdb=" N ILE F 219 " --> pdb=" O VAL F 215 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU F 222 " --> pdb=" O THR F 218 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 249 removed outlier: 4.365A pdb=" N GLN F 241 " --> pdb=" O PHE F 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 35 removed outlier: 3.793A pdb=" N TRP I 21 " --> pdb=" O ILE I 17 " (cutoff:3.500A) Proline residue: I 22 - end of helix Processing helix chain 'I' and resid 36 through 38 No H-bonds generated for 'chain 'I' and resid 36 through 38' Processing helix chain 'I' and resid 48 through 62 removed outlier: 5.383A pdb=" N ILE I 54 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU I 60 " --> pdb=" O VAL I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 84 removed outlier: 4.268A pdb=" N LEU I 71 " --> pdb=" O TYR I 67 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET I 79 " --> pdb=" O CYS I 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 20 removed outlier: 3.636A pdb=" N LEU G 16 " --> pdb=" O LEU G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 36 Processing helix chain 'G' and resid 48 through 62 removed outlier: 4.512A pdb=" N ILE G 54 " --> pdb=" O GLY G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 84 removed outlier: 4.127A pdb=" N LEU G 71 " --> pdb=" O TYR G 67 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU G 77 " --> pdb=" O SER G 73 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET G 79 " --> pdb=" O CYS G 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 19 Processing helix chain 'H' and resid 20 through 35 Processing helix chain 'H' and resid 36 through 38 No H-bonds generated for 'chain 'H' and resid 36 through 38' Processing helix chain 'H' and resid 46 through 62 removed outlier: 4.548A pdb=" N ILE H 54 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU H 60 " --> pdb=" O VAL H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 82 removed outlier: 4.094A pdb=" N LEU H 71 " --> pdb=" O TYR H 67 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU H 77 " --> pdb=" O SER H 73 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET H 79 " --> pdb=" O CYS H 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 18 Processing helix chain 'J' and resid 19 through 33 removed outlier: 3.568A pdb=" N VAL J 23 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU J 31 " --> pdb=" O THR J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 62 removed outlier: 3.881A pdb=" N GLY J 50 " --> pdb=" O THR J 46 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LYS J 52 " --> pdb=" O PRO J 48 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE J 54 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER J 59 " --> pdb=" O GLY J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 66 Processing helix chain 'J' and resid 70 through 82 675 hydrogen bonds defined for protein. 2019 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3237 1.34 - 1.46: 2874 1.46 - 1.58: 5421 1.58 - 1.70: 1 1.70 - 1.82: 135 Bond restraints: 11668 Sorted by residual: bond pdb=" C LEU A 109 " pdb=" N GLU A 110 " ideal model delta sigma weight residual 1.334 1.467 -0.133 1.61e-02 3.86e+03 6.86e+01 bond pdb=" CA VAL F 67 " pdb=" C VAL F 67 " ideal model delta sigma weight residual 1.523 1.590 -0.067 1.27e-02 6.20e+03 2.78e+01 bond pdb=" C LEU C 159 " pdb=" N PRO C 160 " ideal model delta sigma weight residual 1.334 1.369 -0.035 8.40e-03 1.42e+04 1.73e+01 bond pdb=" N VAL F 67 " pdb=" CA VAL F 67 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.25e-02 6.40e+03 1.48e+01 bond pdb=" C LEU J 47 " pdb=" N PRO J 48 " ideal model delta sigma weight residual 1.334 1.423 -0.089 2.34e-02 1.83e+03 1.44e+01 ... (remaining 11663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.46: 15638 5.46 - 10.93: 167 10.93 - 16.39: 7 16.39 - 21.86: 1 21.86 - 27.32: 1 Bond angle restraints: 15814 Sorted by residual: angle pdb=" C VAL F 67 " pdb=" N PHE F 68 " pdb=" CA PHE F 68 " ideal model delta sigma weight residual 126.86 154.18 -27.32 1.57e+00 4.06e-01 3.03e+02 angle pdb=" C SER F 86 " pdb=" CA SER F 86 " pdb=" CB SER F 86 " ideal model delta sigma weight residual 110.67 127.27 -16.60 1.92e+00 2.71e-01 7.47e+01 angle pdb=" N LYS H 83 " pdb=" CA LYS H 83 " pdb=" C LYS H 83 " ideal model delta sigma weight residual 113.38 103.69 9.69 1.23e+00 6.61e-01 6.21e+01 angle pdb=" N SER F 66 " pdb=" CA SER F 66 " pdb=" C SER F 66 " ideal model delta sigma weight residual 108.76 121.99 -13.23 1.69e+00 3.50e-01 6.12e+01 angle pdb=" N ILE C 67 " pdb=" CA ILE C 67 " pdb=" C ILE C 67 " ideal model delta sigma weight residual 112.96 107.06 5.90 1.00e+00 1.00e+00 3.48e+01 ... (remaining 15809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.92: 6090 13.92 - 27.85: 538 27.85 - 41.77: 188 41.77 - 55.70: 36 55.70 - 69.62: 3 Dihedral angle restraints: 6855 sinusoidal: 2640 harmonic: 4215 Sorted by residual: dihedral pdb=" C SER F 86 " pdb=" N SER F 86 " pdb=" CA SER F 86 " pdb=" CB SER F 86 " ideal model delta harmonic sigma weight residual -122.60 -146.11 23.51 0 2.50e+00 1.60e-01 8.84e+01 dihedral pdb=" CA THR G 38 " pdb=" C THR G 38 " pdb=" N VAL G 39 " pdb=" CA VAL G 39 " ideal model delta harmonic sigma weight residual -180.00 -139.00 -41.00 0 5.00e+00 4.00e-02 6.72e+01 dihedral pdb=" CA GLY I 68 " pdb=" C GLY I 68 " pdb=" N GLU I 69 " pdb=" CA GLU I 69 " ideal model delta harmonic sigma weight residual -180.00 -146.02 -33.98 0 5.00e+00 4.00e-02 4.62e+01 ... (remaining 6852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 1890 0.166 - 0.332: 36 0.332 - 0.498: 0 0.498 - 0.664: 0 0.664 - 0.830: 1 Chirality restraints: 1927 Sorted by residual: chirality pdb=" CA SER F 86 " pdb=" N SER F 86 " pdb=" C SER F 86 " pdb=" CB SER F 86 " both_signs ideal model delta sigma weight residual False 2.51 1.68 0.83 2.00e-01 2.50e+01 1.72e+01 chirality pdb=" CA VAL C 46 " pdb=" N VAL C 46 " pdb=" C VAL C 46 " pdb=" CB VAL C 46 " both_signs ideal model delta sigma weight residual False 2.44 2.14 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB ILE G 51 " pdb=" CA ILE G 51 " pdb=" CG1 ILE G 51 " pdb=" CG2 ILE G 51 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1924 not shown) Planarity restraints: 1877 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 109 " -0.033 2.00e-02 2.50e+03 6.10e-02 3.73e+01 pdb=" C LEU A 109 " 0.106 2.00e-02 2.50e+03 pdb=" O LEU A 109 " -0.039 2.00e-02 2.50e+03 pdb=" N GLU A 110 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 62 " -0.028 2.00e-02 2.50e+03 5.93e-02 3.52e+01 pdb=" C ASP F 62 " 0.102 2.00e-02 2.50e+03 pdb=" O ASP F 62 " -0.041 2.00e-02 2.50e+03 pdb=" N ILE F 63 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 67 " 0.019 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C VAL F 67 " -0.068 2.00e-02 2.50e+03 pdb=" O VAL F 67 " 0.025 2.00e-02 2.50e+03 pdb=" N PHE F 68 " 0.024 2.00e-02 2.50e+03 ... (remaining 1874 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 30 2.40 - 3.02: 5866 3.02 - 3.65: 17695 3.65 - 4.27: 25556 4.27 - 4.90: 42126 Nonbonded interactions: 91273 Sorted by model distance: nonbonded pdb=" O PHE A 115 " pdb=" OG SER A 137 " model vdw 1.771 3.040 nonbonded pdb=" OE1 GLU B 209 " pdb=" CE LYS H 83 " model vdw 1.812 3.440 nonbonded pdb=" OE1 GLU B 209 " pdb=" CD LYS H 83 " model vdw 1.926 3.440 nonbonded pdb=" OG SER A 134 " pdb=" N LEU A 135 " model vdw 2.120 3.120 nonbonded pdb=" O GLY A 24 " pdb=" OH TYR A 99 " model vdw 2.260 3.040 ... (remaining 91268 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' and (resid 11 through 73 or resid 96 through 116 or resid 133 through \ 213)) selection = (chain 'B' and (resid 11 through 73 or resid 96 through 116 or resid 133 through \ 213)) selection = (chain 'C' and (resid 11 through 116 or resid 133 through 213)) selection = (chain 'D' and (resid 11 through 116 or resid 133 through 213)) selection = (chain 'E' and (resid 11 through 116 or resid 133 through 213)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.580 Find NCS groups from input model: 0.190 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 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 : 0.010 0.133 11668 Z= 0.413 Angle : 1.362 27.323 15814 Z= 0.693 Chirality : 0.067 0.830 1927 Planarity : 0.009 0.071 1877 Dihedral : 12.493 69.623 4135 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.56 % Favored : 91.09 % Rotamer: Outliers : 1.97 % Allowed : 6.54 % Favored : 91.50 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.29 % 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: -5.15 (0.17), residues: 1414 helix: -3.10 (0.11), residues: 1064 sheet: None (None), residues: 0 loop : -3.66 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG B 38 TYR 0.024 0.003 TYR D 133 PHE 0.037 0.003 PHE F 133 TRP 0.033 0.003 TRP D 200 HIS 0.007 0.002 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.01001 (11668) covalent geometry : angle 1.36174 (15814) hydrogen bonds : bond 0.20668 ( 675) hydrogen bonds : angle 8.66439 ( 2019) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 531 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 LYS cc_start: 0.8346 (mtpt) cc_final: 0.7752 (mtpt) REVERT: B 29 LYS cc_start: 0.7992 (tptt) cc_final: 0.7516 (tptm) REVERT: B 172 LEU cc_start: 0.7698 (tt) cc_final: 0.7117 (tt) REVERT: C 175 LEU cc_start: 0.8309 (tp) cc_final: 0.8046 (tt) REVERT: C 177 MET cc_start: 0.6126 (ptp) cc_final: 0.5718 (ptm) REVERT: D 197 LEU cc_start: 0.6869 (tp) cc_final: 0.6583 (tt) REVERT: I 59 SER cc_start: 0.8387 (p) cc_final: 0.8118 (t) REVERT: G 59 SER cc_start: 0.7745 (p) cc_final: 0.7429 (t) outliers start: 25 outliers final: 2 residues processed: 546 average time/residue: 0.1016 time to fit residues: 78.9406 Evaluate side-chains 303 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 301 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain H residue 21 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 101 GLN ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN F 156 ASN F 247 HIS ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.066746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.051019 restraints weight = 47601.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.052653 restraints weight = 26799.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.053637 restraints weight = 18635.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.054382 restraints weight = 15058.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.054719 restraints weight = 12806.624| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11668 Z= 0.177 Angle : 0.904 12.900 15814 Z= 0.443 Chirality : 0.045 0.179 1927 Planarity : 0.005 0.058 1877 Dihedral : 6.315 44.801 1518 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.00 % Favored : 92.93 % Rotamer: Outliers : 4.80 % Allowed : 20.16 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.20), residues: 1414 helix: -1.49 (0.14), residues: 1085 sheet: None (None), residues: 0 loop : -3.26 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 113 TYR 0.025 0.002 TYR C 27 PHE 0.027 0.002 PHE F 76 TRP 0.015 0.001 TRP D 200 HIS 0.012 0.001 HIS F 247 Details of bonding type rmsd covalent geometry : bond 0.00399 (11668) covalent geometry : angle 0.90393 (15814) hydrogen bonds : bond 0.04744 ( 675) hydrogen bonds : angle 5.29278 ( 2019) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 356 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.9143 (ttm) cc_final: 0.8893 (ttm) REVERT: A 49 ASN cc_start: 0.8827 (t0) cc_final: 0.8565 (t0) REVERT: A 108 ASP cc_start: 0.8281 (m-30) cc_final: 0.7771 (m-30) REVERT: A 171 ILE cc_start: 0.9559 (pt) cc_final: 0.9334 (pt) REVERT: A 178 MET cc_start: 0.8017 (ppp) cc_final: 0.6977 (ppp) REVERT: A 179 MET cc_start: 0.7895 (tpt) cc_final: 0.7354 (tpp) REVERT: B 46 VAL cc_start: 0.8238 (OUTLIER) cc_final: 0.7980 (p) REVERT: B 158 TYR cc_start: 0.8855 (t80) cc_final: 0.8386 (t80) REVERT: B 177 MET cc_start: 0.8364 (ptp) cc_final: 0.8106 (ptp) REVERT: C 50 MET cc_start: 0.8256 (tpt) cc_final: 0.8056 (tpp) REVERT: C 178 MET cc_start: 0.8247 (ppp) cc_final: 0.7797 (ppp) REVERT: C 198 ASP cc_start: 0.8188 (t0) cc_final: 0.7964 (t70) REVERT: D 50 MET cc_start: 0.8747 (tmm) cc_final: 0.8464 (tmm) REVERT: D 64 MET cc_start: 0.9225 (mmp) cc_final: 0.8989 (mmp) REVERT: D 142 TYR cc_start: 0.8238 (t80) cc_final: 0.7887 (t80) REVERT: D 146 GLU cc_start: 0.9497 (OUTLIER) cc_final: 0.9154 (mt-10) REVERT: D 149 ASP cc_start: 0.9206 (t0) cc_final: 0.8971 (t0) REVERT: D 178 MET cc_start: 0.7887 (ppp) cc_final: 0.6613 (ppp) REVERT: D 179 MET cc_start: 0.8303 (mmm) cc_final: 0.7434 (mpp) REVERT: E 36 MET cc_start: 0.9196 (ttm) cc_final: 0.8972 (ttm) REVERT: E 177 MET cc_start: 0.8926 (pmm) cc_final: 0.8513 (pmm) REVERT: E 180 MET cc_start: 0.7672 (ppp) cc_final: 0.7163 (ppp) REVERT: E 205 LYS cc_start: 0.8953 (tmmt) cc_final: 0.8586 (tptm) REVERT: F 83 LEU cc_start: 0.9727 (OUTLIER) cc_final: 0.9386 (tt) REVERT: F 87 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8789 (m-80) REVERT: I 72 LEU cc_start: 0.9529 (tt) cc_final: 0.9301 (mm) REVERT: G 33 ILE cc_start: 0.9717 (tt) cc_final: 0.9237 (tt) REVERT: H 52 LYS cc_start: 0.9642 (mtpt) cc_final: 0.9400 (ptpt) REVERT: H 59 SER cc_start: 0.9512 (t) cc_final: 0.9304 (p) REVERT: J 7 MET cc_start: 0.8749 (mmt) cc_final: 0.8443 (mmt) REVERT: J 42 LEU cc_start: 0.2803 (OUTLIER) cc_final: 0.2588 (mm) REVERT: J 67 TYR cc_start: 0.9049 (m-80) cc_final: 0.8849 (m-80) REVERT: J 79 MET cc_start: 0.8929 (ppp) cc_final: 0.8612 (ppp) outliers start: 61 outliers final: 20 residues processed: 402 average time/residue: 0.0918 time to fit residues: 54.5391 Evaluate side-chains 328 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 303 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 75 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 132 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 49 optimal weight: 0.1980 chunk 93 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 HIS E 101 GLN ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.068065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.052379 restraints weight = 48686.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.053940 restraints weight = 27197.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.054928 restraints weight = 18645.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.055628 restraints weight = 14942.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.056138 restraints weight = 12893.635| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11668 Z= 0.157 Angle : 0.859 11.921 15814 Z= 0.415 Chirality : 0.045 0.201 1927 Planarity : 0.005 0.063 1877 Dihedral : 5.718 45.534 1516 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.79 % Favored : 93.14 % Rotamer: Outliers : 4.80 % Allowed : 22.28 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.22), residues: 1414 helix: -0.77 (0.15), residues: 1089 sheet: None (None), residues: 0 loop : -3.11 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 113 TYR 0.025 0.002 TYR E 27 PHE 0.026 0.002 PHE F 76 TRP 0.012 0.001 TRP D 200 HIS 0.004 0.001 HIS C 106 Details of bonding type rmsd covalent geometry : bond 0.00357 (11668) covalent geometry : angle 0.85887 (15814) hydrogen bonds : bond 0.04041 ( 675) hydrogen bonds : angle 4.93944 ( 2019) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 343 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 THR cc_start: 0.7069 (p) cc_final: 0.6856 (p) REVERT: A 36 MET cc_start: 0.9119 (ttm) cc_final: 0.8835 (ttm) REVERT: A 171 ILE cc_start: 0.9528 (pt) cc_final: 0.9298 (pt) REVERT: B 46 VAL cc_start: 0.8232 (OUTLIER) cc_final: 0.8030 (p) REVERT: B 108 ASP cc_start: 0.8694 (t0) cc_final: 0.8092 (t0) REVERT: B 111 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9071 (tt) REVERT: B 149 ASP cc_start: 0.8938 (t0) cc_final: 0.8569 (t0) REVERT: B 175 LEU cc_start: 0.9433 (tp) cc_final: 0.9174 (tp) REVERT: B 177 MET cc_start: 0.8752 (ptp) cc_final: 0.8462 (ptp) REVERT: B 178 MET cc_start: 0.8717 (ppp) cc_final: 0.7682 (ppp) REVERT: C 48 SER cc_start: 0.8793 (t) cc_final: 0.8359 (p) REVERT: C 50 MET cc_start: 0.8418 (tpt) cc_final: 0.8198 (tpp) REVERT: C 135 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7737 (pp) REVERT: C 175 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8149 (tt) REVERT: C 177 MET cc_start: 0.8661 (ppp) cc_final: 0.8060 (pmm) REVERT: C 178 MET cc_start: 0.8225 (ppp) cc_final: 0.7949 (ppp) REVERT: D 50 MET cc_start: 0.8695 (tmm) cc_final: 0.8471 (tmm) REVERT: D 64 MET cc_start: 0.9293 (mmp) cc_final: 0.8994 (mmp) REVERT: D 149 ASP cc_start: 0.9249 (t0) cc_final: 0.8898 (t0) REVERT: D 159 LEU cc_start: 0.9539 (tp) cc_final: 0.9338 (pp) REVERT: D 190 LYS cc_start: 0.9336 (mtmt) cc_final: 0.8946 (mtmm) REVERT: D 197 LEU cc_start: 0.8735 (tt) cc_final: 0.8474 (mt) REVERT: E 180 MET cc_start: 0.7706 (ppp) cc_final: 0.7300 (ppp) REVERT: E 205 LYS cc_start: 0.8958 (tmmt) cc_final: 0.8736 (tptm) REVERT: F 83 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9329 (tt) REVERT: F 87 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8810 (m-80) REVERT: F 210 MET cc_start: 0.8652 (ppp) cc_final: 0.8405 (ppp) REVERT: F 220 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.8836 (tmmt) REVERT: F 227 ILE cc_start: 0.9805 (mm) cc_final: 0.9597 (tt) REVERT: I 19 SER cc_start: 0.9547 (t) cc_final: 0.9189 (p) REVERT: I 72 LEU cc_start: 0.9589 (tt) cc_final: 0.9366 (mm) REVERT: H 3 ASP cc_start: 0.8911 (p0) cc_final: 0.8641 (p0) REVERT: H 44 GLU cc_start: 0.6407 (mp0) cc_final: 0.6033 (mp0) REVERT: H 45 GLN cc_start: 0.8856 (pm20) cc_final: 0.7957 (mm-40) REVERT: H 52 LYS cc_start: 0.9611 (mtpt) cc_final: 0.9257 (ptpp) REVERT: H 59 SER cc_start: 0.9509 (t) cc_final: 0.9298 (p) REVERT: J 79 MET cc_start: 0.9146 (ppp) cc_final: 0.8802 (ppp) outliers start: 61 outliers final: 24 residues processed: 384 average time/residue: 0.0854 time to fit residues: 49.2961 Evaluate side-chains 328 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 297 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 156 TYR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 12 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 51 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.067362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.051737 restraints weight = 48464.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.053273 restraints weight = 26748.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.054315 restraints weight = 18449.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.054893 restraints weight = 14558.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.055355 restraints weight = 12776.072| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11668 Z= 0.159 Angle : 0.818 10.801 15814 Z= 0.399 Chirality : 0.044 0.188 1927 Planarity : 0.004 0.057 1877 Dihedral : 5.434 44.614 1516 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.72 % Favored : 93.21 % Rotamer: Outliers : 4.57 % Allowed : 24.09 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.49 (0.23), residues: 1414 helix: -0.41 (0.16), residues: 1113 sheet: None (None), residues: 0 loop : -2.79 (0.39), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 117 TYR 0.024 0.002 TYR D 142 PHE 0.033 0.001 PHE F 33 TRP 0.011 0.001 TRP D 200 HIS 0.003 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00368 (11668) covalent geometry : angle 0.81769 (15814) hydrogen bonds : bond 0.03676 ( 675) hydrogen bonds : angle 4.68440 ( 2019) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 332 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.9132 (ptp-110) cc_final: 0.8820 (ptp90) REVERT: B 45 GLN cc_start: 0.8833 (tp40) cc_final: 0.8614 (tp-100) REVERT: B 108 ASP cc_start: 0.8636 (t0) cc_final: 0.8368 (t0) REVERT: B 149 ASP cc_start: 0.8884 (t0) cc_final: 0.8376 (t0) REVERT: B 178 MET cc_start: 0.8884 (ppp) cc_final: 0.7903 (ppp) REVERT: B 179 MET cc_start: 0.8746 (mmm) cc_final: 0.8304 (mmm) REVERT: C 48 SER cc_start: 0.8794 (t) cc_final: 0.8341 (p) REVERT: C 50 MET cc_start: 0.8671 (tpt) cc_final: 0.8281 (tpt) REVERT: C 135 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7756 (pp) REVERT: C 198 ASP cc_start: 0.8260 (t0) cc_final: 0.7991 (t70) REVERT: D 50 MET cc_start: 0.8763 (tmm) cc_final: 0.8508 (tmm) REVERT: D 142 TYR cc_start: 0.8220 (t80) cc_final: 0.7884 (t80) REVERT: D 146 GLU cc_start: 0.9409 (OUTLIER) cc_final: 0.9117 (mt-10) REVERT: D 149 ASP cc_start: 0.9274 (t0) cc_final: 0.8879 (t0) REVERT: D 190 LYS cc_start: 0.9369 (mtmt) cc_final: 0.9027 (mtmm) REVERT: E 39 ASN cc_start: 0.9036 (m-40) cc_final: 0.8756 (m110) REVERT: E 180 MET cc_start: 0.7950 (ppp) cc_final: 0.7307 (ppp) REVERT: E 205 LYS cc_start: 0.8944 (tmmt) cc_final: 0.8579 (tptm) REVERT: F 75 MET cc_start: 0.8650 (mmp) cc_final: 0.8335 (mmp) REVERT: F 83 LEU cc_start: 0.9677 (OUTLIER) cc_final: 0.9310 (tt) REVERT: F 87 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8761 (m-80) REVERT: F 175 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9176 (tp) REVERT: I 19 SER cc_start: 0.9600 (t) cc_final: 0.9239 (p) REVERT: I 72 LEU cc_start: 0.9596 (tt) cc_final: 0.9356 (mm) REVERT: G 52 LYS cc_start: 0.9566 (mtpt) cc_final: 0.9268 (ttpp) REVERT: G 63 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9168 (tt) REVERT: H 3 ASP cc_start: 0.8935 (p0) cc_final: 0.8723 (p0) REVERT: H 45 GLN cc_start: 0.8900 (pm20) cc_final: 0.7820 (mm-40) REVERT: H 52 LYS cc_start: 0.9669 (mtpt) cc_final: 0.9359 (ptpp) REVERT: H 59 SER cc_start: 0.9634 (t) cc_final: 0.9429 (p) REVERT: J 67 TYR cc_start: 0.9011 (m-80) cc_final: 0.8680 (m-80) REVERT: J 83 LYS cc_start: 0.9425 (mttt) cc_final: 0.9130 (mttp) outliers start: 58 outliers final: 25 residues processed: 374 average time/residue: 0.0891 time to fit residues: 50.4031 Evaluate side-chains 339 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 308 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 156 TYR Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain H residue 21 TRP Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 12 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 105 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.065848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.050481 restraints weight = 48916.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.052140 restraints weight = 26536.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.053263 restraints weight = 17992.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.053947 restraints weight = 13962.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.054476 restraints weight = 11959.420| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11668 Z= 0.153 Angle : 0.838 13.364 15814 Z= 0.406 Chirality : 0.044 0.199 1927 Planarity : 0.004 0.061 1877 Dihedral : 5.331 45.837 1516 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.72 % Favored : 93.21 % Rotamer: Outliers : 3.78 % Allowed : 26.93 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.19 (0.23), residues: 1414 helix: -0.16 (0.16), residues: 1102 sheet: None (None), residues: 0 loop : -2.76 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 113 TYR 0.033 0.002 TYR A 158 PHE 0.030 0.001 PHE H 49 TRP 0.008 0.001 TRP D 200 HIS 0.002 0.001 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00360 (11668) covalent geometry : angle 0.83771 (15814) hydrogen bonds : bond 0.03529 ( 675) hydrogen bonds : angle 4.61106 ( 2019) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 323 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.9150 (ttm) cc_final: 0.8870 (ttm) REVERT: A 93 ASP cc_start: 0.8891 (m-30) cc_final: 0.8492 (p0) REVERT: A 175 LEU cc_start: 0.9521 (tp) cc_final: 0.9027 (pp) REVERT: A 209 GLU cc_start: 0.8382 (tp30) cc_final: 0.7868 (tp30) REVERT: B 45 GLN cc_start: 0.8927 (tp40) cc_final: 0.8710 (tp-100) REVERT: B 108 ASP cc_start: 0.8728 (t0) cc_final: 0.8389 (t0) REVERT: B 111 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8965 (tt) REVERT: B 149 ASP cc_start: 0.8951 (t0) cc_final: 0.8403 (t0) REVERT: B 178 MET cc_start: 0.9000 (ppp) cc_final: 0.8352 (ppp) REVERT: B 179 MET cc_start: 0.8839 (mmm) cc_final: 0.8234 (mmm) REVERT: C 27 TYR cc_start: 0.9534 (t80) cc_final: 0.9234 (t80) REVERT: C 48 SER cc_start: 0.8705 (t) cc_final: 0.8243 (p) REVERT: C 50 MET cc_start: 0.8672 (tpt) cc_final: 0.8276 (tpt) REVERT: C 135 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7788 (pp) REVERT: C 178 MET cc_start: 0.8196 (ppp) cc_final: 0.7852 (ppp) REVERT: C 179 MET cc_start: 0.8549 (mmm) cc_final: 0.8201 (mmm) REVERT: C 198 ASP cc_start: 0.8386 (t0) cc_final: 0.8029 (t0) REVERT: D 50 MET cc_start: 0.8804 (tmm) cc_final: 0.8578 (tmm) REVERT: D 108 ASP cc_start: 0.7719 (t0) cc_final: 0.6967 (t70) REVERT: D 111 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8962 (tt) REVERT: D 142 TYR cc_start: 0.8324 (t80) cc_final: 0.7935 (t80) REVERT: D 146 GLU cc_start: 0.9474 (OUTLIER) cc_final: 0.9195 (mt-10) REVERT: D 149 ASP cc_start: 0.9329 (t0) cc_final: 0.8902 (t0) REVERT: D 190 LYS cc_start: 0.9347 (mtmt) cc_final: 0.9026 (mtmm) REVERT: E 39 ASN cc_start: 0.9176 (m-40) cc_final: 0.8794 (m110) REVERT: E 180 MET cc_start: 0.7839 (ppp) cc_final: 0.7631 (ppp) REVERT: E 205 LYS cc_start: 0.8813 (tmmt) cc_final: 0.8581 (tptm) REVERT: F 75 MET cc_start: 0.8676 (mmp) cc_final: 0.8332 (mmp) REVERT: F 83 LEU cc_start: 0.9664 (OUTLIER) cc_final: 0.9288 (tt) REVERT: F 87 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8770 (m-80) REVERT: F 210 MET cc_start: 0.8599 (ppp) cc_final: 0.8219 (ppp) REVERT: F 220 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8705 (tmmt) REVERT: I 19 SER cc_start: 0.9618 (OUTLIER) cc_final: 0.9349 (p) REVERT: I 72 LEU cc_start: 0.9583 (tt) cc_final: 0.9323 (mm) REVERT: G 52 LYS cc_start: 0.9543 (mtpt) cc_final: 0.9287 (ttpp) REVERT: G 63 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9198 (tt) REVERT: H 3 ASP cc_start: 0.9053 (p0) cc_final: 0.8829 (p0) REVERT: H 52 LYS cc_start: 0.9636 (mtpt) cc_final: 0.9401 (ptpp) REVERT: J 67 TYR cc_start: 0.9133 (m-80) cc_final: 0.8821 (m-80) REVERT: J 79 MET cc_start: 0.9178 (ppp) cc_final: 0.8843 (ppp) outliers start: 48 outliers final: 28 residues processed: 357 average time/residue: 0.0911 time to fit residues: 48.6259 Evaluate side-chains 332 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 295 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 75 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 128 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.064748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.048690 restraints weight = 50082.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.050325 restraints weight = 27278.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.051410 restraints weight = 18601.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.052164 restraints weight = 14513.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.052535 restraints weight = 12325.433| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.5752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11668 Z= 0.178 Angle : 0.829 13.979 15814 Z= 0.404 Chirality : 0.044 0.200 1927 Planarity : 0.004 0.062 1877 Dihedral : 5.236 46.171 1516 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.79 % Favored : 93.14 % Rotamer: Outliers : 4.88 % Allowed : 26.14 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.90 (0.23), residues: 1414 helix: 0.05 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -2.73 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 44 TYR 0.022 0.001 TYR G 13 PHE 0.022 0.001 PHE F 33 TRP 0.007 0.001 TRP D 200 HIS 0.003 0.001 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00411 (11668) covalent geometry : angle 0.82866 (15814) hydrogen bonds : bond 0.03485 ( 675) hydrogen bonds : angle 4.51793 ( 2019) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 320 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.9158 (ttm) cc_final: 0.8850 (ttm) REVERT: A 81 LYS cc_start: 0.8764 (tmtt) cc_final: 0.8546 (tppt) REVERT: A 93 ASP cc_start: 0.8998 (m-30) cc_final: 0.8606 (p0) REVERT: A 97 MET cc_start: 0.7646 (mpp) cc_final: 0.7394 (mpp) REVERT: A 175 LEU cc_start: 0.9560 (tp) cc_final: 0.9171 (pp) REVERT: B 108 ASP cc_start: 0.8789 (t0) cc_final: 0.8436 (t0) REVERT: B 111 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8948 (tt) REVERT: B 149 ASP cc_start: 0.8960 (t0) cc_final: 0.8431 (t0) REVERT: B 168 ILE cc_start: 0.9518 (tp) cc_final: 0.9298 (pt) REVERT: B 178 MET cc_start: 0.9056 (ppp) cc_final: 0.8458 (ppp) REVERT: C 27 TYR cc_start: 0.9569 (t80) cc_final: 0.9335 (t80) REVERT: C 48 SER cc_start: 0.8749 (t) cc_final: 0.8307 (p) REVERT: C 50 MET cc_start: 0.8726 (tpt) cc_final: 0.8325 (tpt) REVERT: C 135 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7886 (pp) REVERT: C 198 ASP cc_start: 0.8501 (t0) cc_final: 0.8156 (t0) REVERT: D 50 MET cc_start: 0.8811 (tmm) cc_final: 0.8580 (tmm) REVERT: D 108 ASP cc_start: 0.7850 (t0) cc_final: 0.7556 (t0) REVERT: D 142 TYR cc_start: 0.8387 (t80) cc_final: 0.8030 (t80) REVERT: D 146 GLU cc_start: 0.9500 (OUTLIER) cc_final: 0.9197 (mt-10) REVERT: D 149 ASP cc_start: 0.9334 (t0) cc_final: 0.8897 (t0) REVERT: D 159 LEU cc_start: 0.9530 (mt) cc_final: 0.9228 (mt) REVERT: D 190 LYS cc_start: 0.9368 (mtmt) cc_final: 0.9063 (mtmm) REVERT: E 205 LYS cc_start: 0.8881 (tmmt) cc_final: 0.8545 (tptm) REVERT: F 22 PHE cc_start: 0.8834 (m-80) cc_final: 0.8366 (m-80) REVERT: F 35 ASN cc_start: 0.6938 (t0) cc_final: 0.6174 (m110) REVERT: F 106 GLN cc_start: 0.9568 (tp40) cc_final: 0.9286 (tp-100) REVERT: F 248 LYS cc_start: 0.9319 (mmtt) cc_final: 0.8979 (mmtm) REVERT: G 45 GLN cc_start: 0.8471 (mm110) cc_final: 0.8130 (mm-40) REVERT: G 52 LYS cc_start: 0.9508 (mtpt) cc_final: 0.9191 (ttpp) REVERT: G 63 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9238 (tt) REVERT: H 4 ILE cc_start: 0.9387 (mp) cc_final: 0.9182 (mp) REVERT: H 41 GLN cc_start: 0.7756 (tp40) cc_final: 0.7507 (tp-100) REVERT: H 44 GLU cc_start: 0.6350 (mp0) cc_final: 0.5778 (mp0) REVERT: H 45 GLN cc_start: 0.8782 (pm20) cc_final: 0.7964 (mp10) REVERT: H 52 LYS cc_start: 0.9659 (mtpt) cc_final: 0.9443 (ptpp) REVERT: J 67 TYR cc_start: 0.9035 (m-80) cc_final: 0.8723 (m-80) REVERT: J 79 MET cc_start: 0.9259 (ppp) cc_final: 0.8826 (ppp) outliers start: 62 outliers final: 32 residues processed: 363 average time/residue: 0.0874 time to fit residues: 47.9578 Evaluate side-chains 330 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 294 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 45 GLN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 75 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 94 optimal weight: 8.9990 chunk 134 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 chunk 135 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN F 209 GLN ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.065871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.050213 restraints weight = 49410.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.051855 restraints weight = 26891.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.052986 restraints weight = 18237.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.053667 restraints weight = 14126.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.054192 restraints weight = 12079.444| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.5995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11668 Z= 0.150 Angle : 0.878 14.016 15814 Z= 0.416 Chirality : 0.044 0.210 1927 Planarity : 0.005 0.070 1877 Dihedral : 5.216 45.628 1516 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.36 % Favored : 93.56 % Rotamer: Outliers : 4.09 % Allowed : 28.43 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.85 (0.23), residues: 1414 helix: 0.11 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -2.76 (0.37), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 90 TYR 0.028 0.001 TYR A 158 PHE 0.023 0.001 PHE H 49 TRP 0.007 0.001 TRP D 200 HIS 0.003 0.001 HIS F 70 Details of bonding type rmsd covalent geometry : bond 0.00349 (11668) covalent geometry : angle 0.87774 (15814) hydrogen bonds : bond 0.03390 ( 675) hydrogen bonds : angle 4.52660 ( 2019) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 314 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.9142 (ttm) cc_final: 0.8870 (ttm) REVERT: A 50 MET cc_start: 0.9156 (tpp) cc_final: 0.8819 (tpt) REVERT: A 69 GLU cc_start: 0.7736 (mm-30) cc_final: 0.6806 (mm-30) REVERT: A 93 ASP cc_start: 0.8913 (m-30) cc_final: 0.8527 (p0) REVERT: A 175 LEU cc_start: 0.9560 (tp) cc_final: 0.9170 (pp) REVERT: A 179 MET cc_start: 0.7855 (mmm) cc_final: 0.7554 (tpp) REVERT: B 108 ASP cc_start: 0.8775 (t0) cc_final: 0.8409 (t0) REVERT: B 111 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8926 (tt) REVERT: B 149 ASP cc_start: 0.8941 (t0) cc_final: 0.8411 (t0) REVERT: B 168 ILE cc_start: 0.9500 (tp) cc_final: 0.9273 (pt) REVERT: B 178 MET cc_start: 0.8873 (ppp) cc_final: 0.8446 (ppp) REVERT: C 48 SER cc_start: 0.8635 (t) cc_final: 0.8198 (p) REVERT: C 50 MET cc_start: 0.8713 (tpt) cc_final: 0.8292 (tpt) REVERT: C 135 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7856 (pp) REVERT: C 198 ASP cc_start: 0.8505 (t0) cc_final: 0.8169 (t0) REVERT: D 64 MET cc_start: 0.9313 (mmp) cc_final: 0.9067 (mmp) REVERT: D 142 TYR cc_start: 0.8343 (t80) cc_final: 0.7892 (t80) REVERT: D 146 GLU cc_start: 0.9498 (OUTLIER) cc_final: 0.9169 (mt-10) REVERT: D 149 ASP cc_start: 0.9328 (t0) cc_final: 0.8847 (t0) REVERT: D 159 LEU cc_start: 0.9499 (mt) cc_final: 0.9216 (mt) REVERT: D 179 MET cc_start: 0.8933 (mmm) cc_final: 0.8601 (tpp) REVERT: D 190 LYS cc_start: 0.9354 (mtmt) cc_final: 0.9042 (mtmm) REVERT: F 22 PHE cc_start: 0.8730 (m-80) cc_final: 0.8289 (m-80) REVERT: F 35 ASN cc_start: 0.6528 (t0) cc_final: 0.5943 (m-40) REVERT: F 87 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8795 (m-80) REVERT: F 106 GLN cc_start: 0.9529 (tp40) cc_final: 0.9266 (tp-100) REVERT: F 220 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8717 (tmmt) REVERT: F 248 LYS cc_start: 0.9342 (mmtt) cc_final: 0.8960 (mmtm) REVERT: I 13 TYR cc_start: 0.8394 (t80) cc_final: 0.8097 (m-80) REVERT: G 52 LYS cc_start: 0.9510 (mtpt) cc_final: 0.9252 (ttpp) REVERT: G 63 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9252 (tt) REVERT: J 67 TYR cc_start: 0.9077 (m-80) cc_final: 0.8797 (m-80) REVERT: J 79 MET cc_start: 0.9320 (ppp) cc_final: 0.8917 (ppp) outliers start: 52 outliers final: 32 residues processed: 353 average time/residue: 0.0843 time to fit residues: 45.0909 Evaluate side-chains 325 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 287 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 164 CYS Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 75 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 86 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN F 209 GLN ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.065661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.049890 restraints weight = 49543.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.051560 restraints weight = 27064.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.052610 restraints weight = 18406.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.053378 restraints weight = 14455.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.053823 restraints weight = 12196.229| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11668 Z= 0.160 Angle : 0.927 15.331 15814 Z= 0.437 Chirality : 0.045 0.250 1927 Planarity : 0.005 0.074 1877 Dihedral : 5.181 45.941 1516 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.44 % Favored : 93.49 % Rotamer: Outliers : 4.09 % Allowed : 29.06 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.76 (0.23), residues: 1414 helix: 0.18 (0.16), residues: 1108 sheet: None (None), residues: 0 loop : -2.82 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 44 TYR 0.037 0.002 TYR C 27 PHE 0.031 0.001 PHE H 49 TRP 0.014 0.001 TRP D 200 HIS 0.003 0.001 HIS F 70 Details of bonding type rmsd covalent geometry : bond 0.00382 (11668) covalent geometry : angle 0.92686 (15814) hydrogen bonds : bond 0.03470 ( 675) hydrogen bonds : angle 4.54175 ( 2019) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 298 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.9141 (ttm) cc_final: 0.8863 (ttm) REVERT: A 50 MET cc_start: 0.9121 (tpp) cc_final: 0.8758 (tpt) REVERT: A 90 ARG cc_start: 0.9179 (ptp-110) cc_final: 0.8879 (ptp90) REVERT: A 175 LEU cc_start: 0.9542 (tp) cc_final: 0.9197 (pp) REVERT: A 179 MET cc_start: 0.7576 (mmm) cc_final: 0.7253 (tpp) REVERT: B 108 ASP cc_start: 0.8791 (t0) cc_final: 0.8449 (t0) REVERT: B 111 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8946 (tt) REVERT: B 149 ASP cc_start: 0.8960 (t0) cc_final: 0.8419 (t0) REVERT: B 168 ILE cc_start: 0.9514 (tp) cc_final: 0.9291 (pt) REVERT: B 178 MET cc_start: 0.8803 (ppp) cc_final: 0.8207 (ppp) REVERT: B 180 MET cc_start: 0.9194 (ppp) cc_final: 0.8603 (ppp) REVERT: C 48 SER cc_start: 0.8664 (t) cc_final: 0.8215 (p) REVERT: C 50 MET cc_start: 0.8713 (tpt) cc_final: 0.8274 (tpt) REVERT: C 135 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7855 (pp) REVERT: C 179 MET cc_start: 0.8715 (mmm) cc_final: 0.8388 (mmm) REVERT: C 198 ASP cc_start: 0.8531 (t0) cc_final: 0.8201 (t70) REVERT: D 64 MET cc_start: 0.9314 (mmp) cc_final: 0.9055 (mmp) REVERT: D 142 TYR cc_start: 0.8412 (t80) cc_final: 0.7981 (t80) REVERT: D 146 GLU cc_start: 0.9525 (OUTLIER) cc_final: 0.9218 (mt-10) REVERT: D 149 ASP cc_start: 0.9345 (t0) cc_final: 0.8854 (t0) REVERT: D 159 LEU cc_start: 0.9495 (mt) cc_final: 0.9209 (mt) REVERT: D 179 MET cc_start: 0.8980 (mmm) cc_final: 0.8317 (tpp) REVERT: E 179 MET cc_start: 0.8325 (mtm) cc_final: 0.7540 (tpp) REVERT: E 205 LYS cc_start: 0.9203 (tptm) cc_final: 0.8902 (tptp) REVERT: F 22 PHE cc_start: 0.8694 (m-80) cc_final: 0.8290 (m-80) REVERT: F 35 ASN cc_start: 0.6430 (t0) cc_final: 0.5826 (m-40) REVERT: F 87 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8803 (m-80) REVERT: F 106 GLN cc_start: 0.9528 (tp40) cc_final: 0.9250 (tp-100) REVERT: F 220 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8700 (tmmt) REVERT: F 248 LYS cc_start: 0.9372 (mmtt) cc_final: 0.9106 (mmtt) REVERT: I 19 SER cc_start: 0.9581 (t) cc_final: 0.9218 (p) REVERT: G 52 LYS cc_start: 0.9543 (mtpt) cc_final: 0.9278 (ttpp) REVERT: G 63 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9264 (tt) REVERT: H 45 GLN cc_start: 0.8821 (pm20) cc_final: 0.8167 (mm-40) REVERT: J 67 TYR cc_start: 0.9052 (m-80) cc_final: 0.8773 (m-80) REVERT: J 83 LYS cc_start: 0.9454 (mttt) cc_final: 0.9168 (mttp) outliers start: 52 outliers final: 36 residues processed: 336 average time/residue: 0.0843 time to fit residues: 42.9807 Evaluate side-chains 328 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 286 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 164 CYS Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 75 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.4980 chunk 26 optimal weight: 7.9990 chunk 16 optimal weight: 0.0870 chunk 118 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 59 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.066439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.050658 restraints weight = 48953.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.052300 restraints weight = 26764.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.053446 restraints weight = 18237.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.054117 restraints weight = 14192.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.054668 restraints weight = 12162.788| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.6311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11668 Z= 0.154 Angle : 0.941 16.483 15814 Z= 0.441 Chirality : 0.044 0.225 1927 Planarity : 0.005 0.077 1877 Dihedral : 5.176 45.746 1516 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.72 % Favored : 93.21 % Rotamer: Outliers : 4.02 % Allowed : 29.13 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.72 (0.23), residues: 1414 helix: 0.19 (0.16), residues: 1103 sheet: None (None), residues: 0 loop : -2.70 (0.38), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 TYR 0.039 0.002 TYR A 158 PHE 0.026 0.001 PHE J 74 TRP 0.012 0.001 TRP D 200 HIS 0.003 0.000 HIS F 70 Details of bonding type rmsd covalent geometry : bond 0.00359 (11668) covalent geometry : angle 0.94088 (15814) hydrogen bonds : bond 0.03480 ( 675) hydrogen bonds : angle 4.55608 ( 2019) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 307 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.9125 (ttm) cc_final: 0.8852 (ttm) REVERT: A 50 MET cc_start: 0.9062 (tpp) cc_final: 0.8697 (tpt) REVERT: A 146 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8580 (mm-30) REVERT: A 175 LEU cc_start: 0.9523 (tp) cc_final: 0.9274 (pp) REVERT: B 108 ASP cc_start: 0.8780 (t0) cc_final: 0.8441 (t0) REVERT: B 110 GLU cc_start: 0.8778 (pp20) cc_final: 0.8563 (pp20) REVERT: B 111 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.8943 (tt) REVERT: B 149 ASP cc_start: 0.8935 (t0) cc_final: 0.8386 (t0) REVERT: B 168 ILE cc_start: 0.9505 (tp) cc_final: 0.9293 (pt) REVERT: C 48 SER cc_start: 0.8624 (t) cc_final: 0.8175 (p) REVERT: C 50 MET cc_start: 0.8706 (tpt) cc_final: 0.8274 (tpt) REVERT: C 135 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7849 (pp) REVERT: C 158 TYR cc_start: 0.9078 (t80) cc_final: 0.8695 (t80) REVERT: C 179 MET cc_start: 0.8768 (mmm) cc_final: 0.8317 (mmm) REVERT: C 198 ASP cc_start: 0.8570 (t0) cc_final: 0.8220 (t70) REVERT: D 64 MET cc_start: 0.9296 (mmp) cc_final: 0.9050 (mmp) REVERT: D 142 TYR cc_start: 0.8389 (t80) cc_final: 0.7959 (t80) REVERT: D 146 GLU cc_start: 0.9529 (OUTLIER) cc_final: 0.9245 (mt-10) REVERT: D 149 ASP cc_start: 0.9318 (t0) cc_final: 0.8941 (t0) REVERT: D 159 LEU cc_start: 0.9509 (mt) cc_final: 0.9252 (mt) REVERT: D 179 MET cc_start: 0.8979 (mmm) cc_final: 0.8429 (tpp) REVERT: D 190 LYS cc_start: 0.9291 (mtmt) cc_final: 0.8922 (mtmm) REVERT: E 15 THR cc_start: 0.9176 (m) cc_final: 0.8925 (p) REVERT: E 179 MET cc_start: 0.8462 (mtm) cc_final: 0.7675 (tpp) REVERT: E 205 LYS cc_start: 0.9147 (tptm) cc_final: 0.8854 (tptp) REVERT: F 22 PHE cc_start: 0.8654 (m-80) cc_final: 0.8257 (m-80) REVERT: F 35 ASN cc_start: 0.6426 (t0) cc_final: 0.5925 (m-40) REVERT: F 87 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8796 (m-80) REVERT: F 106 GLN cc_start: 0.9510 (tp40) cc_final: 0.9216 (tp-100) REVERT: F 128 LYS cc_start: 0.9184 (ttpp) cc_final: 0.8977 (ttpp) REVERT: F 220 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8709 (tmmt) REVERT: F 248 LYS cc_start: 0.9375 (mmtt) cc_final: 0.9080 (mmtp) REVERT: I 19 SER cc_start: 0.9565 (t) cc_final: 0.9209 (p) REVERT: G 52 LYS cc_start: 0.9528 (mtpt) cc_final: 0.9268 (ttpp) REVERT: G 59 SER cc_start: 0.9496 (t) cc_final: 0.9240 (p) REVERT: G 63 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9244 (tt) REVERT: J 67 TYR cc_start: 0.9017 (m-80) cc_final: 0.8760 (m-80) outliers start: 51 outliers final: 40 residues processed: 340 average time/residue: 0.0854 time to fit residues: 43.6885 Evaluate side-chains 339 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 293 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 45 GLN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 164 CYS Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 75 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 68 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 125 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN F 209 GLN ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.066240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.050400 restraints weight = 49645.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.052111 restraints weight = 27255.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.053222 restraints weight = 18549.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.054005 restraints weight = 14468.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.054353 restraints weight = 12270.766| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.6481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11668 Z= 0.160 Angle : 0.951 16.666 15814 Z= 0.447 Chirality : 0.045 0.219 1927 Planarity : 0.005 0.080 1877 Dihedral : 5.200 45.870 1516 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.86 % Favored : 93.07 % Rotamer: Outliers : 3.70 % Allowed : 29.92 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.63 (0.23), residues: 1414 helix: 0.24 (0.16), residues: 1118 sheet: None (None), residues: 0 loop : -2.71 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 38 TYR 0.029 0.001 TYR C 27 PHE 0.024 0.001 PHE H 49 TRP 0.012 0.001 TRP D 200 HIS 0.003 0.001 HIS F 70 Details of bonding type rmsd covalent geometry : bond 0.00379 (11668) covalent geometry : angle 0.95073 (15814) hydrogen bonds : bond 0.03579 ( 675) hydrogen bonds : angle 4.57182 ( 2019) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 296 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.9172 (ttm) cc_final: 0.8887 (ttm) REVERT: A 50 MET cc_start: 0.9022 (tpp) cc_final: 0.8651 (tpt) REVERT: A 146 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8619 (mm-30) REVERT: A 175 LEU cc_start: 0.9535 (tp) cc_final: 0.9267 (pp) REVERT: B 108 ASP cc_start: 0.8789 (t0) cc_final: 0.8430 (t0) REVERT: B 111 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8933 (tt) REVERT: B 149 ASP cc_start: 0.8980 (t0) cc_final: 0.8422 (t0) REVERT: B 168 ILE cc_start: 0.9505 (tp) cc_final: 0.9279 (pt) REVERT: C 48 SER cc_start: 0.8608 (t) cc_final: 0.8165 (p) REVERT: C 50 MET cc_start: 0.8707 (tpt) cc_final: 0.8263 (tpt) REVERT: C 135 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7858 (pp) REVERT: C 158 TYR cc_start: 0.9086 (t80) cc_final: 0.8698 (t80) REVERT: C 179 MET cc_start: 0.8791 (mmm) cc_final: 0.8310 (mmm) REVERT: C 198 ASP cc_start: 0.8670 (t0) cc_final: 0.8284 (t70) REVERT: D 64 MET cc_start: 0.9347 (mmp) cc_final: 0.9101 (mmp) REVERT: D 142 TYR cc_start: 0.8459 (t80) cc_final: 0.8012 (t80) REVERT: D 146 GLU cc_start: 0.9568 (OUTLIER) cc_final: 0.9250 (mt-10) REVERT: D 149 ASP cc_start: 0.9414 (t0) cc_final: 0.8967 (t0) REVERT: D 159 LEU cc_start: 0.9499 (mt) cc_final: 0.9232 (mt) REVERT: D 190 LYS cc_start: 0.9287 (mtmt) cc_final: 0.8928 (mtmm) REVERT: E 15 THR cc_start: 0.9158 (m) cc_final: 0.8908 (p) REVERT: E 179 MET cc_start: 0.8507 (mtm) cc_final: 0.8260 (ttt) REVERT: E 205 LYS cc_start: 0.9176 (tptm) cc_final: 0.8922 (tptp) REVERT: F 22 PHE cc_start: 0.8733 (m-80) cc_final: 0.8326 (m-80) REVERT: F 35 ASN cc_start: 0.6627 (t0) cc_final: 0.6068 (m-40) REVERT: F 106 GLN cc_start: 0.9544 (tp40) cc_final: 0.9255 (tp-100) REVERT: F 220 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8671 (tmmt) REVERT: F 248 LYS cc_start: 0.9406 (mmtt) cc_final: 0.9115 (mmtp) REVERT: I 19 SER cc_start: 0.9558 (t) cc_final: 0.9212 (p) REVERT: G 52 LYS cc_start: 0.9514 (mtpt) cc_final: 0.9263 (ttpp) REVERT: G 59 SER cc_start: 0.9490 (t) cc_final: 0.9237 (p) REVERT: G 63 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9245 (tt) REVERT: G 79 MET cc_start: 0.9542 (mmm) cc_final: 0.8969 (mmm) REVERT: J 67 TYR cc_start: 0.8978 (m-80) cc_final: 0.8738 (m-80) outliers start: 47 outliers final: 37 residues processed: 329 average time/residue: 0.0835 time to fit residues: 42.0224 Evaluate side-chains 327 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 285 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 45 GLN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 164 CYS Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 75 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 90 optimal weight: 5.9990 chunk 100 optimal weight: 0.0470 chunk 6 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 124 optimal weight: 0.0040 chunk 36 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 112 optimal weight: 0.4980 chunk 110 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.4490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN E 213 ASN F 209 GLN ** G 43 GLN ** 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 = 0.3331 r_free = 0.3331 target = 0.066865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.051288 restraints weight = 49402.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.052908 restraints weight = 27119.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.053938 restraints weight = 18375.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.054760 restraints weight = 14473.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.055119 restraints weight = 12114.794| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.6568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11668 Z= 0.158 Angle : 0.969 16.653 15814 Z= 0.452 Chirality : 0.045 0.279 1927 Planarity : 0.005 0.078 1877 Dihedral : 5.172 45.930 1516 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.79 % Favored : 93.14 % Rotamer: Outliers : 3.39 % Allowed : 30.39 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.62 (0.23), residues: 1414 helix: 0.24 (0.16), residues: 1118 sheet: None (None), residues: 0 loop : -2.67 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 38 TYR 0.039 0.002 TYR A 158 PHE 0.024 0.001 PHE F 76 TRP 0.009 0.001 TRP D 200 HIS 0.003 0.001 HIS F 70 Details of bonding type rmsd covalent geometry : bond 0.00369 (11668) covalent geometry : angle 0.96891 (15814) hydrogen bonds : bond 0.03580 ( 675) hydrogen bonds : angle 4.55162 ( 2019) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2067.65 seconds wall clock time: 36 minutes 29.87 seconds (2189.87 seconds total)