Starting phenix.real_space_refine on Sat Mar 7 03:23:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z18_14444/03_2026/7z18_14444_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z18_14444/03_2026/7z18_14444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z18_14444/03_2026/7z18_14444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z18_14444/03_2026/7z18_14444.map" model { file = "/net/cci-nas-00/data/ceres_data/7z18_14444/03_2026/7z18_14444_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z18_14444/03_2026/7z18_14444_neut_trim.cif" } resolution = 1.98 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= 0.001 sd= 0.022 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: 8 Type Number sf(0) Gaussians Zn 4 6.06 5 P 10 5.49 5 Mg 2 5.21 5 S 86 5.16 5 C 11895 2.51 5 N 3360 2.21 5 O 3642 1.98 5 H 18660 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37659 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2187 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "B" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 2942 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 178} Chain: "C" Number of atoms: 5395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5395 Classifications: {'peptide': 353} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Chain: "D" Number of atoms: 4357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4357 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 20, 'TRANS': 257} Chain: "E" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2187 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "F" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 2956 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 178} Chain: "G" Number of atoms: 5395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5395 Classifications: {'peptide': 353} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Chain: "H" Number of atoms: 4357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4357 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 20, 'TRANS': 257} Chain: "I" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 3903 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 11, 'TRANS': 238} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 3872 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {' ZN': 1, 'I9X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {' ZN': 1, 'I9X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14322 SG CYS D 241 57.637 16.454 77.069 1.00 11.08 S ATOM 14361 SG CYS D 244 54.212 14.865 76.654 1.00 12.88 S ATOM 14681 SG CYS D 266 54.722 18.369 75.570 1.00 8.23 S ATOM 14761 SG CYS D 272 54.914 17.506 79.374 1.00 11.29 S ATOM 29217 SG CYS H 241 75.111 105.234 77.069 1.00 11.01 S ATOM 29256 SG CYS H 244 78.535 106.824 76.654 1.00 12.76 S ATOM 29576 SG CYS H 266 78.026 103.320 75.570 1.00 8.35 S ATOM 29656 SG CYS H 272 77.835 104.183 79.374 1.00 11.18 S Time building chain proxies: 5.96, per 1000 atoms: 0.16 Number of scatterers: 37659 At special positions: 0 Unit cell: (133.674, 122.612, 129.065, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 S 86 16.00 P 10 15.00 Mg 2 11.99 O 3642 8.00 N 3360 7.00 C 11895 6.00 H 18660 1.00 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: 2.89 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 328 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 333 " pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 241 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 244 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 266 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 272 " pdb=" ZN G1000 " pdb="ZN ZN G1000 " - pdb=" NE2 HIS G 328 " pdb="ZN ZN G1000 " - pdb=" NE2 HIS G 333 " pdb=" ZN H1000 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 241 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 244 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 266 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 272 " Number of angles added : 12 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4516 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 22 sheets defined 46.8% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 88 through 103 removed outlier: 3.589A pdb=" N GLN A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 115 removed outlier: 4.510A pdb=" N GLN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASN A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 136 removed outlier: 3.749A pdb=" N ALA A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 27 Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 66 through 69 Processing helix chain 'B' and resid 70 through 82 Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 102 through 109 Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.765A pdb=" N GLY B 120 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 164 Processing helix chain 'C' and resid 7 through 25 Processing helix chain 'C' and resid 33 through 41 Processing helix chain 'C' and resid 41 through 53 Processing helix chain 'C' and resid 56 through 67 Processing helix chain 'C' and resid 70 through 84 removed outlier: 3.613A pdb=" N THR C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 188 through 199 Processing helix chain 'C' and resid 200 through 213 Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 305 through 308 Processing helix chain 'C' and resid 309 through 316 removed outlier: 3.774A pdb=" N HIS C 316 " --> pdb=" O PHE C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 333 through 353 Processing helix chain 'D' and resid 8 through 12 removed outlier: 4.093A pdb=" N LEU D 12 " --> pdb=" O PHE D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 30 Processing helix chain 'D' and resid 49 through 60 Processing helix chain 'D' and resid 76 through 91 Processing helix chain 'D' and resid 137 through 147 removed outlier: 4.204A pdb=" N THR D 143 " --> pdb=" O THR D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 Processing helix chain 'D' and resid 189 through 197 Proline residue: D 194 - end of helix Processing helix chain 'D' and resid 268 through 279 Processing helix chain 'E' and resid 4 through 18 Processing helix chain 'E' and resid 19 through 31 Processing helix chain 'E' and resid 54 through 56 No H-bonds generated for 'chain 'E' and resid 54 through 56' Processing helix chain 'E' and resid 88 through 103 removed outlier: 3.590A pdb=" N GLN E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 115 removed outlier: 4.502A pdb=" N GLN E 109 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ASN E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 136 removed outlier: 3.749A pdb=" N ALA E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 27 Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'F' and resid 66 through 69 Processing helix chain 'F' and resid 70 through 82 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 102 through 109 Processing helix chain 'F' and resid 116 through 120 removed outlier: 3.766A pdb=" N GLY F 120 " --> pdb=" O PRO F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 164 Processing helix chain 'G' and resid 7 through 25 Processing helix chain 'G' and resid 33 through 41 Processing helix chain 'G' and resid 41 through 53 Processing helix chain 'G' and resid 56 through 67 Processing helix chain 'G' and resid 70 through 84 removed outlier: 3.613A pdb=" N THR G 84 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 99 Processing helix chain 'G' and resid 130 through 135 Processing helix chain 'G' and resid 154 through 162 Processing helix chain 'G' and resid 188 through 199 Processing helix chain 'G' and resid 200 through 213 Processing helix chain 'G' and resid 281 through 295 Processing helix chain 'G' and resid 295 through 300 Processing helix chain 'G' and resid 305 through 308 Processing helix chain 'G' and resid 309 through 316 removed outlier: 3.775A pdb=" N HIS G 316 " --> pdb=" O PHE G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 328 Processing helix chain 'G' and resid 329 through 331 No H-bonds generated for 'chain 'G' and resid 329 through 331' Processing helix chain 'G' and resid 333 through 353 Processing helix chain 'H' and resid 8 through 12 removed outlier: 4.093A pdb=" N LEU H 12 " --> pdb=" O PHE H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 30 Processing helix chain 'H' and resid 49 through 60 Processing helix chain 'H' and resid 76 through 91 Processing helix chain 'H' and resid 137 through 147 removed outlier: 4.205A pdb=" N THR H 143 " --> pdb=" O THR H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 165 Processing helix chain 'H' and resid 189 through 197 Proline residue: H 194 - end of helix Processing helix chain 'H' and resid 268 through 279 Processing helix chain 'I' and resid 43 through 52 Processing helix chain 'I' and resid 73 through 84 Processing helix chain 'I' and resid 91 through 96 Processing helix chain 'I' and resid 101 through 113 removed outlier: 4.202A pdb=" N ARG I 109 " --> pdb=" O ASN I 105 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU I 110 " --> pdb=" O ILE I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 132 Processing helix chain 'I' and resid 135 through 139 Processing helix chain 'I' and resid 142 through 146 Processing helix chain 'I' and resid 147 through 161 Processing helix chain 'I' and resid 177 through 196 Processing helix chain 'I' and resid 205 through 213 removed outlier: 3.508A pdb=" N ALA I 209 " --> pdb=" O ASP I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 236 Processing helix chain 'I' and resid 239 through 249 removed outlier: 3.549A pdb=" N VAL I 249 " --> pdb=" O LEU I 245 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 73 through 84 Processing helix chain 'J' and resid 91 through 96 Processing helix chain 'J' and resid 101 through 113 removed outlier: 4.201A pdb=" N ARG J 109 " --> pdb=" O ASN J 105 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU J 110 " --> pdb=" O ILE J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 132 Processing helix chain 'J' and resid 135 through 139 Processing helix chain 'J' and resid 142 through 146 Processing helix chain 'J' and resid 147 through 161 Processing helix chain 'J' and resid 177 through 196 Processing helix chain 'J' and resid 205 through 213 removed outlier: 3.508A pdb=" N ALA J 209 " --> pdb=" O ASP J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 230 through 236 Processing helix chain 'J' and resid 239 through 249 removed outlier: 3.548A pdb=" N VAL J 249 " --> pdb=" O LEU J 245 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 85 removed outlier: 5.340A pdb=" N PHE A 61 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA A 51 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLY A 63 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ALA A 71 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ALA A 41 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ARG A 73 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE A 39 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LYS C 87 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU A 46 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA C 89 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 4.693A pdb=" N GLN C 116 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 144 Processing sheet with id=AA4, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.288A pdb=" N LEU B 123 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N THR B 177 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 125 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA B 95 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLN B 126 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR B 97 " --> pdb=" O GLN B 126 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP B 63 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 147 through 149 Processing sheet with id=AA6, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.713A pdb=" N SER C 227 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG C 104 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE C 225 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ALA C 222 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL C 256 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY C 246 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE C 234 " --> pdb=" O ASN C 244 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASN C 244 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLU C 252 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL C 276 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLU C 254 " --> pdb=" O GLY C 274 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLY C 274 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL C 256 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N GLY C 272 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLY C 258 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR C 270 " --> pdb=" O GLY C 258 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 35 through 36 removed outlier: 6.418A pdb=" N ILE D 104 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N GLN D 124 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N THR D 106 " --> pdb=" O GLN D 124 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AB1, first strand: chain 'D' and resid 251 through 255 Processing sheet with id=AB2, first strand: chain 'E' and resid 79 through 85 removed outlier: 5.340A pdb=" N PHE E 61 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA E 51 " --> pdb=" O PHE E 61 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY E 63 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ALA E 71 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ALA E 41 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ARG E 73 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE E 39 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LYS G 87 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU E 46 " --> pdb=" O LYS G 87 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA G 89 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 138 through 139 removed outlier: 4.699A pdb=" N GLN G 116 " --> pdb=" O VAL E 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 32 through 33 removed outlier: 6.288A pdb=" N LEU F 123 " --> pdb=" O ILE F 175 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR F 177 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU F 125 " --> pdb=" O THR F 177 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA F 95 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLN F 126 " --> pdb=" O ALA F 95 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR F 97 " --> pdb=" O GLN F 126 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP F 63 " --> pdb=" O VAL F 96 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 147 through 149 Processing sheet with id=AB6, first strand: chain 'G' and resid 100 through 105 removed outlier: 6.712A pdb=" N SER G 227 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG G 104 " --> pdb=" O ILE G 225 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE G 225 " --> pdb=" O ARG G 104 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ALA G 222 " --> pdb=" O VAL G 256 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL G 256 " --> pdb=" O ALA G 222 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY G 246 " --> pdb=" O VAL G 232 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE G 234 " --> pdb=" O ASN G 244 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASN G 244 " --> pdb=" O ILE G 234 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLU G 252 " --> pdb=" O VAL G 276 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL G 276 " --> pdb=" O GLU G 252 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLU G 254 " --> pdb=" O GLY G 274 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLY G 274 " --> pdb=" O GLU G 254 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL G 256 " --> pdb=" O GLY G 272 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLY G 272 " --> pdb=" O VAL G 256 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLY G 258 " --> pdb=" O THR G 270 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR G 270 " --> pdb=" O GLY G 258 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 35 through 36 removed outlier: 6.418A pdb=" N ILE H 104 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N GLN H 124 " --> pdb=" O ILE H 104 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N THR H 106 " --> pdb=" O GLN H 124 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 181 through 183 Processing sheet with id=AB9, first strand: chain 'H' and resid 251 through 255 Processing sheet with id=AC1, first strand: chain 'I' and resid 19 through 28 removed outlier: 3.525A pdb=" N ALA I 16 " --> pdb=" O LYS I 19 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE I 21 " --> pdb=" O LEU I 14 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU I 14 " --> pdb=" O PHE I 21 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASP I 23 " --> pdb=" O THR I 12 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR I 12 " --> pdb=" O ASP I 23 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER I 25 " --> pdb=" O ASN I 10 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN I 10 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASP I 27 " --> pdb=" O VAL I 8 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL I 8 " --> pdb=" O ASP I 27 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU I 11 " --> pdb=" O GLN I 59 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLN I 59 " --> pdb=" O LEU I 11 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 85 through 88 removed outlier: 6.273A pdb=" N VAL I 33 " --> pdb=" O ARG I 215 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU I 217 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLY I 35 " --> pdb=" O LEU I 217 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N MET I 219 " --> pdb=" O GLY I 35 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL I 37 " --> pdb=" O MET I 219 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU I 226 " --> pdb=" O VAL I 218 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS I 220 " --> pdb=" O VAL I 224 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL I 224 " --> pdb=" O LYS I 220 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 19 through 28 removed outlier: 3.525A pdb=" N ALA J 16 " --> pdb=" O LYS J 19 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N PHE J 21 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU J 14 " --> pdb=" O PHE J 21 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASP J 23 " --> pdb=" O THR J 12 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR J 12 " --> pdb=" O ASP J 23 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER J 25 " --> pdb=" O ASN J 10 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN J 10 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASP J 27 " --> pdb=" O VAL J 8 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL J 8 " --> pdb=" O ASP J 27 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU J 11 " --> pdb=" O GLN J 59 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLN J 59 " --> pdb=" O LEU J 11 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 85 through 88 removed outlier: 6.273A pdb=" N VAL J 33 " --> pdb=" O ARG J 215 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU J 217 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLY J 35 " --> pdb=" O LEU J 217 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N MET J 219 " --> pdb=" O GLY J 35 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL J 37 " --> pdb=" O MET J 219 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU J 226 " --> pdb=" O VAL J 218 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS J 220 " --> pdb=" O VAL J 224 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL J 224 " --> pdb=" O LYS J 220 " (cutoff:3.500A) 915 hydrogen bonds defined for protein. 2535 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: 9.27 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.14: 18650 1.14 - 1.44: 8136 1.44 - 1.74: 11085 1.74 - 2.04: 152 2.04 - 2.34: 4 Bond restraints: 38027 Sorted by residual: bond pdb=" C03 I9X D1001 " pdb=" C04 I9X D1001 " ideal model delta sigma weight residual 1.545 1.214 0.331 2.00e-02 2.50e+03 2.74e+02 bond pdb=" C03 I9X H1001 " pdb=" C04 I9X H1001 " ideal model delta sigma weight residual 1.545 1.215 0.330 2.00e-02 2.50e+03 2.73e+02 bond pdb=" C05 I9X D1001 " pdb=" O07 I9X D1001 " ideal model delta sigma weight residual 1.471 1.214 0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" C05 I9X H1001 " pdb=" O07 I9X H1001 " ideal model delta sigma weight residual 1.471 1.214 0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" O10 I9X H1001 " pdb=" P08 I9X H1001 " ideal model delta sigma weight residual 1.559 1.331 0.228 2.00e-02 2.50e+03 1.30e+02 ... (remaining 38022 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.08: 68647 8.08 - 16.16: 13 16.16 - 24.24: 12 24.24 - 32.32: 18 32.32 - 40.40: 18 Bond angle restraints: 68708 Sorted by residual: angle pdb=" H1 MET G 1 " pdb=" N MET G 1 " pdb=" H3 MET G 1 " ideal model delta sigma weight residual 109.47 149.87 -40.40 3.00e+00 1.11e-01 1.81e+02 angle pdb=" N ALA A 3 " pdb=" CA ALA A 3 " pdb=" HA ALA A 3 " ideal model delta sigma weight residual 110.00 71.86 38.14 3.00e+00 1.11e-01 1.62e+02 angle pdb=" N ASP A 4 " pdb=" CA ASP A 4 " pdb=" HA ASP A 4 " ideal model delta sigma weight residual 110.00 72.97 37.03 3.00e+00 1.11e-01 1.52e+02 angle pdb=" CB ASP A 4 " pdb=" CA ASP A 4 " pdb=" HA ASP A 4 " ideal model delta sigma weight residual 109.00 71.99 37.01 3.00e+00 1.11e-01 1.52e+02 angle pdb=" N THR F 2 " pdb=" CA THR F 2 " pdb=" HA THR F 2 " ideal model delta sigma weight residual 110.00 73.51 36.49 3.00e+00 1.11e-01 1.48e+02 ... (remaining 68703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 16322 17.99 - 35.98: 1066 35.98 - 53.96: 400 53.96 - 71.95: 139 71.95 - 89.94: 58 Dihedral angle restraints: 17985 sinusoidal: 10025 harmonic: 7960 Sorted by residual: dihedral pdb=" CA ARG H 180 " pdb=" C ARG H 180 " pdb=" N TYR H 181 " pdb=" CA TYR H 181 " ideal model delta harmonic sigma weight residual -180.00 -161.99 -18.01 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ARG D 180 " pdb=" C ARG D 180 " pdb=" N TYR D 181 " pdb=" CA TYR D 181 " ideal model delta harmonic sigma weight residual 180.00 -162.01 -17.99 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CG ARG J 98 " pdb=" CD ARG J 98 " pdb=" NE ARG J 98 " pdb=" CZ ARG J 98 " ideal model delta sinusoidal sigma weight residual 90.00 41.06 48.94 2 1.50e+01 4.44e-03 1.21e+01 ... (remaining 17982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2780 0.102 - 0.205: 186 0.205 - 0.307: 18 0.307 - 0.410: 2 0.410 - 0.512: 6 Chirality restraints: 2992 Sorted by residual: chirality pdb=" CB THR C 143 " pdb=" CA THR C 143 " pdb=" OG1 THR C 143 " pdb=" CG2 THR C 143 " both_signs ideal model delta sigma weight residual False 2.55 2.04 0.51 2.00e-01 2.50e+01 6.56e+00 chirality pdb=" CB THR G 143 " pdb=" CA THR G 143 " pdb=" OG1 THR G 143 " pdb=" CG2 THR G 143 " both_signs ideal model delta sigma weight residual False 2.55 2.04 0.51 2.00e-01 2.50e+01 6.50e+00 chirality pdb=" CB THR F 5 " pdb=" CA THR F 5 " pdb=" OG1 THR F 5 " pdb=" CG2 THR F 5 " both_signs ideal model delta sigma weight residual False 2.55 2.05 0.51 2.00e-01 2.50e+01 6.40e+00 ... (remaining 2989 not shown) Planarity restraints: 5748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN J 159 " -0.018 2.00e-02 2.50e+03 4.43e-01 2.94e+03 pdb=" CG ASN J 159 " 0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN J 159 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN J 159 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN J 159 " 0.764 2.00e-02 2.50e+03 pdb="HD22 ASN J 159 " -0.769 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 159 " 0.010 2.00e-02 2.50e+03 4.42e-01 2.93e+03 pdb=" CG ASN I 159 " -0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN I 159 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN I 159 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN I 159 " -0.764 2.00e-02 2.50e+03 pdb="HD22 ASN I 159 " 0.768 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 150 " -0.046 2.00e-02 2.50e+03 4.40e-01 2.91e+03 pdb=" CD GLN C 150 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN C 150 " 0.042 2.00e-02 2.50e+03 pdb=" NE2 GLN C 150 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN C 150 " 0.758 2.00e-02 2.50e+03 pdb="HE22 GLN C 150 " -0.765 2.00e-02 2.50e+03 ... (remaining 5745 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.16: 1500 2.16 - 2.77: 72648 2.77 - 3.38: 115381 3.38 - 3.99: 153282 3.99 - 4.60: 233759 Nonbonded interactions: 576570 Sorted by model distance: nonbonded pdb=" HB THR F 5 " pdb="HG23 THR F 5 " model vdw 1.544 1.952 nonbonded pdb=" O PHE H 9 " pdb=" HZ1 LYS H 17 " model vdw 1.588 2.450 nonbonded pdb=" O PHE D 9 " pdb=" HZ1 LYS D 17 " model vdw 1.589 2.450 nonbonded pdb="HH22 ARG C 282 " pdb=" OD2 ASP G 70 " model vdw 1.606 2.450 nonbonded pdb=" OD2 ASP C 70 " pdb="HH22 ARG G 282 " model vdw 1.610 2.450 ... (remaining 576565 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and (resid 2 through 187 or (resid 188 through 189 and (name N or nam \ e CA or name C or name O or name CB or name OG1 or name CG2)) or resid 190 throu \ gh 194)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 3 through 250 or resid 1000 through 1001)) 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.220 Extract box with map and model: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 43.030 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.331 19379 Z= 0.489 Angle : 0.940 16.663 26359 Z= 0.590 Chirality : 0.057 0.512 2992 Planarity : 0.005 0.068 3462 Dihedral : 15.453 89.913 7295 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.19 % Allowed : 6.68 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.17), residues: 2412 helix: 1.89 (0.18), residues: 944 sheet: 0.34 (0.26), residues: 376 loop : 0.49 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 104 TYR 0.012 0.002 TYR H 150 PHE 0.016 0.002 PHE C 337 TRP 0.009 0.002 TRP I 85 HIS 0.010 0.001 HIS D 145 Details of bonding type rmsd covalent geometry : bond 0.00823 (19367) covalent geometry : angle 0.93845 (26347) hydrogen bonds : bond 0.14152 ( 915) hydrogen bonds : angle 6.66568 ( 2535) metal coordination : bond 0.00399 ( 12) metal coordination : angle 2.98607 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 319 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 295 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7725 (mt0) outliers start: 24 outliers final: 5 residues processed: 310 average time/residue: 1.7027 time to fit residues: 581.6570 Evaluate side-chains 239 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 233 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 133 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN D 3 ASN F 91 GLN H 3 ASN I 159 ASN I 181 GLN J 159 ASN J 181 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.113342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.079773 restraints weight = 62263.699| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.47 r_work: 0.2906 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19379 Z= 0.200 Angle : 0.607 11.007 26359 Z= 0.319 Chirality : 0.061 1.336 2992 Planarity : 0.005 0.058 3462 Dihedral : 7.646 77.228 2797 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.84 % Allowed : 7.43 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 1.44 (0.17), residues: 2412 helix: 1.91 (0.17), residues: 950 sheet: 0.15 (0.26), residues: 378 loop : 0.54 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 153 TYR 0.016 0.002 TYR C 209 PHE 0.014 0.002 PHE F 18 TRP 0.017 0.001 TRP A 11 HIS 0.015 0.001 HIS I 91 Details of bonding type rmsd covalent geometry : bond 0.00437 (19367) covalent geometry : angle 0.60460 (26347) hydrogen bonds : bond 0.04957 ( 915) hydrogen bonds : angle 5.39151 ( 2535) metal coordination : bond 0.00680 ( 12) metal coordination : angle 2.57442 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 242 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 225 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7521 (tpp) REVERT: B 135 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8176 (tpt) REVERT: C 298 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7834 (mt-10) REVERT: F 8 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7514 (tpp) REVERT: F 194 CYS cc_start: 0.7818 (m) cc_final: 0.7423 (m) REVERT: G 298 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: G 349 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7678 (mt0) REVERT: I 61 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7324 (tp30) REVERT: I 98 ARG cc_start: 0.8515 (mmt90) cc_final: 0.8255 (mmt90) REVERT: I 127 LYS cc_start: 0.8296 (tmmt) cc_final: 0.7970 (tmtt) REVERT: J 61 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7374 (tp30) REVERT: J 98 ARG cc_start: 0.8471 (mmt90) cc_final: 0.8204 (mmt90) REVERT: J 127 LYS cc_start: 0.8295 (tmmt) cc_final: 0.7973 (tmtt) outliers start: 17 outliers final: 2 residues processed: 236 average time/residue: 1.6311 time to fit residues: 425.6494 Evaluate side-chains 227 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 217 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain F residue 8 MET Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain G residue 349 GLN Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain J residue 61 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 47 optimal weight: 2.9990 chunk 3 optimal weight: 0.0030 chunk 1 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 208 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN E 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.112896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.079579 restraints weight = 62239.242| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.44 r_work: 0.2916 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19379 Z= 0.171 Angle : 0.564 11.492 26359 Z= 0.297 Chirality : 0.062 1.419 2992 Planarity : 0.004 0.055 3462 Dihedral : 7.269 80.764 2786 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.99 % Allowed : 7.72 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 1.35 (0.17), residues: 2412 helix: 1.89 (0.17), residues: 958 sheet: -0.00 (0.26), residues: 380 loop : 0.46 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 161 TYR 0.014 0.002 TYR G 209 PHE 0.014 0.002 PHE F 18 TRP 0.015 0.001 TRP A 11 HIS 0.008 0.001 HIS I 91 Details of bonding type rmsd covalent geometry : bond 0.00378 (19367) covalent geometry : angle 0.56160 (26347) hydrogen bonds : bond 0.04649 ( 915) hydrogen bonds : angle 5.18012 ( 2535) metal coordination : bond 0.00715 ( 12) metal coordination : angle 2.73477 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 228 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 CYS cc_start: 0.7883 (m) cc_final: 0.7431 (m) REVERT: C 349 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7276 (mp10) REVERT: F 194 CYS cc_start: 0.7912 (m) cc_final: 0.7474 (m) REVERT: I 61 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7472 (tp30) REVERT: I 127 LYS cc_start: 0.8363 (tmmt) cc_final: 0.8056 (tmtt) REVERT: J 127 LYS cc_start: 0.8358 (tmmt) cc_final: 0.8051 (tmtt) outliers start: 20 outliers final: 5 residues processed: 239 average time/residue: 1.5807 time to fit residues: 418.9396 Evaluate side-chains 220 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 213 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain C residue 349 GLN Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 61 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 236 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 193 optimal weight: 7.9990 chunk 80 optimal weight: 0.5980 chunk 117 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN B 152 GLN I 159 ASN J 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.112662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.079191 restraints weight = 62315.312| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.47 r_work: 0.2904 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19379 Z= 0.162 Angle : 0.555 11.507 26359 Z= 0.291 Chirality : 0.062 1.443 2992 Planarity : 0.004 0.040 3462 Dihedral : 7.044 78.003 2786 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.84 % Allowed : 8.51 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 1.37 (0.17), residues: 2412 helix: 1.95 (0.17), residues: 956 sheet: -0.06 (0.26), residues: 376 loop : 0.46 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 82 TYR 0.013 0.001 TYR G 209 PHE 0.014 0.002 PHE B 18 TRP 0.014 0.001 TRP A 11 HIS 0.009 0.001 HIS I 91 Details of bonding type rmsd covalent geometry : bond 0.00355 (19367) covalent geometry : angle 0.55175 (26347) hydrogen bonds : bond 0.04372 ( 915) hydrogen bonds : angle 5.05784 ( 2535) metal coordination : bond 0.00610 ( 12) metal coordination : angle 2.64623 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 212 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 194 CYS cc_start: 0.7804 (m) cc_final: 0.7316 (m) REVERT: C 349 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7222 (mp10) REVERT: F 194 CYS cc_start: 0.7812 (m) cc_final: 0.7335 (m) REVERT: I 127 LYS cc_start: 0.8342 (tmmt) cc_final: 0.8044 (tmtt) REVERT: I 194 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7190 (mm-30) REVERT: J 127 LYS cc_start: 0.8340 (tmmt) cc_final: 0.8044 (tmtt) REVERT: J 194 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7184 (mm-30) outliers start: 17 outliers final: 4 residues processed: 224 average time/residue: 1.6118 time to fit residues: 400.5911 Evaluate side-chains 217 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 212 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain C residue 349 GLN Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain G residue 328 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 155 optimal weight: 2.9990 chunk 234 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 236 optimal weight: 7.9990 chunk 229 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN I 159 ASN J 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.112542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.078944 restraints weight = 62139.183| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.47 r_work: 0.2901 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19379 Z= 0.166 Angle : 0.554 11.530 26359 Z= 0.290 Chirality : 0.062 1.433 2992 Planarity : 0.004 0.038 3462 Dihedral : 7.129 77.325 2786 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.54 % Allowed : 8.47 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 1.36 (0.17), residues: 2412 helix: 1.95 (0.17), residues: 956 sheet: -0.07 (0.26), residues: 376 loop : 0.45 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 153 TYR 0.013 0.002 TYR G 209 PHE 0.015 0.002 PHE F 18 TRP 0.012 0.001 TRP A 11 HIS 0.008 0.001 HIS I 91 Details of bonding type rmsd covalent geometry : bond 0.00368 (19367) covalent geometry : angle 0.55065 (26347) hydrogen bonds : bond 0.04394 ( 915) hydrogen bonds : angle 5.02920 ( 2535) metal coordination : bond 0.00601 ( 12) metal coordination : angle 2.74655 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 215 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8295 (tpt) REVERT: C 349 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7200 (mp10) REVERT: F 135 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8328 (tpt) REVERT: F 145 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7805 (mm-30) REVERT: I 127 LYS cc_start: 0.8353 (tmmt) cc_final: 0.8057 (tmtt) REVERT: J 127 LYS cc_start: 0.8359 (tmmt) cc_final: 0.8066 (tmtt) outliers start: 11 outliers final: 4 residues processed: 221 average time/residue: 1.5803 time to fit residues: 388.1848 Evaluate side-chains 217 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 209 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain C residue 349 GLN Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain G residue 328 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 0 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 209 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 145 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN I 159 ASN J 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.113377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.079962 restraints weight = 62432.711| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.45 r_work: 0.2919 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19379 Z= 0.125 Angle : 0.530 11.512 26359 Z= 0.277 Chirality : 0.061 1.428 2992 Planarity : 0.004 0.051 3462 Dihedral : 6.924 76.401 2786 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.74 % Allowed : 8.47 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 1.46 (0.17), residues: 2412 helix: 2.06 (0.17), residues: 956 sheet: -0.10 (0.26), residues: 380 loop : 0.51 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 73 TYR 0.012 0.001 TYR H 214 PHE 0.014 0.001 PHE F 18 TRP 0.014 0.001 TRP A 11 HIS 0.007 0.001 HIS I 91 Details of bonding type rmsd covalent geometry : bond 0.00271 (19367) covalent geometry : angle 0.52739 (26347) hydrogen bonds : bond 0.04037 ( 915) hydrogen bonds : angle 4.90452 ( 2535) metal coordination : bond 0.00492 ( 12) metal coordination : angle 2.61442 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 217 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8291 (tpt) REVERT: C 349 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7216 (mp10) REVERT: D 221 ARG cc_start: 0.8190 (mtp-110) cc_final: 0.7799 (mmm160) REVERT: H 221 ARG cc_start: 0.8180 (mtp-110) cc_final: 0.7786 (mmm160) REVERT: I 127 LYS cc_start: 0.8362 (tmmt) cc_final: 0.8065 (tmtt) REVERT: J 127 LYS cc_start: 0.8355 (tmmt) cc_final: 0.8066 (tmtt) outliers start: 15 outliers final: 5 residues processed: 229 average time/residue: 1.5657 time to fit residues: 398.0937 Evaluate side-chains 216 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 209 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain C residue 349 GLN Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 61 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 158 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN B 152 GLN F 42 GLN I 159 ASN J 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.112744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.079258 restraints weight = 62475.047| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.46 r_work: 0.2906 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19379 Z= 0.162 Angle : 0.546 11.492 26359 Z= 0.286 Chirality : 0.062 1.425 2992 Planarity : 0.004 0.050 3462 Dihedral : 7.012 76.551 2786 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.69 % Allowed : 8.96 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 1.42 (0.17), residues: 2412 helix: 2.00 (0.17), residues: 956 sheet: -0.07 (0.26), residues: 376 loop : 0.48 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 73 TYR 0.013 0.001 TYR G 209 PHE 0.015 0.002 PHE F 18 TRP 0.013 0.001 TRP A 11 HIS 0.007 0.001 HIS I 91 Details of bonding type rmsd covalent geometry : bond 0.00360 (19367) covalent geometry : angle 0.54303 (26347) hydrogen bonds : bond 0.04269 ( 915) hydrogen bonds : angle 4.93559 ( 2535) metal coordination : bond 0.00591 ( 12) metal coordination : angle 2.70243 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 206 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8009 (tpt) REVERT: B 145 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7895 (mm-30) REVERT: C 349 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7230 (mp10) REVERT: F 135 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8029 (tpt) REVERT: F 145 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7834 (mm-30) REVERT: G 349 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7424 (mp10) REVERT: I 127 LYS cc_start: 0.8363 (tmmt) cc_final: 0.8070 (tmtt) REVERT: J 127 LYS cc_start: 0.8366 (tmmt) cc_final: 0.8082 (tmtt) outliers start: 14 outliers final: 7 residues processed: 214 average time/residue: 1.5387 time to fit residues: 364.5032 Evaluate side-chains 219 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 206 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain C residue 349 GLN Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain G residue 349 GLN Chi-restraints excluded: chain I residue 61 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 30 optimal weight: 0.4980 chunk 212 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN B 152 GLN I 159 ASN J 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.113089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.079671 restraints weight = 62087.262| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.45 r_work: 0.2915 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19379 Z= 0.138 Angle : 0.537 11.519 26359 Z= 0.281 Chirality : 0.062 1.432 2992 Planarity : 0.004 0.052 3462 Dihedral : 6.933 76.632 2786 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.64 % Allowed : 8.96 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 1.46 (0.17), residues: 2412 helix: 2.05 (0.17), residues: 956 sheet: -0.06 (0.26), residues: 376 loop : 0.51 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 153 TYR 0.012 0.001 TYR G 209 PHE 0.014 0.001 PHE B 18 TRP 0.014 0.001 TRP A 11 HIS 0.007 0.001 HIS I 91 Details of bonding type rmsd covalent geometry : bond 0.00303 (19367) covalent geometry : angle 0.53378 (26347) hydrogen bonds : bond 0.04104 ( 915) hydrogen bonds : angle 4.88665 ( 2535) metal coordination : bond 0.00540 ( 12) metal coordination : angle 2.66119 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 209 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8046 (tpt) REVERT: B 145 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7884 (mm-30) REVERT: C 349 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7218 (mp10) REVERT: G 349 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7341 (mp10) REVERT: I 127 LYS cc_start: 0.8369 (tmmt) cc_final: 0.8078 (tmtt) REVERT: J 127 LYS cc_start: 0.8364 (tmmt) cc_final: 0.8081 (tmtt) outliers start: 13 outliers final: 7 residues processed: 217 average time/residue: 1.5457 time to fit residues: 372.6539 Evaluate side-chains 218 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 207 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain C residue 349 GLN Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain G residue 349 GLN Chi-restraints excluded: chain I residue 61 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 202 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN B 152 GLN I 89 HIS I 159 ASN J 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.112744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.079287 restraints weight = 62741.056| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.46 r_work: 0.2908 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19379 Z= 0.159 Angle : 0.549 11.483 26359 Z= 0.287 Chirality : 0.062 1.423 2992 Planarity : 0.004 0.057 3462 Dihedral : 6.985 76.807 2786 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.69 % Allowed : 9.01 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 1.43 (0.17), residues: 2412 helix: 2.01 (0.17), residues: 956 sheet: -0.07 (0.26), residues: 376 loop : 0.50 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 153 TYR 0.013 0.001 TYR G 209 PHE 0.015 0.002 PHE B 18 TRP 0.013 0.001 TRP A 11 HIS 0.007 0.001 HIS I 91 Details of bonding type rmsd covalent geometry : bond 0.00353 (19367) covalent geometry : angle 0.54639 (26347) hydrogen bonds : bond 0.04238 ( 915) hydrogen bonds : angle 4.91315 ( 2535) metal coordination : bond 0.00600 ( 12) metal coordination : angle 2.69583 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 211 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7896 (mm-30) REVERT: C 349 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7220 (mp10) REVERT: F 145 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7854 (mm-30) REVERT: G 349 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7328 (mp10) REVERT: I 127 LYS cc_start: 0.8369 (tmmt) cc_final: 0.8077 (tmtt) REVERT: J 127 LYS cc_start: 0.8369 (tmmt) cc_final: 0.8082 (tmtt) outliers start: 14 outliers final: 6 residues processed: 219 average time/residue: 1.5303 time to fit residues: 371.9091 Evaluate side-chains 215 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 205 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain C residue 349 GLN Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain G residue 349 GLN Chi-restraints excluded: chain I residue 61 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 5 optimal weight: 1.9990 chunk 237 optimal weight: 9.9990 chunk 185 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 chunk 71 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN B 152 GLN I 159 ASN J 89 HIS J 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.112488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.078996 restraints weight = 62461.068| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.46 r_work: 0.2904 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19379 Z= 0.169 Angle : 0.556 11.529 26359 Z= 0.291 Chirality : 0.062 1.435 2992 Planarity : 0.004 0.061 3462 Dihedral : 7.035 77.159 2786 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.79 % Allowed : 9.11 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 1.41 (0.17), residues: 2412 helix: 1.98 (0.17), residues: 956 sheet: -0.06 (0.26), residues: 376 loop : 0.49 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 153 TYR 0.013 0.002 TYR G 209 PHE 0.015 0.002 PHE B 18 TRP 0.014 0.001 TRP A 11 HIS 0.007 0.001 HIS I 91 Details of bonding type rmsd covalent geometry : bond 0.00375 (19367) covalent geometry : angle 0.55263 (26347) hydrogen bonds : bond 0.04320 ( 915) hydrogen bonds : angle 4.93436 ( 2535) metal coordination : bond 0.00635 ( 12) metal coordination : angle 2.77062 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8146 (tpt) REVERT: B 145 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7906 (mm-30) REVERT: C 349 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7223 (mp10) REVERT: F 145 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7887 (mm-30) REVERT: G 349 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7370 (mp10) REVERT: I 127 LYS cc_start: 0.8366 (tmmt) cc_final: 0.8073 (tmtt) REVERT: J 127 LYS cc_start: 0.8365 (tmmt) cc_final: 0.8076 (tmtt) outliers start: 16 outliers final: 6 residues processed: 219 average time/residue: 1.5994 time to fit residues: 387.7079 Evaluate side-chains 218 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 207 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain C residue 349 GLN Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain G residue 349 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 206 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 222 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 130 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN B 152 GLN F 42 GLN I 159 ASN J 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.113473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.080198 restraints weight = 62342.588| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.46 r_work: 0.2925 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19379 Z= 0.118 Angle : 0.530 11.513 26359 Z= 0.277 Chirality : 0.061 1.432 2992 Planarity : 0.004 0.057 3462 Dihedral : 6.874 76.715 2786 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.54 % Allowed : 9.16 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 1.50 (0.17), residues: 2412 helix: 2.10 (0.17), residues: 956 sheet: -0.07 (0.26), residues: 376 loop : 0.51 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 98 TYR 0.012 0.001 TYR D 214 PHE 0.014 0.001 PHE B 18 TRP 0.014 0.001 TRP A 11 HIS 0.007 0.001 HIS I 91 Details of bonding type rmsd covalent geometry : bond 0.00255 (19367) covalent geometry : angle 0.52736 (26347) hydrogen bonds : bond 0.03933 ( 915) hydrogen bonds : angle 4.82994 ( 2535) metal coordination : bond 0.00485 ( 12) metal coordination : angle 2.66426 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17485.54 seconds wall clock time: 294 minutes 59.59 seconds (17699.59 seconds total)