Starting phenix.real_space_refine on Tue Nov 18 05:01:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r6b_4734/11_2025/6r6b_4734.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r6b_4734/11_2025/6r6b_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 { model { file = "/net/cci-nas-00/data/ceres_data/6r6b_4734/11_2025/6r6b_4734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r6b_4734/11_2025/6r6b_4734.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6r6b_4734/11_2025/6r6b_4734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r6b_4734/11_2025/6r6b_4734.map" } 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-2.0-5881/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: 3.05, per 1000 atoms: 0.27 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: 1.22 Conformation dependent library (CDL) restraints added in 566.8 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: 0.24 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: 1.76 Time building geometry restraints manager: 1.53 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.070 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.890 ------------------------------------------------------------------------------- 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 : 0.457 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: 0.7753 (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: 0.7118 (tt) REVERT: C 175 LEU cc_start: 0.8309 (tp) cc_final: 0.8046 (tt) REVERT: C 177 MET cc_start: 0.6125 (ptp) cc_final: 0.5718 (ptm) REVERT: D 197 LEU cc_start: 0.6869 (tp) cc_final: 0.6582 (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: 0.1082 time to fit residues: 84.2709 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 : 0.390 ------------------------------------------------------------------------------- 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 : 0.447 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: 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: 0.8280 (m-30) cc_final: 0.7771 (m-30) REVERT: A 171 ILE cc_start: 0.9559 (pt) cc_final: 0.9333 (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: 0.8363 (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: 0.8463 (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: 0.9496 (OUTLIER) cc_final: 0.9154 (mt-10) REVERT: D 149 ASP cc_start: 0.9206 (t0) cc_final: 0.8972 (t0) REVERT: D 178 MET cc_start: 0.7887 (ppp) cc_final: 0.6613 (ppp) REVERT: D 179 MET cc_start: 0.8304 (mmm) cc_final: 0.7434 (mpp) REVERT: E 36 MET cc_start: 0.9196 (ttm) cc_final: 0.8972 (ttm) REVERT: E 64 MET cc_start: 0.9386 (mmp) cc_final: 0.9185 (mmp) REVERT: E 177 MET cc_start: 0.8926 (pmm) cc_final: 0.8513 (pmm) REVERT: E 180 MET cc_start: 0.7673 (ppp) cc_final: 0.7164 (ppp) REVERT: E 205 LYS cc_start: 0.8952 (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: 0.8748 (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: 0.0940 time to fit residues: 55.5581 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 : 0.520 ------------------------------------------------------------------------------- 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** E 101 GLN ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.067986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.052309 restraints weight = 48660.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.053869 restraints weight = 27484.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.054855 restraints weight = 18748.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.055591 restraints weight = 15035.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.056023 restraints weight = 12837.809| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11668 Z= 0.158 Angle : 0.859 12.031 15814 Z= 0.416 Chirality : 0.045 0.193 1927 Planarity : 0.005 0.069 1877 Dihedral : 5.726 45.426 1516 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.79 % Favored : 93.14 % Rotamer: Outliers : 4.72 % Allowed : 22.76 % Favored : 72.52 % 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: -2.09 (0.22), residues: 1414 helix: -0.77 (0.15), residues: 1090 sheet: None (None), residues: 0 loop : -3.11 (0.35), residues: 324 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 0.011 0.001 TRP D 200 HIS 0.004 0.001 HIS C 106 Details of bonding type rmsd covalent geometry : bond 0.00358 (11668) covalent geometry : angle 0.85918 (15814) hydrogen bonds : bond 0.04049 ( 675) hydrogen bonds : angle 4.95293 ( 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: 60 poor density : 344 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 THR cc_start: 0.7089 (p) cc_final: 0.6868 (p) REVERT: A 36 MET cc_start: 0.9121 (ttm) cc_final: 0.8837 (ttm) REVERT: A 165 ASP cc_start: 0.8616 (m-30) cc_final: 0.8413 (m-30) REVERT: A 171 ILE cc_start: 0.9529 (pt) cc_final: 0.9299 (pt) REVERT: B 46 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.8026 (p) REVERT: B 108 ASP cc_start: 0.8684 (t0) cc_final: 0.8057 (t0) REVERT: B 149 ASP cc_start: 0.8951 (t0) cc_final: 0.8597 (t0) REVERT: B 175 LEU cc_start: 0.9431 (tp) cc_final: 0.9164 (tp) REVERT: C 48 SER cc_start: 0.8803 (t) cc_final: 0.8366 (p) REVERT: C 50 MET cc_start: 0.8418 (tpt) cc_final: 0.8210 (tpp) REVERT: C 135 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7739 (pp) REVERT: C 175 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8701 (tp) REVERT: C 177 MET cc_start: 0.8643 (ppp) cc_final: 0.8141 (pmm) REVERT: C 178 MET cc_start: 0.8226 (ppp) cc_final: 0.7941 (ppp) REVERT: D 50 MET cc_start: 0.8706 (tmm) cc_final: 0.8482 (tmm) REVERT: D 64 MET cc_start: 0.9288 (mmp) cc_final: 0.8982 (mmp) REVERT: D 142 TYR cc_start: 0.8231 (t80) cc_final: 0.7895 (t80) REVERT: D 149 ASP cc_start: 0.9259 (t0) cc_final: 0.8929 (t0) REVERT: D 159 LEU cc_start: 0.9540 (tp) cc_final: 0.9334 (pp) REVERT: D 190 LYS cc_start: 0.9331 (mtmt) cc_final: 0.8934 (mtmm) REVERT: D 197 LEU cc_start: 0.8749 (tt) cc_final: 0.8465 (mt) REVERT: E 64 MET cc_start: 0.9476 (mmp) cc_final: 0.9254 (mmp) REVERT: E 180 MET cc_start: 0.7702 (ppp) cc_final: 0.7303 (ppp) REVERT: E 205 LYS cc_start: 0.8954 (tmmt) cc_final: 0.8727 (tptm) REVERT: F 83 LEU cc_start: 0.9686 (OUTLIER) cc_final: 0.9322 (tt) REVERT: F 87 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8814 (m-80) REVERT: F 209 GLN cc_start: 0.8575 (mp10) cc_final: 0.8271 (mp10) REVERT: F 210 MET cc_start: 0.8662 (ppp) cc_final: 0.8435 (ppp) REVERT: F 220 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8842 (tmmt) REVERT: F 227 ILE cc_start: 0.9809 (mm) cc_final: 0.9594 (tt) REVERT: I 19 SER cc_start: 0.9547 (t) cc_final: 0.9185 (p) REVERT: I 72 LEU cc_start: 0.9586 (tt) cc_final: 0.9363 (mm) REVERT: H 3 ASP cc_start: 0.8908 (p0) cc_final: 0.8639 (p0) REVERT: H 45 GLN cc_start: 0.8849 (pm20) cc_final: 0.7881 (mm-40) REVERT: H 52 LYS cc_start: 0.9606 (mtpt) cc_final: 0.9241 (ptpp) REVERT: H 59 SER cc_start: 0.9515 (t) cc_final: 0.9302 (p) REVERT: J 79 MET cc_start: 0.9123 (ppp) cc_final: 0.8785 (ppp) outliers start: 60 outliers final: 24 residues processed: 384 average time/residue: 0.0938 time to fit residues: 53.7258 Evaluate side-chains 331 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 301 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 79 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 48 optimal weight: 0.0270 chunk 102 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- 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** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN C 106 HIS ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3403 r_free = 0.3403 target = 0.067956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.052356 restraints weight = 48152.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.053901 restraints weight = 26904.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.054927 restraints weight = 18392.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.055657 restraints weight = 14583.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.056132 restraints weight = 12543.852| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11668 Z= 0.150 Angle : 0.829 11.156 15814 Z= 0.401 Chirality : 0.044 0.192 1927 Planarity : 0.005 0.057 1877 Dihedral : 5.450 44.756 1516 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.65 % Favored : 93.28 % Rotamer: Outliers : 4.57 % Allowed : 24.88 % Favored : 70.55 % 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: -1.52 (0.23), residues: 1414 helix: -0.43 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : -2.74 (0.38), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 117 TYR 0.020 0.002 TYR E 27 PHE 0.034 0.001 PHE F 33 TRP 0.011 0.001 TRP D 200 HIS 0.003 0.001 HIS C 106 Details of bonding type rmsd covalent geometry : bond 0.00350 (11668) covalent geometry : angle 0.82860 (15814) hydrogen bonds : bond 0.03682 ( 675) hydrogen bonds : angle 4.70765 ( 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 395 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 337 time to evaluate : 0.466 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 90 ARG cc_start: 0.9086 (ptp-110) cc_final: 0.8778 (ptp90) REVERT: A 165 ASP cc_start: 0.8580 (m-30) cc_final: 0.8286 (m-30) REVERT: B 108 ASP cc_start: 0.8576 (t0) cc_final: 0.8330 (t0) REVERT: B 111 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9043 (tt) REVERT: B 149 ASP cc_start: 0.8875 (t0) cc_final: 0.8369 (t0) REVERT: C 48 SER cc_start: 0.8758 (t) cc_final: 0.8310 (p) REVERT: C 50 MET cc_start: 0.8618 (tpt) cc_final: 0.8228 (tpt) REVERT: C 135 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7696 (pp) REVERT: C 158 TYR cc_start: 0.9167 (t80) cc_final: 0.8666 (t80) REVERT: C 198 ASP cc_start: 0.8238 (t0) cc_final: 0.7966 (t70) REVERT: D 50 MET cc_start: 0.8749 (tmm) cc_final: 0.8491 (tmm) REVERT: D 108 ASP cc_start: 0.7549 (t0) cc_final: 0.6786 (t70) REVERT: D 142 TYR cc_start: 0.8236 (t80) cc_final: 0.7934 (t80) REVERT: D 146 GLU cc_start: 0.9408 (OUTLIER) cc_final: 0.9145 (mt-10) REVERT: D 149 ASP cc_start: 0.9246 (t0) cc_final: 0.8849 (t0) REVERT: D 190 LYS cc_start: 0.9349 (mtmt) cc_final: 0.9000 (mtmm) REVERT: E 39 ASN cc_start: 0.9004 (m-40) cc_final: 0.8794 (m110) REVERT: E 180 MET cc_start: 0.7909 (ppp) cc_final: 0.7291 (ppp) REVERT: E 205 LYS cc_start: 0.8924 (tmmt) cc_final: 0.8558 (tptm) REVERT: F 75 MET cc_start: 0.8629 (mmp) cc_final: 0.8320 (mmp) REVERT: F 83 LEU cc_start: 0.9665 (OUTLIER) cc_final: 0.9305 (tt) REVERT: F 87 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8735 (m-80) REVERT: F 220 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8716 (tmmt) REVERT: I 19 SER cc_start: 0.9582 (t) cc_final: 0.9211 (p) REVERT: I 72 LEU cc_start: 0.9589 (tt) cc_final: 0.9346 (mm) REVERT: G 42 LEU cc_start: 0.9453 (mm) cc_final: 0.9249 (mm) REVERT: G 52 LYS cc_start: 0.9576 (mtpt) cc_final: 0.9263 (ttpp) REVERT: G 63 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9179 (tt) REVERT: H 44 GLU cc_start: 0.6322 (mp0) cc_final: 0.5803 (mp0) REVERT: H 45 GLN cc_start: 0.8868 (pm20) cc_final: 0.7768 (mm-40) REVERT: H 52 LYS cc_start: 0.9664 (mtpt) cc_final: 0.9358 (ptpp) REVERT: H 59 SER cc_start: 0.9613 (t) cc_final: 0.9406 (p) REVERT: J 67 TYR cc_start: 0.8991 (m-80) cc_final: 0.8672 (m-80) REVERT: J 79 MET cc_start: 0.9184 (ppp) cc_final: 0.8953 (ppp) outliers start: 58 outliers final: 22 residues processed: 380 average time/residue: 0.0931 time to fit residues: 52.7655 Evaluate side-chains 343 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 314 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 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 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 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 140 TYR Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain G residue 36 LEU 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 Chi-restraints excluded: chain J residue 75 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 105 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** B 45 GLN C 39 ASN G 37 GLN ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.065689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.049928 restraints weight = 49569.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.051599 restraints weight = 27288.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.052725 restraints weight = 18620.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.053357 restraints weight = 14473.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.053963 restraints weight = 12503.952| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11668 Z= 0.158 Angle : 0.842 13.397 15814 Z= 0.408 Chirality : 0.044 0.200 1927 Planarity : 0.005 0.061 1877 Dihedral : 5.341 46.073 1516 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.58 % Favored : 93.35 % Rotamer: Outliers : 3.94 % Allowed : 26.61 % Favored : 69.45 % 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: -1.22 (0.23), residues: 1414 helix: -0.20 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : -2.70 (0.38), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 113 TYR 0.033 0.002 TYR A 158 PHE 0.032 0.001 PHE H 49 TRP 0.008 0.001 TRP D 200 HIS 0.002 0.001 HIS F 247 Details of bonding type rmsd covalent geometry : bond 0.00372 (11668) covalent geometry : angle 0.84192 (15814) hydrogen bonds : bond 0.03546 ( 675) hydrogen bonds : angle 4.61498 ( 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 370 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 320 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.9172 (ttm) cc_final: 0.8884 (ttm) REVERT: A 50 MET cc_start: 0.9037 (tpp) cc_final: 0.8830 (tpt) REVERT: A 93 ASP cc_start: 0.8942 (m-30) cc_final: 0.8546 (p0) REVERT: A 98 GLU cc_start: 0.8472 (pp20) cc_final: 0.8248 (pp20) REVERT: A 165 ASP cc_start: 0.8628 (m-30) cc_final: 0.8340 (m-30) REVERT: A 171 ILE cc_start: 0.9537 (pt) cc_final: 0.9287 (pt) REVERT: A 175 LEU cc_start: 0.9513 (tp) cc_final: 0.9021 (pp) REVERT: A 209 GLU cc_start: 0.8385 (tp30) cc_final: 0.7868 (tp30) REVERT: B 45 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8485 (tp40) REVERT: B 108 ASP cc_start: 0.8734 (t0) cc_final: 0.8382 (t0) REVERT: B 111 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8931 (tt) REVERT: B 149 ASP cc_start: 0.8980 (t0) cc_final: 0.8457 (t0) REVERT: B 178 MET cc_start: 0.8836 (ppp) cc_final: 0.8268 (ppp) REVERT: B 179 MET cc_start: 0.8958 (mmm) cc_final: 0.8269 (mmm) REVERT: C 27 TYR cc_start: 0.9535 (t80) cc_final: 0.9224 (t80) REVERT: C 48 SER cc_start: 0.8725 (t) cc_final: 0.8286 (p) REVERT: C 50 MET cc_start: 0.8680 (tpt) cc_final: 0.8260 (tpt) REVERT: C 135 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7775 (pp) REVERT: C 158 TYR cc_start: 0.9175 (t80) cc_final: 0.8742 (t80) REVERT: C 178 MET cc_start: 0.8237 (ppp) cc_final: 0.7927 (ppp) REVERT: C 179 MET cc_start: 0.8593 (mmm) cc_final: 0.8202 (mmm) REVERT: C 198 ASP cc_start: 0.8442 (t0) cc_final: 0.8049 (t0) REVERT: D 50 MET cc_start: 0.8773 (tmm) cc_final: 0.8522 (tmm) REVERT: D 61 LEU cc_start: 0.9637 (mp) cc_final: 0.9405 (mt) REVERT: D 108 ASP cc_start: 0.7758 (t0) cc_final: 0.7486 (t0) REVERT: D 142 TYR cc_start: 0.8412 (t80) cc_final: 0.8059 (t80) REVERT: D 146 GLU cc_start: 0.9504 (OUTLIER) cc_final: 0.9193 (mt-10) REVERT: D 149 ASP cc_start: 0.9344 (t0) cc_final: 0.8921 (t0) REVERT: D 190 LYS cc_start: 0.9323 (mtmt) cc_final: 0.9004 (mtmm) REVERT: E 39 ASN cc_start: 0.9156 (m-40) cc_final: 0.8804 (m110) REVERT: E 205 LYS cc_start: 0.8818 (tmmt) cc_final: 0.8600 (tptm) REVERT: F 75 MET cc_start: 0.8685 (mmp) cc_final: 0.8332 (mmp) REVERT: F 83 LEU cc_start: 0.9659 (OUTLIER) cc_final: 0.9282 (tt) REVERT: F 87 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8788 (m-80) REVERT: F 175 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9133 (tp) REVERT: I 72 LEU cc_start: 0.9575 (tt) cc_final: 0.9313 (mm) REVERT: G 52 LYS cc_start: 0.9535 (mtpt) cc_final: 0.9287 (ttpp) REVERT: G 63 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9180 (tt) REVERT: H 52 LYS cc_start: 0.9623 (mtpt) cc_final: 0.9396 (ptpp) REVERT: H 59 SER cc_start: 0.9645 (t) cc_final: 0.9436 (p) REVERT: J 67 TYR cc_start: 0.9097 (m-80) cc_final: 0.8811 (m-80) REVERT: J 79 MET cc_start: 0.9285 (ppp) cc_final: 0.9008 (ppp) outliers start: 50 outliers final: 28 residues processed: 357 average time/residue: 0.0919 time to fit residues: 49.2637 Evaluate side-chains 333 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 297 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 39 ASN Chi-restraints excluded: chain B residue 45 GLN 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 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 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 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 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 63 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 128 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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** ** 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 = 0.065745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.050186 restraints weight = 48982.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.051823 restraints weight = 26908.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.052816 restraints weight = 18376.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.053616 restraints weight = 14683.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.054055 restraints weight = 12324.994| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11668 Z= 0.165 Angle : 0.841 13.832 15814 Z= 0.407 Chirality : 0.044 0.200 1927 Planarity : 0.004 0.066 1877 Dihedral : 5.223 46.076 1516 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.58 % Favored : 93.35 % Rotamer: Outliers : 4.72 % Allowed : 26.61 % Favored : 68.66 % 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: -0.97 (0.23), residues: 1414 helix: -0.01 (0.16), residues: 1108 sheet: None (None), residues: 0 loop : -2.73 (0.39), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 113 TYR 0.020 0.001 TYR G 13 PHE 0.024 0.001 PHE H 49 TRP 0.013 0.001 TRP D 200 HIS 0.002 0.001 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00390 (11668) covalent geometry : angle 0.84098 (15814) hydrogen bonds : bond 0.03483 ( 675) hydrogen bonds : angle 4.51850 ( 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 389 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 329 time to evaluate : 0.434 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: 0.9098 (ttm) cc_final: 0.8851 (ttm) REVERT: A 50 MET cc_start: 0.8982 (tpp) cc_final: 0.8724 (tpt) REVERT: A 93 ASP cc_start: 0.8867 (m-30) cc_final: 0.8457 (p0) REVERT: A 165 ASP cc_start: 0.8586 (m-30) cc_final: 0.8311 (m-30) REVERT: A 171 ILE cc_start: 0.9581 (pt) cc_final: 0.9267 (pt) REVERT: A 175 LEU cc_start: 0.9548 (tp) cc_final: 0.9100 (pp) REVERT: A 177 MET cc_start: 0.8247 (ptp) cc_final: 0.8014 (ptp) REVERT: B 108 ASP cc_start: 0.8751 (t0) cc_final: 0.8424 (t0) REVERT: B 111 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8992 (tt) REVERT: B 149 ASP cc_start: 0.8881 (t0) cc_final: 0.8339 (t0) REVERT: B 178 MET cc_start: 0.8946 (ppp) cc_final: 0.8431 (ppp) REVERT: B 179 MET cc_start: 0.8923 (mmm) cc_final: 0.8585 (mmm) REVERT: C 27 TYR cc_start: 0.9513 (t80) cc_final: 0.9247 (t80) REVERT: C 48 SER cc_start: 0.8720 (t) cc_final: 0.8301 (p) REVERT: C 50 MET cc_start: 0.8708 (tpt) cc_final: 0.8333 (tpt) REVERT: C 135 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7764 (pp) REVERT: C 198 ASP cc_start: 0.8313 (t0) cc_final: 0.8031 (t0) REVERT: D 50 MET cc_start: 0.8791 (tmm) cc_final: 0.8579 (tmm) REVERT: D 142 TYR cc_start: 0.8323 (t80) cc_final: 0.8020 (t80) REVERT: D 146 GLU cc_start: 0.9435 (OUTLIER) cc_final: 0.9125 (mt-10) REVERT: D 149 ASP cc_start: 0.9263 (t0) cc_final: 0.8818 (t0) REVERT: D 190 LYS cc_start: 0.9390 (mtmt) cc_final: 0.9069 (mtmm) REVERT: E 39 ASN cc_start: 0.9221 (m-40) cc_final: 0.8799 (m110) REVERT: E 173 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9257 (tt) REVERT: E 205 LYS cc_start: 0.8819 (tmmt) cc_final: 0.8493 (tptm) REVERT: F 22 PHE cc_start: 0.8756 (m-80) cc_final: 0.8319 (m-80) REVERT: F 106 GLN cc_start: 0.9517 (tp40) cc_final: 0.9269 (tp-100) REVERT: F 220 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8764 (tmmt) REVERT: F 248 LYS cc_start: 0.9262 (mmtt) cc_final: 0.8900 (mmtm) REVERT: G 1 MET cc_start: 0.7971 (mmm) cc_final: 0.7646 (mmp) REVERT: G 52 LYS cc_start: 0.9554 (mtpt) cc_final: 0.9237 (ttpp) REVERT: G 63 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9227 (tt) REVERT: H 41 GLN cc_start: 0.7602 (tp-100) cc_final: 0.7382 (tp-100) REVERT: H 44 GLU cc_start: 0.6444 (mp0) cc_final: 0.5843 (mp0) REVERT: H 45 GLN cc_start: 0.8774 (pm20) cc_final: 0.7967 (mm-40) REVERT: H 52 LYS cc_start: 0.9663 (mtpt) cc_final: 0.9423 (ptpp) REVERT: H 59 SER cc_start: 0.9665 (t) cc_final: 0.9422 (p) REVERT: H 81 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9044 (tt) REVERT: J 49 PHE cc_start: 0.8896 (t80) cc_final: 0.8194 (t80) REVERT: J 52 LYS cc_start: 0.8980 (mtmm) cc_final: 0.8769 (ptpt) REVERT: J 67 TYR cc_start: 0.9090 (m-80) cc_final: 0.8811 (m-80) REVERT: J 79 MET cc_start: 0.9301 (ppp) cc_final: 0.9035 (ppp) outliers start: 60 outliers final: 33 residues processed: 370 average time/residue: 0.0914 time to fit residues: 50.9819 Evaluate side-chains 340 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 300 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 45 GLN 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 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 173 LEU 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 140 TYR Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 25 ILE 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 H residue 81 LEU 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: 0.0970 chunk 16 optimal weight: 0.7980 chunk 135 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 42 optimal weight: 0.0870 chunk 46 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.066516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.050658 restraints weight = 49401.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.052336 restraints weight = 27086.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.053497 restraints weight = 18464.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.054121 restraints weight = 14298.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.054733 restraints weight = 12339.828| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.5951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11668 Z= 0.146 Angle : 0.859 10.433 15814 Z= 0.410 Chirality : 0.044 0.210 1927 Planarity : 0.005 0.071 1877 Dihedral : 5.214 45.599 1516 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.36 % Favored : 93.56 % Rotamer: Outliers : 4.02 % Allowed : 28.11 % Favored : 67.87 % 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: 0.08 (0.16), residues: 1092 sheet: None (None), residues: 0 loop : -2.58 (0.38), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 90 TYR 0.022 0.001 TYR D 27 PHE 0.030 0.001 PHE H 49 TRP 0.011 0.001 TRP D 200 HIS 0.003 0.001 HIS F 70 Details of bonding type rmsd covalent geometry : bond 0.00340 (11668) covalent geometry : angle 0.85904 (15814) hydrogen bonds : bond 0.03424 ( 675) hydrogen bonds : angle 4.55266 ( 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 370 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 319 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.9139 (ttm) cc_final: 0.8898 (ttm) REVERT: A 50 MET cc_start: 0.8920 (tpp) cc_final: 0.8578 (tpt) REVERT: A 93 ASP cc_start: 0.8915 (m-30) cc_final: 0.8443 (p0) REVERT: A 146 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8563 (mm-30) REVERT: A 165 ASP cc_start: 0.8633 (m-30) cc_final: 0.8353 (m-30) REVERT: A 171 ILE cc_start: 0.9547 (pt) cc_final: 0.9244 (pt) REVERT: A 175 LEU cc_start: 0.9543 (tp) cc_final: 0.9103 (pp) REVERT: A 177 MET cc_start: 0.8207 (ptp) cc_final: 0.7951 (ptp) REVERT: B 45 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8519 (tp40) REVERT: B 108 ASP cc_start: 0.8736 (t0) cc_final: 0.8377 (t0) REVERT: B 111 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8940 (tt) REVERT: B 149 ASP cc_start: 0.8921 (t0) cc_final: 0.8397 (t0) REVERT: B 179 MET cc_start: 0.8803 (mmm) cc_final: 0.8544 (mmm) REVERT: B 180 MET cc_start: 0.9232 (ppp) cc_final: 0.8604 (ppp) REVERT: C 48 SER cc_start: 0.8629 (t) cc_final: 0.8192 (p) REVERT: C 50 MET cc_start: 0.8651 (tpt) cc_final: 0.8241 (tpt) REVERT: C 135 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7783 (pp) REVERT: C 158 TYR cc_start: 0.9072 (t80) cc_final: 0.8700 (t80) REVERT: C 198 ASP cc_start: 0.8495 (t0) cc_final: 0.8130 (t0) REVERT: D 64 MET cc_start: 0.9307 (mmp) cc_final: 0.9061 (mmp) REVERT: D 142 TYR cc_start: 0.8391 (t80) cc_final: 0.7990 (t80) REVERT: D 146 GLU cc_start: 0.9509 (OUTLIER) cc_final: 0.9210 (mt-10) REVERT: D 149 ASP cc_start: 0.9311 (t0) cc_final: 0.8820 (t0) REVERT: D 190 LYS cc_start: 0.9328 (mtmt) cc_final: 0.9023 (mtmm) REVERT: E 39 ASN cc_start: 0.9205 (m-40) cc_final: 0.8719 (m110) REVERT: F 22 PHE cc_start: 0.8715 (m-80) cc_final: 0.8285 (m-80) REVERT: F 35 ASN cc_start: 0.7335 (t0) cc_final: 0.6239 (m110) REVERT: F 78 GLU cc_start: 0.9333 (mm-30) cc_final: 0.9093 (mm-30) REVERT: F 87 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8785 (m-80) REVERT: F 106 GLN cc_start: 0.9525 (tp40) cc_final: 0.9247 (tp-100) REVERT: F 220 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8692 (tmmt) REVERT: F 248 LYS cc_start: 0.9315 (mmtt) cc_final: 0.8965 (mmtm) REVERT: I 13 TYR cc_start: 0.8437 (t80) cc_final: 0.8121 (m-80) REVERT: G 52 LYS cc_start: 0.9510 (mtpt) cc_final: 0.9211 (ttpp) REVERT: G 63 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9217 (tt) REVERT: H 59 SER cc_start: 0.9671 (t) cc_final: 0.9471 (p) REVERT: J 67 TYR cc_start: 0.9067 (m-80) cc_final: 0.8811 (m-80) REVERT: J 79 MET cc_start: 0.9355 (ppp) cc_final: 0.9072 (ppp) outliers start: 51 outliers final: 28 residues processed: 354 average time/residue: 0.0933 time to fit residues: 49.3842 Evaluate side-chains 324 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 289 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 B residue 45 GLN 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 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 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 160 LEU 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 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: 0.3980 chunk 3 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 38 optimal weight: 0.3980 chunk 125 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 GLN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 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 = 0.3318 r_free = 0.3318 target = 0.066498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.050698 restraints weight = 48984.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.052369 restraints weight = 26779.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.053534 restraints weight = 18225.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.054136 restraints weight = 14111.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.054737 restraints weight = 12234.093| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.6163 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= 0.153 Angle : 0.905 12.723 15814 Z= 0.427 Chirality : 0.044 0.216 1927 Planarity : 0.005 0.074 1877 Dihedral : 5.179 46.251 1516 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.36 % Favored : 93.56 % Rotamer: Outliers : 3.46 % Allowed : 29.61 % Favored : 66.93 % 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: -0.83 (0.23), residues: 1414 helix: 0.09 (0.16), residues: 1115 sheet: None (None), residues: 0 loop : -2.75 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 38 TYR 0.039 0.002 TYR A 158 PHE 0.022 0.001 PHE H 49 TRP 0.010 0.001 TRP D 200 HIS 0.003 0.001 HIS F 70 Details of bonding type rmsd covalent geometry : bond 0.00360 (11668) covalent geometry : angle 0.90470 (15814) hydrogen bonds : bond 0.03436 ( 675) hydrogen bonds : angle 4.52080 ( 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 348 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 304 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.9147 (ttm) cc_final: 0.8870 (ttm) REVERT: A 50 MET cc_start: 0.8884 (tpp) cc_final: 0.8516 (tpt) REVERT: A 146 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8562 (mm-30) REVERT: A 165 ASP cc_start: 0.8596 (m-30) cc_final: 0.8320 (m-30) REVERT: A 171 ILE cc_start: 0.9546 (pt) cc_final: 0.9228 (pt) REVERT: A 175 LEU cc_start: 0.9526 (tp) cc_final: 0.9143 (pp) REVERT: B 108 ASP cc_start: 0.8723 (t0) cc_final: 0.8346 (t0) REVERT: B 111 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8911 (tt) REVERT: B 149 ASP cc_start: 0.8936 (t0) cc_final: 0.8395 (t0) REVERT: B 180 MET cc_start: 0.9205 (ppp) cc_final: 0.8483 (ppp) REVERT: C 48 SER cc_start: 0.8637 (t) cc_final: 0.8210 (p) REVERT: C 50 MET cc_start: 0.8673 (tpt) cc_final: 0.8256 (tpt) REVERT: C 135 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7794 (pp) REVERT: C 158 TYR cc_start: 0.9073 (t80) cc_final: 0.8606 (t80) REVERT: C 198 ASP cc_start: 0.8526 (t0) cc_final: 0.8183 (t70) REVERT: D 64 MET cc_start: 0.9287 (mmp) cc_final: 0.9029 (mmp) REVERT: D 142 TYR cc_start: 0.8397 (t80) cc_final: 0.7989 (t80) REVERT: D 146 GLU cc_start: 0.9520 (OUTLIER) cc_final: 0.9261 (mt-10) REVERT: D 149 ASP cc_start: 0.9315 (t0) cc_final: 0.8804 (t0) REVERT: E 15 THR cc_start: 0.9171 (m) cc_final: 0.8914 (p) REVERT: E 39 ASN cc_start: 0.9180 (m-40) cc_final: 0.8695 (m110) REVERT: E 179 MET cc_start: 0.8384 (mtm) cc_final: 0.8137 (ttp) REVERT: E 190 LYS cc_start: 0.9480 (mtmt) cc_final: 0.8732 (mtmm) REVERT: E 205 LYS cc_start: 0.9161 (tptm) cc_final: 0.8875 (tptp) REVERT: F 22 PHE cc_start: 0.8629 (m-80) cc_final: 0.8255 (m-80) REVERT: F 35 ASN cc_start: 0.7147 (t0) cc_final: 0.5930 (m110) REVERT: F 78 GLU cc_start: 0.9323 (mm-30) cc_final: 0.9051 (mm-30) REVERT: F 87 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8785 (m-80) REVERT: F 106 GLN cc_start: 0.9513 (tp40) cc_final: 0.9216 (tp-100) REVERT: F 220 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8659 (tmmt) REVERT: F 248 LYS cc_start: 0.9347 (mmtt) cc_final: 0.8995 (mmtm) REVERT: I 19 SER cc_start: 0.9562 (t) cc_final: 0.9204 (p) REVERT: G 45 GLN cc_start: 0.8369 (mm110) cc_final: 0.8133 (mm110) REVERT: G 52 LYS cc_start: 0.9525 (mtpt) cc_final: 0.9311 (ttpp) REVERT: G 63 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9302 (tp) REVERT: H 45 GLN cc_start: 0.8929 (pm20) cc_final: 0.8645 (mm-40) REVERT: H 59 SER cc_start: 0.9656 (t) cc_final: 0.9444 (p) REVERT: J 67 TYR cc_start: 0.9076 (m-80) cc_final: 0.8817 (m-80) REVERT: J 79 MET cc_start: 0.9356 (ppp) cc_final: 0.9114 (ppp) outliers start: 44 outliers final: 31 residues processed: 338 average time/residue: 0.0923 time to fit residues: 46.8583 Evaluate side-chains 329 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 292 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 B residue 111 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 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 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 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 24 LEU Chi-restraints excluded: chain F residue 39 ILE 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 160 LEU 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 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: 0.7980 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.066651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.050768 restraints weight = 49189.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.052411 restraints weight = 27197.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.053571 restraints weight = 18666.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.054256 restraints weight = 14531.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.054776 restraints weight = 12468.043| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.6283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11668 Z= 0.155 Angle : 0.919 12.324 15814 Z= 0.434 Chirality : 0.044 0.232 1927 Planarity : 0.005 0.077 1877 Dihedral : 5.134 46.073 1516 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.44 % Favored : 93.49 % Rotamer: Outliers : 3.78 % Allowed : 29.53 % Favored : 66.69 % 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: -0.69 (0.23), residues: 1414 helix: 0.19 (0.16), residues: 1115 sheet: None (None), residues: 0 loop : -2.67 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 44 TYR 0.023 0.001 TYR D 27 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 0.00372 (11668) covalent geometry : angle 0.91866 (15814) hydrogen bonds : bond 0.03372 ( 675) hydrogen bonds : angle 4.51381 ( 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 351 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 303 time to evaluate : 0.457 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: 0.9174 (ttm) cc_final: 0.8877 (ttm) REVERT: A 165 ASP cc_start: 0.8652 (m-30) cc_final: 0.8404 (m-30) REVERT: A 171 ILE cc_start: 0.9535 (pt) cc_final: 0.9222 (pt) REVERT: A 175 LEU cc_start: 0.9510 (tp) cc_final: 0.9156 (pp) REVERT: B 108 ASP cc_start: 0.8736 (t0) cc_final: 0.8398 (t0) REVERT: B 111 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8911 (tt) REVERT: B 149 ASP cc_start: 0.8970 (t0) cc_final: 0.8419 (t0) REVERT: B 180 MET cc_start: 0.9178 (ppp) cc_final: 0.8448 (ppp) REVERT: C 48 SER cc_start: 0.8640 (t) cc_final: 0.8217 (p) REVERT: C 50 MET cc_start: 0.8687 (tpt) cc_final: 0.8268 (tpt) REVERT: C 135 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7873 (pp) REVERT: C 158 TYR cc_start: 0.9037 (t80) cc_final: 0.8612 (t80) REVERT: C 198 ASP cc_start: 0.8568 (t0) cc_final: 0.8215 (t70) REVERT: D 64 MET cc_start: 0.9331 (mmp) cc_final: 0.9073 (mmp) REVERT: D 142 TYR cc_start: 0.8437 (t80) cc_final: 0.8032 (t80) REVERT: D 146 GLU cc_start: 0.9536 (OUTLIER) cc_final: 0.9254 (mt-10) REVERT: D 149 ASP cc_start: 0.9340 (t0) cc_final: 0.8827 (t0) REVERT: D 190 LYS cc_start: 0.9255 (mtmt) cc_final: 0.8887 (mtmm) REVERT: E 15 THR cc_start: 0.9165 (m) cc_final: 0.8908 (p) REVERT: E 36 MET cc_start: 0.9260 (ttm) cc_final: 0.9037 (ttm) REVERT: E 39 ASN cc_start: 0.9152 (m-40) cc_final: 0.8659 (m110) REVERT: E 179 MET cc_start: 0.8480 (mtm) cc_final: 0.8176 (ttp) REVERT: E 190 LYS cc_start: 0.9487 (mtmt) cc_final: 0.8743 (mtmm) REVERT: E 205 LYS cc_start: 0.9154 (tptm) cc_final: 0.8888 (tptp) REVERT: F 22 PHE cc_start: 0.8679 (m-80) cc_final: 0.8287 (m-80) REVERT: F 35 ASN cc_start: 0.6678 (t0) cc_final: 0.6055 (m-40) REVERT: F 78 GLU cc_start: 0.9359 (mm-30) cc_final: 0.9093 (mm-30) REVERT: F 87 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.8832 (m-80) REVERT: F 220 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8659 (tmmt) REVERT: F 248 LYS cc_start: 0.9382 (mmtt) cc_final: 0.9092 (mmtm) REVERT: I 19 SER cc_start: 0.9549 (t) cc_final: 0.9209 (p) REVERT: G 52 LYS cc_start: 0.9544 (mtpt) cc_final: 0.9285 (ttpp) REVERT: G 63 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9248 (tt) REVERT: H 1 MET cc_start: 0.7481 (ptt) cc_final: 0.7052 (tmm) REVERT: H 44 GLU cc_start: 0.7499 (pp20) cc_final: 0.6877 (mp0) REVERT: H 59 SER cc_start: 0.9666 (t) cc_final: 0.9412 (p) REVERT: J 3 ASP cc_start: 0.9130 (OUTLIER) cc_final: 0.8925 (t0) REVERT: J 67 TYR cc_start: 0.9031 (m-80) cc_final: 0.8760 (m-80) REVERT: J 79 MET cc_start: 0.9363 (ppp) cc_final: 0.9131 (ppp) outliers start: 48 outliers final: 35 residues processed: 338 average time/residue: 0.0895 time to fit residues: 45.6228 Evaluate side-chains 335 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 293 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 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 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 197 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 E residue 213 ASN Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 39 ILE 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 160 LEU Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 222 LEU 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 3 ASP 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: 1.9990 chunk 132 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 125 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 GLN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 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 = 0.3312 r_free = 0.3312 target = 0.066249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.050362 restraints weight = 49428.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.052009 restraints weight = 27416.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.053143 restraints weight = 18778.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.053812 restraints weight = 14628.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.054348 restraints weight = 12572.525| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.6391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 11668 Z= 0.165 Angle : 0.949 14.591 15814 Z= 0.446 Chirality : 0.045 0.222 1927 Planarity : 0.005 0.079 1877 Dihedral : 5.117 46.113 1516 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.65 % Favored : 93.28 % Rotamer: Outliers : 3.46 % Allowed : 29.76 % Favored : 66.77 % 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: -0.57 (0.23), residues: 1414 helix: 0.27 (0.16), residues: 1113 sheet: None (None), residues: 0 loop : -2.61 (0.39), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 38 TYR 0.040 0.002 TYR A 158 PHE 0.026 0.001 PHE J 74 TRP 0.008 0.001 TRP D 200 HIS 0.003 0.001 HIS F 70 Details of bonding type rmsd covalent geometry : bond 0.00400 (11668) covalent geometry : angle 0.94876 (15814) hydrogen bonds : bond 0.03449 ( 675) hydrogen bonds : angle 4.52319 ( 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: 44 poor density : 299 time to evaluate : 0.552 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: 0.9167 (ttm) cc_final: 0.8886 (ttm) REVERT: A 50 MET cc_start: 0.8723 (tpp) cc_final: 0.8474 (tpp) REVERT: A 165 ASP cc_start: 0.8673 (m-30) cc_final: 0.8416 (m-30) REVERT: A 175 LEU cc_start: 0.9496 (tp) cc_final: 0.9266 (pp) REVERT: B 108 ASP cc_start: 0.8772 (t0) cc_final: 0.8406 (t0) REVERT: B 111 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8920 (tt) REVERT: B 149 ASP cc_start: 0.8974 (t0) cc_final: 0.8422 (t0) REVERT: C 48 SER cc_start: 0.8636 (t) cc_final: 0.8206 (p) REVERT: C 50 MET cc_start: 0.8700 (tpt) cc_final: 0.8212 (tpt) REVERT: C 135 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7822 (pp) REVERT: C 158 TYR cc_start: 0.9068 (t80) cc_final: 0.8646 (t80) REVERT: C 198 ASP cc_start: 0.8647 (t0) cc_final: 0.8275 (t70) REVERT: D 64 MET cc_start: 0.9336 (mmp) cc_final: 0.9087 (mmp) REVERT: D 142 TYR cc_start: 0.8479 (t80) cc_final: 0.8067 (t80) REVERT: D 146 GLU cc_start: 0.9544 (OUTLIER) cc_final: 0.9242 (mt-10) REVERT: D 149 ASP cc_start: 0.9332 (t0) cc_final: 0.8953 (t0) REVERT: D 190 LYS cc_start: 0.9270 (mtmt) cc_final: 0.8918 (mtmm) REVERT: E 15 THR cc_start: 0.9171 (m) cc_final: 0.8916 (p) REVERT: E 39 ASN cc_start: 0.9171 (m-40) cc_final: 0.8656 (m110) REVERT: E 179 MET cc_start: 0.8509 (mtm) cc_final: 0.8163 (ttt) REVERT: E 190 LYS cc_start: 0.9483 (mtmt) cc_final: 0.8735 (mtmm) REVERT: E 205 LYS cc_start: 0.9176 (tptm) cc_final: 0.8937 (tptp) REVERT: F 22 PHE cc_start: 0.8701 (m-80) cc_final: 0.8302 (m-80) REVERT: F 35 ASN cc_start: 0.6459 (t0) cc_final: 0.5763 (m-40) REVERT: F 78 GLU cc_start: 0.9374 (mm-30) cc_final: 0.9108 (mm-30) REVERT: F 87 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8895 (m-80) REVERT: F 220 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8647 (tmmt) REVERT: F 248 LYS cc_start: 0.9397 (mmtt) cc_final: 0.9110 (mmtm) REVERT: I 19 SER cc_start: 0.9549 (t) cc_final: 0.9218 (p) REVERT: G 52 LYS cc_start: 0.9524 (mtpt) cc_final: 0.9299 (ttpp) REVERT: G 63 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9249 (tt) REVERT: H 1 MET cc_start: 0.7584 (ptt) cc_final: 0.7113 (tmm) REVERT: H 44 GLU cc_start: 0.7434 (pp20) cc_final: 0.7032 (mp0) REVERT: H 59 SER cc_start: 0.9638 (t) cc_final: 0.9373 (p) REVERT: J 67 TYR cc_start: 0.9005 (m-80) cc_final: 0.8798 (m-80) REVERT: J 79 MET cc_start: 0.9373 (ppp) cc_final: 0.9110 (ppp) outliers start: 44 outliers final: 33 residues processed: 329 average time/residue: 0.0899 time to fit residues: 44.6253 Evaluate side-chains 331 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 292 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 45 GLN 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 177 MET 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 197 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 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 160 LEU Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain I residue 15 ILE 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 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 90 optimal weight: 10.0000 chunk 100 optimal weight: 0.0870 chunk 6 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 GLN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.066416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.050377 restraints weight = 49795.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.052081 restraints weight = 27302.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.053211 restraints weight = 18621.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.053856 restraints weight = 14475.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.054367 restraints weight = 12465.092| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.6387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.198 11668 Z= 0.225 Angle : 1.152 59.191 15814 Z= 0.606 Chirality : 0.045 0.256 1927 Planarity : 0.006 0.148 1877 Dihedral : 5.121 46.087 1516 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.44 % Favored : 93.49 % Rotamer: Outliers : 3.23 % Allowed : 29.76 % Favored : 67.01 % Cbeta Deviations : 0.07 % 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: -0.55 (0.23), residues: 1414 helix: 0.28 (0.16), residues: 1113 sheet: None (None), residues: 0 loop : -2.60 (0.39), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 38 TYR 0.029 0.002 TYR C 142 PHE 0.024 0.001 PHE J 74 TRP 0.008 0.001 TRP D 200 HIS 0.003 0.001 HIS F 70 Details of bonding type rmsd covalent geometry : bond 0.00523 (11668) covalent geometry : angle 1.15174 (15814) hydrogen bonds : bond 0.03450 ( 675) hydrogen bonds : angle 4.52424 ( 2019) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2230.40 seconds wall clock time: 39 minutes 22.78 seconds (2362.78 seconds total)