Starting phenix.real_space_refine on Sun Mar 17 15:03:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyk_34372/03_2024/8gyk_34372_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyk_34372/03_2024/8gyk_34372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyk_34372/03_2024/8gyk_34372.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyk_34372/03_2024/8gyk_34372.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyk_34372/03_2024/8gyk_34372_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyk_34372/03_2024/8gyk_34372_updated.pdb" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.004 sd= 0.073 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 96 5.16 5 C 11290 2.51 5 N 3211 2.21 5 O 3482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18103 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2233 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 6, 'TRANS': 283} Chain breaks: 2 Chain: "B" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2249 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 6, 'TRANS': 286} Chain breaks: 2 Chain: "C" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2241 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 6, 'TRANS': 285} Chain breaks: 2 Chain: "D" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2225 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 6, 'TRANS': 282} Chain breaks: 2 Chain: "E" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2232 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 283} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2233 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 6, 'TRANS': 283} Chain breaks: 2 Chain: "G" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2241 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 6, 'TRANS': 285} Chain breaks: 2 Chain: "H" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2225 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 6, 'TRANS': 282} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.36, per 1000 atoms: 0.52 Number of scatterers: 18103 At special positions: 0 Unit cell: (124.5, 122.84, 146.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 16 15.00 Mg 8 11.99 O 3482 8.00 N 3211 7.00 C 11290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 6.99 Conformation dependent library (CDL) restraints added in 3.4 seconds 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4238 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 14 sheets defined 42.4% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'A' and resid 25 through 28 Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 68 through 81 Processing helix chain 'A' and resid 89 through 96 Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 133 through 145 removed outlier: 4.642A pdb=" N GLN A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 168 through 178 Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 197 through 210 removed outlier: 3.605A pdb=" N THR A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.570A pdb=" N ASP A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 259 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 68 through 79 Processing helix chain 'B' and resid 89 through 96 Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 133 through 145 removed outlier: 4.668A pdb=" N GLN B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 198 through 213 removed outlier: 3.937A pdb=" N ALA B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 239 through 259 Processing helix chain 'B' and resid 291 through 295 removed outlier: 4.125A pdb=" N ALA B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 291 through 295' Processing helix chain 'C' and resid 25 through 28 Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 68 through 81 Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 133 through 145 removed outlier: 4.543A pdb=" N GLN C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 168 through 178 Processing helix chain 'C' and resid 182 through 188 removed outlier: 3.698A pdb=" N LEU C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 213 removed outlier: 3.711A pdb=" N THR C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA C 209 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET C 210 " --> pdb=" O GLN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 230 Processing helix chain 'C' and resid 235 through 259 removed outlier: 4.172A pdb=" N LEU C 238 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER C 239 " --> pdb=" O GLY C 236 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE C 259 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 28 Processing helix chain 'D' and resid 36 through 44 removed outlier: 3.832A pdb=" N GLU D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 54 Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 68 through 81 Processing helix chain 'D' and resid 89 through 96 Processing helix chain 'D' and resid 133 through 145 removed outlier: 3.531A pdb=" N VAL D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLN D 145 " --> pdb=" O ALA D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 178 Processing helix chain 'D' and resid 182 through 188 removed outlier: 3.628A pdb=" N ASN D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 210 removed outlier: 3.820A pdb=" N THR D 201 " --> pdb=" O THR D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 231 removed outlier: 3.507A pdb=" N THR D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 259 Processing helix chain 'E' and resid 25 through 28 Processing helix chain 'E' and resid 38 through 43 Processing helix chain 'E' and resid 49 through 53 Processing helix chain 'E' and resid 57 through 61 Processing helix chain 'E' and resid 68 through 81 removed outlier: 3.612A pdb=" N LEU E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 96 Processing helix chain 'E' and resid 107 through 112 Processing helix chain 'E' and resid 133 through 145 removed outlier: 3.577A pdb=" N CYS E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN E 145 " --> pdb=" O ALA E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 168 through 177 removed outlier: 3.537A pdb=" N GLU E 176 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 188 Processing helix chain 'E' and resid 197 through 211 removed outlier: 3.623A pdb=" N THR E 201 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 231 removed outlier: 3.566A pdb=" N THR E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 226 through 231' Processing helix chain 'E' and resid 238 through 259 removed outlier: 4.490A pdb=" N GLU E 258 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 28 Processing helix chain 'F' and resid 36 through 42 removed outlier: 3.582A pdb=" N LYS F 40 " --> pdb=" O ASN F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 53 Processing helix chain 'F' and resid 57 through 61 Processing helix chain 'F' and resid 68 through 81 removed outlier: 3.691A pdb=" N LYS F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 96 Processing helix chain 'F' and resid 133 through 143 removed outlier: 3.512A pdb=" N CYS F 137 " --> pdb=" O LYS F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 150 No H-bonds generated for 'chain 'F' and resid 148 through 150' Processing helix chain 'F' and resid 168 through 178 removed outlier: 4.083A pdb=" N ARG F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR F 178 " --> pdb=" O VAL F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 186 removed outlier: 3.819A pdb=" N LEU F 186 " --> pdb=" O GLY F 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 182 through 186' Processing helix chain 'F' and resid 199 through 213 removed outlier: 3.855A pdb=" N ALA F 209 " --> pdb=" O TYR F 205 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 231 Processing helix chain 'F' and resid 237 through 259 removed outlier: 4.027A pdb=" N MET F 243 " --> pdb=" O ALA F 240 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS F 244 " --> pdb=" O ARG F 241 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET F 251 " --> pdb=" O PHE F 248 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU F 253 " --> pdb=" O ARG F 250 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP F 257 " --> pdb=" O ARG F 254 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU F 258 " --> pdb=" O LEU F 255 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE F 259 " --> pdb=" O ALA F 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 28 Processing helix chain 'G' and resid 38 through 42 Processing helix chain 'G' and resid 49 through 53 Processing helix chain 'G' and resid 57 through 61 Processing helix chain 'G' and resid 68 through 81 Processing helix chain 'G' and resid 89 through 96 Processing helix chain 'G' and resid 107 through 112 Processing helix chain 'G' and resid 133 through 145 removed outlier: 4.763A pdb=" N GLN G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 150 No H-bonds generated for 'chain 'G' and resid 148 through 150' Processing helix chain 'G' and resid 168 through 177 removed outlier: 3.689A pdb=" N ARG G 177 " --> pdb=" O ALA G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 188 removed outlier: 4.055A pdb=" N LEU G 186 " --> pdb=" O GLY G 182 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP G 187 " --> pdb=" O SER G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 213 removed outlier: 3.973A pdb=" N THR G 201 " --> pdb=" O THR G 197 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA G 209 " --> pdb=" O TYR G 205 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 230 Processing helix chain 'G' and resid 235 through 259 removed outlier: 3.830A pdb=" N LEU G 238 " --> pdb=" O ARG G 235 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER G 239 " --> pdb=" O GLY G 236 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN G 242 " --> pdb=" O SER G 239 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU G 245 " --> pdb=" O GLN G 242 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG G 254 " --> pdb=" O MET G 251 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU G 258 " --> pdb=" O LEU G 255 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE G 259 " --> pdb=" O ALA G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 295 removed outlier: 4.410A pdb=" N ALA G 295 " --> pdb=" O ILE G 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 291 through 295' Processing helix chain 'H' and resid 25 through 28 Processing helix chain 'H' and resid 35 through 44 removed outlier: 3.752A pdb=" N GLU H 43 " --> pdb=" O LYS H 39 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 53 Processing helix chain 'H' and resid 57 through 59 No H-bonds generated for 'chain 'H' and resid 57 through 59' Processing helix chain 'H' and resid 68 through 81 removed outlier: 3.512A pdb=" N LEU H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU H 81 " --> pdb=" O GLU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 97 Processing helix chain 'H' and resid 133 through 145 removed outlier: 4.716A pdb=" N GLN H 145 " --> pdb=" O ALA H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 177 removed outlier: 3.516A pdb=" N LEU H 172 " --> pdb=" O PRO H 168 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 188 removed outlier: 3.673A pdb=" N ASN H 188 " --> pdb=" O ASP H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 210 removed outlier: 3.809A pdb=" N THR H 201 " --> pdb=" O THR H 197 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU H 204 " --> pdb=" O GLN H 200 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR H 205 " --> pdb=" O THR H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 231 removed outlier: 3.594A pdb=" N THR H 230 " --> pdb=" O ALA H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 259 removed outlier: 3.838A pdb=" N MET H 243 " --> pdb=" O SER H 239 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS H 244 " --> pdb=" O ALA H 240 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 123 through 125 removed outlier: 3.648A pdb=" N ILE A 265 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 298 through 300 removed outlier: 3.552A pdb=" N THR B 298 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 263 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N MET B 125 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE B 265 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS B 156 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU B 219 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N MET B 158 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N VAL B 221 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE B 160 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 301 through 303 removed outlier: 3.567A pdb=" N ILE B 311 " --> pdb=" O ARG B 303 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 123 through 125 Processing sheet with id= E, first strand: chain 'C' and resid 311 through 313 Processing sheet with id= F, first strand: chain 'D' and resid 218 through 221 removed outlier: 6.600A pdb=" N ALA D 262 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL D 221 " --> pdb=" O ALA D 262 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL D 264 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N GLU D 124 " --> pdb=" O THR D 297 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG D 299 " --> pdb=" O GLU D 124 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 158 through 161 removed outlier: 6.117A pdb=" N ALA D 190 " --> pdb=" O TYR D 159 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ASP D 161 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA D 192 " --> pdb=" O ASP D 161 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 300 through 303 removed outlier: 3.605A pdb=" N ILE D 311 " --> pdb=" O ARG D 303 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 218 through 220 removed outlier: 7.255A pdb=" N ALA E 262 " --> pdb=" O LEU E 219 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'F' and resid 298 through 300 removed outlier: 6.838A pdb=" N VAL F 263 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N MET F 125 " --> pdb=" O VAL F 263 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE F 265 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 301 through 303 removed outlier: 3.938A pdb=" N PHE F 327 " --> pdb=" O ARG F 310 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS F 312 " --> pdb=" O ALA F 325 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 264 through 266 removed outlier: 6.158A pdb=" N THR G 123 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR G 298 " --> pdb=" O GLU G 124 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N PHE G 126 " --> pdb=" O THR G 298 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU G 300 " --> pdb=" O PHE G 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'H' and resid 122 through 125 removed outlier: 6.875A pdb=" N VAL H 263 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N MET H 125 " --> pdb=" O VAL H 263 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE H 265 " --> pdb=" O MET H 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR H 266 " --> pdb=" O VAL H 221 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS H 156 " --> pdb=" O ALA H 217 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU H 219 " --> pdb=" O LYS H 156 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N MET H 158 " --> pdb=" O LEU H 219 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL H 221 " --> pdb=" O MET H 158 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE H 160 " --> pdb=" O VAL H 221 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA H 190 " --> pdb=" O TYR H 159 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ASP H 161 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA H 192 " --> pdb=" O ASP H 161 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 301 through 303 544 hydrogen bonds defined for protein. 1437 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: 4.61 Time building geometry restraints manager: 7.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6086 1.34 - 1.46: 3112 1.46 - 1.58: 8960 1.58 - 1.69: 25 1.69 - 1.81: 160 Bond restraints: 18343 Sorted by residual: bond pdb=" CG PRO C 83 " pdb=" CD PRO C 83 " ideal model delta sigma weight residual 1.503 1.286 0.217 3.40e-02 8.65e+02 4.06e+01 bond pdb=" CB PRO C 83 " pdb=" CG PRO C 83 " ideal model delta sigma weight residual 1.492 1.688 -0.196 5.00e-02 4.00e+02 1.53e+01 bond pdb=" N PRO C 83 " pdb=" CD PRO C 83 " ideal model delta sigma weight residual 1.473 1.515 -0.042 1.40e-02 5.10e+03 9.02e+00 bond pdb=" N PRO C 83 " pdb=" CA PRO C 83 " ideal model delta sigma weight residual 1.469 1.450 0.019 1.28e-02 6.10e+03 2.22e+00 bond pdb=" C4 ADP B 600 " pdb=" C5 ADP B 600 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.15e+00 ... (remaining 18338 not shown) Histogram of bond angle deviations from ideal: 89.22 - 98.72: 4 98.72 - 108.22: 595 108.22 - 117.72: 13090 117.72 - 127.22: 10950 127.22 - 136.72: 107 Bond angle restraints: 24746 Sorted by residual: angle pdb=" CA PRO C 83 " pdb=" N PRO C 83 " pdb=" CD PRO C 83 " ideal model delta sigma weight residual 112.00 96.48 15.52 1.40e+00 5.10e-01 1.23e+02 angle pdb=" N PRO C 83 " pdb=" CD PRO C 83 " pdb=" CG PRO C 83 " ideal model delta sigma weight residual 103.20 89.22 13.98 1.50e+00 4.44e-01 8.69e+01 angle pdb=" CA PRO C 83 " pdb=" CB PRO C 83 " pdb=" CG PRO C 83 " ideal model delta sigma weight residual 104.50 93.55 10.95 1.90e+00 2.77e-01 3.32e+01 angle pdb=" N ILE A 314 " pdb=" CA ILE A 314 " pdb=" C ILE A 314 " ideal model delta sigma weight residual 113.10 107.75 5.35 9.70e-01 1.06e+00 3.04e+01 angle pdb=" N MET H 326 " pdb=" CA MET H 326 " pdb=" C MET H 326 " ideal model delta sigma weight residual 109.85 115.92 -6.07 1.58e+00 4.01e-01 1.48e+01 ... (remaining 24741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.42: 10579 28.42 - 56.84: 419 56.84 - 85.25: 45 85.25 - 113.67: 8 113.67 - 142.09: 13 Dihedral angle restraints: 11064 sinusoidal: 4445 harmonic: 6619 Sorted by residual: dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 82.09 -142.09 1 2.00e+01 2.50e-03 4.29e+01 dihedral pdb=" O1B ADP B 600 " pdb=" O3A ADP B 600 " pdb=" PB ADP B 600 " pdb=" PA ADP B 600 " ideal model delta sinusoidal sigma weight residual 300.00 162.60 137.40 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" C5' ADP B 600 " pdb=" O5' ADP B 600 " pdb=" PA ADP B 600 " pdb=" O2A ADP B 600 " ideal model delta sinusoidal sigma weight residual -60.00 76.96 -136.96 1 2.00e+01 2.50e-03 4.15e+01 ... (remaining 11061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2213 0.046 - 0.092: 477 0.092 - 0.138: 141 0.138 - 0.184: 8 0.184 - 0.230: 1 Chirality restraints: 2840 Sorted by residual: chirality pdb=" CB ILE G 314 " pdb=" CA ILE G 314 " pdb=" CG1 ILE G 314 " pdb=" CG2 ILE G 314 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB ILE C 314 " pdb=" CA ILE C 314 " pdb=" CG1 ILE C 314 " pdb=" CG2 ILE C 314 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.26e-01 chirality pdb=" CB ILE E 314 " pdb=" CA ILE E 314 " pdb=" CG1 ILE E 314 " pdb=" CG2 ILE E 314 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.91e-01 ... (remaining 2837 not shown) Planarity restraints: 3163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 82 " 0.061 5.00e-02 4.00e+02 8.25e-02 1.09e+01 pdb=" N PRO C 83 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 83 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 83 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 23 " 0.052 5.00e-02 4.00e+02 7.84e-02 9.83e+00 pdb=" N PRO F 24 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO F 24 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 24 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 21 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO B 22 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 22 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 22 " -0.034 5.00e-02 4.00e+02 ... (remaining 3160 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 226 2.58 - 3.16: 15844 3.16 - 3.74: 28447 3.74 - 4.32: 39045 4.32 - 4.90: 63291 Nonbonded interactions: 146853 Sorted by model distance: nonbonded pdb=" O2A ADP G 600 " pdb="MG MG G 601 " model vdw 2.003 2.170 nonbonded pdb=" O1A ADP E 600 " pdb="MG MG E 601 " model vdw 2.004 2.170 nonbonded pdb=" O3B ADP B 600 " pdb="MG MG B 601 " model vdw 2.016 2.170 nonbonded pdb=" O3A ADP H 600 " pdb="MG MG H 601 " model vdw 2.025 2.170 nonbonded pdb=" O3A ADP B 600 " pdb="MG MG B 601 " model vdw 2.030 2.170 ... (remaining 146848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 21 through 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 through 270 or resid 291 through 336 or \ resid 600 through 601)) selection = (chain 'B' and (resid 21 through 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 through 270 or resid 291 through 336 or \ resid 600 through 601)) selection = (chain 'C' and (resid 21 through 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 through 270 or resid 291 through 336 or \ resid 600 through 601)) selection = (chain 'D' and (resid 21 through 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 through 336 or resid 600 through 601)) selection = (chain 'E' and (resid 21 through 270 or resid 291 through 336 or resid 600 throu \ gh 601)) selection = (chain 'F' and (resid 21 through 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 through 270 or resid 291 through 336 or \ resid 600 through 601)) selection = (chain 'G' and (resid 21 through 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 through 270 or resid 291 through 336 or \ resid 600 through 601)) selection = (chain 'H' and (resid 21 through 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 through 336 or resid 600 through 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.290 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 47.730 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 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 : 0.003 0.217 18343 Z= 0.199 Angle : 0.733 15.524 24746 Z= 0.383 Chirality : 0.042 0.230 2840 Planarity : 0.005 0.082 3163 Dihedral : 15.842 142.089 6826 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.70 % Allowed : 6.41 % Favored : 92.89 % Rotamer: Outliers : 0.05 % Allowed : 0.22 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.17), residues: 2277 helix: -0.62 (0.16), residues: 1067 sheet: -1.65 (0.31), residues: 309 loop : -2.09 (0.19), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 244 PHE 0.020 0.001 PHE A 126 TYR 0.022 0.001 TYR C 315 ARG 0.014 0.001 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 473 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.7678 (p) cc_final: 0.7352 (t) REVERT: B 50 GLU cc_start: 0.6821 (mt-10) cc_final: 0.5237 (pt0) REVERT: B 253 LEU cc_start: 0.7411 (mm) cc_final: 0.7060 (mt) REVERT: B 313 LYS cc_start: 0.6027 (mttp) cc_final: 0.5558 (pttp) REVERT: C 97 SER cc_start: 0.6994 (m) cc_final: 0.6657 (p) REVERT: C 111 LYS cc_start: 0.8180 (ttpp) cc_final: 0.7670 (mttm) REVERT: C 118 GLU cc_start: 0.7204 (pt0) cc_final: 0.6915 (tt0) REVERT: C 124 GLU cc_start: 0.7603 (mt-10) cc_final: 0.6970 (tt0) REVERT: C 126 PHE cc_start: 0.7481 (m-10) cc_final: 0.6978 (m-80) REVERT: C 242 GLN cc_start: 0.8005 (mm110) cc_final: 0.7525 (mm-40) REVERT: C 250 ARG cc_start: 0.7751 (ttp-110) cc_final: 0.7317 (mtp-110) REVERT: C 255 LEU cc_start: 0.7774 (tt) cc_final: 0.7572 (tp) REVERT: C 315 TYR cc_start: 0.7331 (t80) cc_final: 0.6962 (t80) REVERT: D 97 SER cc_start: 0.7961 (t) cc_final: 0.7711 (p) REVERT: D 170 ARG cc_start: 0.7558 (tpp-160) cc_final: 0.7247 (tpp80) REVERT: D 178 TYR cc_start: 0.8020 (m-10) cc_final: 0.7812 (m-10) REVERT: D 208 SER cc_start: 0.8620 (t) cc_final: 0.8362 (t) REVERT: D 267 ASN cc_start: 0.7747 (t0) cc_final: 0.7542 (t0) REVERT: D 326 MET cc_start: 0.6806 (mmp) cc_final: 0.6589 (tmm) REVERT: E 140 LEU cc_start: 0.7384 (tp) cc_final: 0.6726 (mt) REVERT: F 124 GLU cc_start: 0.7391 (tt0) cc_final: 0.6950 (tt0) REVERT: F 301 TYR cc_start: 0.7670 (t80) cc_final: 0.7279 (t80) REVERT: G 68 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7317 (mm-30) REVERT: G 126 PHE cc_start: 0.6690 (m-80) cc_final: 0.5868 (m-10) REVERT: G 130 ARG cc_start: 0.6596 (mtt90) cc_final: 0.6177 (mmm160) REVERT: G 154 GLU cc_start: 0.7181 (pt0) cc_final: 0.6339 (tp30) REVERT: G 326 MET cc_start: 0.5126 (mmp) cc_final: 0.4495 (mmp) REVERT: H 210 MET cc_start: 0.8613 (ptm) cc_final: 0.8276 (ptp) REVERT: H 250 ARG cc_start: 0.7418 (ttp-110) cc_final: 0.7162 (ttp-110) REVERT: H 267 ASN cc_start: 0.7491 (t0) cc_final: 0.7143 (t0) outliers start: 1 outliers final: 0 residues processed: 473 average time/residue: 0.3528 time to fit residues: 237.6285 Evaluate side-chains 322 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 0.9990 chunk 174 optimal weight: 6.9990 chunk 96 optimal weight: 0.0070 chunk 59 optimal weight: 0.0040 chunk 117 optimal weight: 5.9990 chunk 93 optimal weight: 0.0050 chunk 180 optimal weight: 0.0670 chunk 69 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 208 optimal weight: 0.6980 overall best weight: 0.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 202 GLN B 23 GLN B 101 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 330 ASN ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN E 188 ASN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 GLN ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 18343 Z= 0.151 Angle : 0.651 7.799 24746 Z= 0.310 Chirality : 0.041 0.209 2840 Planarity : 0.004 0.057 3163 Dihedral : 10.145 135.129 2629 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.53 % Favored : 93.81 % Rotamer: Outliers : 1.46 % Allowed : 9.17 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.17), residues: 2277 helix: -0.43 (0.16), residues: 1072 sheet: -1.58 (0.30), residues: 322 loop : -2.02 (0.19), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 47 PHE 0.030 0.001 PHE A 327 TYR 0.018 0.001 TYR E 315 ARG 0.007 0.001 ARG E 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 333 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7241 (mtt-85) REVERT: A 211 MET cc_start: 0.6198 (mmt) cc_final: 0.5949 (tpp) REVERT: A 229 ARG cc_start: 0.5008 (mmt180) cc_final: 0.4664 (mmp-170) REVERT: B 50 GLU cc_start: 0.6790 (mt-10) cc_final: 0.5478 (pt0) REVERT: B 253 LEU cc_start: 0.7250 (mm) cc_final: 0.6854 (mt) REVERT: C 80 LYS cc_start: 0.8425 (mtmm) cc_final: 0.7957 (mtmm) REVERT: C 97 SER cc_start: 0.7167 (m) cc_final: 0.6834 (p) REVERT: C 118 GLU cc_start: 0.7339 (pt0) cc_final: 0.6913 (tt0) REVERT: C 187 ASP cc_start: 0.7238 (OUTLIER) cc_final: 0.7016 (t0) REVERT: C 205 TYR cc_start: 0.8385 (m-10) cc_final: 0.8075 (m-10) REVERT: C 250 ARG cc_start: 0.7779 (ttp-110) cc_final: 0.7280 (mtp-110) REVERT: D 97 SER cc_start: 0.7998 (t) cc_final: 0.7762 (p) REVERT: D 250 ARG cc_start: 0.7488 (tpt170) cc_final: 0.7172 (ttm110) REVERT: D 301 TYR cc_start: 0.7822 (t80) cc_final: 0.7616 (t80) REVERT: D 304 LYS cc_start: 0.8671 (mmmt) cc_final: 0.7926 (tptp) REVERT: D 315 TYR cc_start: 0.6547 (OUTLIER) cc_final: 0.5690 (m-80) REVERT: D 326 MET cc_start: 0.6448 (mmp) cc_final: 0.6151 (tmm) REVERT: E 258 GLU cc_start: 0.7785 (pp20) cc_final: 0.7103 (pp20) REVERT: F 315 TYR cc_start: 0.6083 (m-10) cc_final: 0.5759 (m-10) REVERT: G 68 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7226 (mm-30) REVERT: G 130 ARG cc_start: 0.6602 (mtt90) cc_final: 0.6156 (mmm160) REVERT: G 156 LYS cc_start: 0.7689 (mtpp) cc_final: 0.7471 (mtpp) REVERT: G 326 MET cc_start: 0.4923 (mmp) cc_final: 0.4104 (mtm) REVERT: H 60 LEU cc_start: 0.6459 (OUTLIER) cc_final: 0.6013 (tt) REVERT: H 118 GLU cc_start: 0.7425 (tt0) cc_final: 0.6868 (pt0) REVERT: H 250 ARG cc_start: 0.7389 (ttp-110) cc_final: 0.7181 (ttp-110) outliers start: 27 outliers final: 10 residues processed: 343 average time/residue: 0.3256 time to fit residues: 162.9936 Evaluate side-chains 314 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 300 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 198 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 330 ASN D 62 ASN D 196 ASN D 200 GLN E 188 ASN E 206 GLN ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 GLN H 196 ASN H 200 GLN H 294 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.084 18343 Z= 0.583 Angle : 0.865 9.735 24746 Z= 0.423 Chirality : 0.053 0.202 2840 Planarity : 0.006 0.058 3163 Dihedral : 10.232 146.567 2629 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.70 % Allowed : 8.17 % Favored : 91.13 % Rotamer: Outliers : 2.91 % Allowed : 14.02 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.16), residues: 2277 helix: -1.08 (0.15), residues: 1088 sheet: -2.40 (0.29), residues: 273 loop : -2.32 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 138 PHE 0.026 0.002 PHE A 327 TYR 0.036 0.003 TYR C 159 ARG 0.006 0.001 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 348 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7579 (mtt-85) REVERT: A 125 MET cc_start: 0.6096 (mmm) cc_final: 0.5044 (mtt) REVERT: A 219 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8593 (tt) REVERT: B 253 LEU cc_start: 0.7491 (mm) cc_final: 0.7142 (mp) REVERT: B 313 LYS cc_start: 0.6430 (mttp) cc_final: 0.5897 (pttp) REVERT: C 68 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7451 (tp30) REVERT: C 163 GLU cc_start: 0.6913 (tp30) cc_final: 0.6087 (tp30) REVERT: C 315 TYR cc_start: 0.7441 (t80) cc_final: 0.6718 (t80) REVERT: D 23 GLN cc_start: 0.7017 (tp-100) cc_final: 0.6701 (tp-100) REVERT: D 97 SER cc_start: 0.8149 (t) cc_final: 0.7891 (p) REVERT: D 208 SER cc_start: 0.8940 (t) cc_final: 0.8719 (t) REVERT: D 315 TYR cc_start: 0.6941 (OUTLIER) cc_final: 0.5985 (m-80) REVERT: D 326 MET cc_start: 0.7029 (mmp) cc_final: 0.6805 (tmm) REVERT: E 94 GLN cc_start: 0.6886 (mt0) cc_final: 0.6464 (mp10) REVERT: E 250 ARG cc_start: 0.7171 (ttp-110) cc_final: 0.6729 (tpp-160) REVERT: E 251 MET cc_start: 0.7391 (tpt) cc_final: 0.7156 (tpt) REVERT: E 336 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.7110 (m-30) REVERT: F 43 GLU cc_start: 0.7339 (mp0) cc_final: 0.6895 (mp0) REVERT: F 48 THR cc_start: 0.8449 (m) cc_final: 0.8094 (p) REVERT: F 112 LEU cc_start: 0.7023 (mp) cc_final: 0.6806 (tp) REVERT: G 118 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7098 (pt0) REVERT: G 130 ARG cc_start: 0.7111 (mtt90) cc_final: 0.6565 (mmm160) REVERT: G 219 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8583 (tt) REVERT: G 326 MET cc_start: 0.6032 (mmp) cc_final: 0.4923 (mtm) REVERT: H 64 LYS cc_start: 0.4958 (tmmt) cc_final: 0.4253 (mmtt) REVERT: H 100 ILE cc_start: 0.7814 (mm) cc_final: 0.7394 (mm) REVERT: H 250 ARG cc_start: 0.7447 (ttp-110) cc_final: 0.7181 (ttp-110) outliers start: 54 outliers final: 27 residues processed: 373 average time/residue: 0.3222 time to fit residues: 177.8692 Evaluate side-chains 336 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 303 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 336 ASP Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 269 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 7.9990 chunk 157 optimal weight: 0.8980 chunk 108 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 99 optimal weight: 0.4980 chunk 140 optimal weight: 0.0980 chunk 209 optimal weight: 1.9990 chunk 222 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 199 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 93 HIS C 206 GLN C 330 ASN E 206 GLN E 242 GLN F 114 GLN ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 GLN H 206 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18343 Z= 0.186 Angle : 0.647 7.084 24746 Z= 0.307 Chirality : 0.041 0.175 2840 Planarity : 0.004 0.054 3163 Dihedral : 9.195 141.068 2629 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.70 % Allowed : 6.19 % Favored : 93.10 % Rotamer: Outliers : 2.64 % Allowed : 17.10 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.17), residues: 2277 helix: -0.69 (0.16), residues: 1076 sheet: -2.05 (0.28), residues: 300 loop : -2.17 (0.18), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 47 PHE 0.026 0.001 PHE A 327 TYR 0.017 0.001 TYR H 315 ARG 0.006 0.000 ARG C 250 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 333 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.6039 (mmm) cc_final: 0.4979 (mtt) REVERT: B 39 LYS cc_start: 0.7613 (mtmm) cc_final: 0.6691 (ttpp) REVERT: B 253 LEU cc_start: 0.7313 (mm) cc_final: 0.6970 (mp) REVERT: C 163 GLU cc_start: 0.6576 (tp30) cc_final: 0.5824 (tp30) REVERT: C 205 TYR cc_start: 0.8245 (m-10) cc_final: 0.7793 (m-10) REVERT: C 315 TYR cc_start: 0.7550 (t80) cc_final: 0.6791 (t80) REVERT: D 315 TYR cc_start: 0.6915 (OUTLIER) cc_final: 0.5964 (m-80) REVERT: D 326 MET cc_start: 0.6960 (mmp) cc_final: 0.6681 (tmm) REVERT: E 126 PHE cc_start: 0.7331 (m-80) cc_final: 0.6946 (m-10) REVERT: E 143 THR cc_start: 0.7701 (OUTLIER) cc_final: 0.7350 (p) REVERT: E 188 ASN cc_start: 0.7814 (m-40) cc_final: 0.7304 (m-40) REVERT: E 250 ARG cc_start: 0.7169 (ttp-110) cc_final: 0.6715 (tpp-160) REVERT: F 43 GLU cc_start: 0.7252 (mp0) cc_final: 0.6724 (mp0) REVERT: F 64 LYS cc_start: 0.7997 (mmmt) cc_final: 0.7735 (mtpp) REVERT: G 118 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6993 (pt0) REVERT: G 130 ARG cc_start: 0.7100 (mtt90) cc_final: 0.6646 (mmt180) REVERT: G 219 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8440 (tt) REVERT: H 64 LYS cc_start: 0.4980 (tmmt) cc_final: 0.4231 (mmtt) REVERT: H 100 ILE cc_start: 0.7652 (mm) cc_final: 0.7223 (mm) REVERT: H 118 GLU cc_start: 0.7348 (tt0) cc_final: 0.6824 (pt0) REVERT: H 250 ARG cc_start: 0.7391 (ttp-110) cc_final: 0.7147 (ttp-110) outliers start: 49 outliers final: 26 residues processed: 360 average time/residue: 0.3310 time to fit residues: 175.0174 Evaluate side-chains 322 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 292 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 210 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 189 optimal weight: 0.2980 chunk 153 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN E 244 HIS H 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18343 Z= 0.289 Angle : 0.688 8.916 24746 Z= 0.326 Chirality : 0.043 0.159 2840 Planarity : 0.004 0.052 3163 Dihedral : 8.605 135.893 2629 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.55 % Favored : 91.79 % Rotamer: Outliers : 3.18 % Allowed : 18.77 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.17), residues: 2277 helix: -0.73 (0.16), residues: 1087 sheet: -2.34 (0.28), residues: 300 loop : -2.18 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 47 PHE 0.025 0.002 PHE A 327 TYR 0.016 0.001 TYR H 315 ARG 0.006 0.000 ARG H 303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 295 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.6183 (mmm) cc_final: 0.5009 (mtt) REVERT: B 253 LEU cc_start: 0.7351 (mm) cc_final: 0.7003 (mp) REVERT: C 94 GLN cc_start: 0.7158 (pp30) cc_final: 0.6675 (mt0) REVERT: C 163 GLU cc_start: 0.6668 (tp30) cc_final: 0.5894 (tp30) REVERT: C 202 GLN cc_start: 0.7394 (mp10) cc_final: 0.7105 (tt0) REVERT: C 242 GLN cc_start: 0.7433 (mm110) cc_final: 0.7081 (mm-40) REVERT: C 315 TYR cc_start: 0.7597 (t80) cc_final: 0.7087 (t80) REVERT: D 23 GLN cc_start: 0.6829 (tp-100) cc_final: 0.6594 (tp-100) REVERT: D 249 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7510 (mm) REVERT: D 315 TYR cc_start: 0.6954 (OUTLIER) cc_final: 0.5991 (m-80) REVERT: E 94 GLN cc_start: 0.6819 (mt0) cc_final: 0.6443 (mp10) REVERT: E 143 THR cc_start: 0.7792 (OUTLIER) cc_final: 0.7313 (p) REVERT: E 247 ARG cc_start: 0.7508 (ptm-80) cc_final: 0.7197 (ttt-90) REVERT: E 250 ARG cc_start: 0.7181 (ttp-110) cc_final: 0.6767 (tpp-160) REVERT: F 43 GLU cc_start: 0.7327 (mp0) cc_final: 0.7000 (mp0) REVERT: F 48 THR cc_start: 0.8385 (m) cc_final: 0.7992 (p) REVERT: F 64 LYS cc_start: 0.8065 (mmmt) cc_final: 0.7705 (mtpp) REVERT: F 126 PHE cc_start: 0.6825 (m-80) cc_final: 0.6574 (m-80) REVERT: F 202 GLN cc_start: 0.7698 (pt0) cc_final: 0.7203 (tp40) REVERT: G 118 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7048 (pt0) REVERT: G 130 ARG cc_start: 0.7170 (mtt90) cc_final: 0.6638 (mmm160) REVERT: G 291 ILE cc_start: 0.4541 (OUTLIER) cc_final: 0.3742 (tp) REVERT: H 100 ILE cc_start: 0.7721 (mm) cc_final: 0.7370 (mm) REVERT: H 118 GLU cc_start: 0.7434 (tt0) cc_final: 0.6870 (pt0) REVERT: H 250 ARG cc_start: 0.7402 (ttp-110) cc_final: 0.7154 (ttp-110) outliers start: 59 outliers final: 37 residues processed: 331 average time/residue: 0.3243 time to fit residues: 158.0930 Evaluate side-chains 325 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 283 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 269 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 222 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 116 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 ASN ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18343 Z= 0.229 Angle : 0.650 8.440 24746 Z= 0.306 Chirality : 0.041 0.155 2840 Planarity : 0.004 0.052 3163 Dihedral : 7.976 129.052 2629 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.70 % Allowed : 6.72 % Favored : 92.58 % Rotamer: Outliers : 3.67 % Allowed : 19.53 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.17), residues: 2277 helix: -0.58 (0.16), residues: 1074 sheet: -2.14 (0.28), residues: 302 loop : -2.11 (0.19), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 47 PHE 0.025 0.001 PHE A 327 TYR 0.016 0.001 TYR B 301 ARG 0.007 0.000 ARG C 250 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 297 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.6182 (mmm) cc_final: 0.5027 (mtt) REVERT: A 243 MET cc_start: 0.7209 (ttt) cc_final: 0.6943 (ttp) REVERT: A 292 ILE cc_start: 0.7125 (tp) cc_final: 0.6859 (mm) REVERT: B 49 VAL cc_start: 0.7934 (OUTLIER) cc_final: 0.7725 (t) REVERT: B 128 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6600 (pt0) REVERT: B 253 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7027 (mp) REVERT: C 94 GLN cc_start: 0.7151 (pp30) cc_final: 0.6691 (mt0) REVERT: C 163 GLU cc_start: 0.6614 (tp30) cc_final: 0.5886 (tp30) REVERT: C 242 GLN cc_start: 0.7331 (mm110) cc_final: 0.6993 (mm-40) REVERT: C 315 TYR cc_start: 0.7541 (t80) cc_final: 0.6960 (t80) REVERT: C 332 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8649 (p0) REVERT: D 249 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7520 (mm) REVERT: D 332 ASP cc_start: 0.8299 (p0) cc_final: 0.7902 (p0) REVERT: E 94 GLN cc_start: 0.6786 (mt0) cc_final: 0.6408 (mp10) REVERT: E 136 ILE cc_start: 0.7824 (pt) cc_final: 0.6942 (mm) REVERT: E 143 THR cc_start: 0.7769 (OUTLIER) cc_final: 0.7307 (p) REVERT: E 247 ARG cc_start: 0.7488 (ptm-80) cc_final: 0.7218 (ttt-90) REVERT: F 43 GLU cc_start: 0.7327 (mp0) cc_final: 0.6968 (mp0) REVERT: F 64 LYS cc_start: 0.8070 (mmmt) cc_final: 0.7795 (mtpp) REVERT: F 126 PHE cc_start: 0.6866 (m-80) cc_final: 0.6659 (m-80) REVERT: F 202 GLN cc_start: 0.7585 (pt0) cc_final: 0.7255 (tp40) REVERT: G 118 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7041 (pt0) REVERT: G 130 ARG cc_start: 0.7206 (mtt90) cc_final: 0.6668 (mmm160) REVERT: G 219 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8426 (tt) REVERT: H 94 GLN cc_start: 0.7347 (mt0) cc_final: 0.6683 (pp30) REVERT: H 100 ILE cc_start: 0.7752 (mm) cc_final: 0.7377 (mm) REVERT: H 118 GLU cc_start: 0.7401 (tt0) cc_final: 0.6806 (pt0) REVERT: H 250 ARG cc_start: 0.7417 (ttp-110) cc_final: 0.7157 (ttp-110) REVERT: H 267 ASN cc_start: 0.8129 (t0) cc_final: 0.7831 (m-40) outliers start: 68 outliers final: 43 residues processed: 341 average time/residue: 0.3157 time to fit residues: 160.1668 Evaluate side-chains 323 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 272 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 292 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 chunk 187 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 221 optimal weight: 0.9990 chunk 138 optimal weight: 0.4980 chunk 135 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN E 290 ASN F 135 GLN ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18343 Z= 0.201 Angle : 0.642 8.612 24746 Z= 0.301 Chirality : 0.041 0.151 2840 Planarity : 0.003 0.049 3163 Dihedral : 7.372 118.705 2629 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.70 % Allowed : 6.72 % Favored : 92.58 % Rotamer: Outliers : 3.72 % Allowed : 19.63 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.17), residues: 2277 helix: -0.42 (0.16), residues: 1064 sheet: -1.97 (0.29), residues: 302 loop : -2.05 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 294 PHE 0.013 0.001 PHE G 327 TYR 0.020 0.001 TYR E 315 ARG 0.008 0.000 ARG C 250 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 288 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.6237 (mmm) cc_final: 0.5004 (mtt) REVERT: A 292 ILE cc_start: 0.7102 (tp) cc_final: 0.6806 (mm) REVERT: B 128 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6482 (pt0) REVERT: B 253 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6960 (mp) REVERT: C 94 GLN cc_start: 0.7117 (pp30) cc_final: 0.6656 (mt0) REVERT: C 163 GLU cc_start: 0.6553 (tp30) cc_final: 0.5827 (tp30) REVERT: C 242 GLN cc_start: 0.7325 (mm110) cc_final: 0.6973 (mm-40) REVERT: C 315 TYR cc_start: 0.7533 (t80) cc_final: 0.6920 (t80) REVERT: D 249 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7533 (mm) REVERT: D 250 ARG cc_start: 0.7543 (tpt170) cc_final: 0.7284 (ttp-110) REVERT: D 332 ASP cc_start: 0.8306 (p0) cc_final: 0.8079 (p0) REVERT: E 94 GLN cc_start: 0.6750 (mt0) cc_final: 0.6401 (mp10) REVERT: E 136 ILE cc_start: 0.7819 (pt) cc_final: 0.6865 (mm) REVERT: E 143 THR cc_start: 0.7767 (OUTLIER) cc_final: 0.7322 (p) REVERT: E 247 ARG cc_start: 0.7501 (ptm-80) cc_final: 0.7206 (ttt-90) REVERT: E 324 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6206 (mm-30) REVERT: F 43 GLU cc_start: 0.7356 (mp0) cc_final: 0.6980 (mp0) REVERT: F 126 PHE cc_start: 0.6939 (m-80) cc_final: 0.6730 (m-80) REVERT: G 68 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7338 (mm-30) REVERT: G 118 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7021 (pt0) REVERT: G 130 ARG cc_start: 0.7242 (mtt90) cc_final: 0.6706 (mmm160) REVERT: H 94 GLN cc_start: 0.7320 (mt0) cc_final: 0.6680 (pp30) REVERT: H 100 ILE cc_start: 0.7652 (mm) cc_final: 0.7290 (mm) REVERT: H 118 GLU cc_start: 0.7371 (tt0) cc_final: 0.6403 (tt0) REVERT: H 250 ARG cc_start: 0.7433 (ttp-110) cc_final: 0.7178 (ttp-110) REVERT: H 267 ASN cc_start: 0.8081 (t0) cc_final: 0.7817 (m-40) outliers start: 69 outliers final: 46 residues processed: 333 average time/residue: 0.3063 time to fit residues: 154.0317 Evaluate side-chains 318 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 267 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 174 optimal weight: 9.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN E 290 ASN F 135 GLN H 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18343 Z= 0.265 Angle : 0.674 9.233 24746 Z= 0.317 Chirality : 0.042 0.195 2840 Planarity : 0.004 0.049 3163 Dihedral : 7.202 112.109 2629 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.47 % Favored : 91.83 % Rotamer: Outliers : 3.88 % Allowed : 19.63 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.17), residues: 2277 helix: -0.53 (0.16), residues: 1076 sheet: -2.01 (0.29), residues: 300 loop : -2.14 (0.19), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 294 PHE 0.014 0.001 PHE G 126 TYR 0.022 0.001 TYR B 301 ARG 0.009 0.000 ARG C 250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 282 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.6228 (mmm) cc_final: 0.5001 (mtt) REVERT: A 243 MET cc_start: 0.7208 (ttt) cc_final: 0.6945 (ttp) REVERT: A 292 ILE cc_start: 0.7091 (tp) cc_final: 0.6793 (mm) REVERT: B 128 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6467 (pt0) REVERT: B 253 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7019 (mp) REVERT: B 258 GLU cc_start: 0.7006 (tt0) cc_final: 0.6698 (pt0) REVERT: C 94 GLN cc_start: 0.7113 (pp30) cc_final: 0.6658 (mt0) REVERT: C 101 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7308 (tp40) REVERT: C 163 GLU cc_start: 0.6627 (tp30) cc_final: 0.5882 (tp30) REVERT: C 242 GLN cc_start: 0.7329 (mm110) cc_final: 0.6962 (mm-40) REVERT: C 315 TYR cc_start: 0.7572 (t80) cc_final: 0.6931 (t80) REVERT: D 249 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7529 (mm) REVERT: D 332 ASP cc_start: 0.8299 (p0) cc_final: 0.8050 (p0) REVERT: E 94 GLN cc_start: 0.6729 (mt0) cc_final: 0.6370 (mp10) REVERT: E 136 ILE cc_start: 0.7831 (pt) cc_final: 0.6938 (mm) REVERT: E 143 THR cc_start: 0.7795 (OUTLIER) cc_final: 0.7290 (p) REVERT: E 247 ARG cc_start: 0.7488 (ptm-80) cc_final: 0.7200 (ttt-90) REVERT: E 324 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6179 (mm-30) REVERT: F 29 GLU cc_start: 0.6428 (pp20) cc_final: 0.6204 (pp20) REVERT: F 43 GLU cc_start: 0.7342 (mp0) cc_final: 0.6956 (mp0) REVERT: F 64 LYS cc_start: 0.8026 (mmmt) cc_final: 0.7655 (mtpp) REVERT: G 118 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7053 (pt0) REVERT: G 130 ARG cc_start: 0.7276 (mtt90) cc_final: 0.6721 (mmm160) REVERT: G 163 GLU cc_start: 0.5955 (tp30) cc_final: 0.5285 (pt0) REVERT: H 100 ILE cc_start: 0.7711 (mm) cc_final: 0.7312 (mm) REVERT: H 118 GLU cc_start: 0.7381 (tt0) cc_final: 0.6425 (tt0) REVERT: H 250 ARG cc_start: 0.7425 (ttp-110) cc_final: 0.7165 (ttp-110) REVERT: H 267 ASN cc_start: 0.8102 (t0) cc_final: 0.7844 (m-40) outliers start: 72 outliers final: 54 residues processed: 331 average time/residue: 0.3060 time to fit residues: 150.2151 Evaluate side-chains 324 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 264 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 292 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 0.9990 chunk 212 optimal weight: 0.0970 chunk 193 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 chunk 162 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 chunk 195 optimal weight: 0.7980 chunk 205 optimal weight: 0.0980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN C 330 ASN ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 18343 Z= 0.163 Angle : 0.641 10.202 24746 Z= 0.299 Chirality : 0.040 0.151 2840 Planarity : 0.004 0.045 3163 Dihedral : 6.642 99.900 2629 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.70 % Allowed : 6.19 % Favored : 93.10 % Rotamer: Outliers : 2.80 % Allowed : 20.98 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.17), residues: 2277 helix: -0.36 (0.16), residues: 1077 sheet: -1.79 (0.30), residues: 302 loop : -2.09 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS H 294 PHE 0.012 0.001 PHE G 126 TYR 0.011 0.001 TYR H 315 ARG 0.010 0.000 ARG C 250 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 286 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.6187 (mmm) cc_final: 0.4936 (mtt) REVERT: A 292 ILE cc_start: 0.6972 (tp) cc_final: 0.6689 (mm) REVERT: B 128 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6311 (pt0) REVERT: B 250 ARG cc_start: 0.6954 (ttp-110) cc_final: 0.6552 (ttm110) REVERT: B 258 GLU cc_start: 0.6912 (tt0) cc_final: 0.6564 (pt0) REVERT: C 94 GLN cc_start: 0.7090 (pp30) cc_final: 0.6600 (mt0) REVERT: C 163 GLU cc_start: 0.6535 (tp30) cc_final: 0.5795 (tp30) REVERT: C 205 TYR cc_start: 0.8177 (m-10) cc_final: 0.7886 (m-10) REVERT: C 242 GLN cc_start: 0.7278 (mm110) cc_final: 0.6935 (mm-40) REVERT: C 315 TYR cc_start: 0.7503 (t80) cc_final: 0.6907 (t80) REVERT: D 249 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7508 (mm) REVERT: D 250 ARG cc_start: 0.7515 (tpt170) cc_final: 0.7271 (ttt-90) REVERT: E 94 GLN cc_start: 0.6728 (mt0) cc_final: 0.6379 (mp10) REVERT: E 136 ILE cc_start: 0.7788 (pt) cc_final: 0.6841 (mm) REVERT: E 143 THR cc_start: 0.7720 (OUTLIER) cc_final: 0.7292 (p) REVERT: E 247 ARG cc_start: 0.7455 (ptm-80) cc_final: 0.7198 (ttt-90) REVERT: F 43 GLU cc_start: 0.7296 (mp0) cc_final: 0.6899 (mp0) REVERT: F 64 LYS cc_start: 0.8036 (mmmt) cc_final: 0.7632 (mtpp) REVERT: G 118 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6995 (pt0) REVERT: G 130 ARG cc_start: 0.7201 (mtt90) cc_final: 0.6671 (mmm160) REVERT: G 163 GLU cc_start: 0.5889 (tp30) cc_final: 0.5275 (pt0) REVERT: H 94 GLN cc_start: 0.7307 (mt0) cc_final: 0.6678 (pp30) REVERT: H 100 ILE cc_start: 0.7593 (mm) cc_final: 0.7203 (mm) REVERT: H 118 GLU cc_start: 0.7330 (tt0) cc_final: 0.6381 (tt0) REVERT: H 250 ARG cc_start: 0.7438 (ttp-110) cc_final: 0.7176 (ttp-110) REVERT: H 267 ASN cc_start: 0.8053 (t0) cc_final: 0.7851 (m-40) outliers start: 52 outliers final: 40 residues processed: 317 average time/residue: 0.3081 time to fit residues: 146.1049 Evaluate side-chains 308 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 264 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 292 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 4.9990 chunk 218 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 151 optimal weight: 0.0770 chunk 229 optimal weight: 5.9990 chunk 210 optimal weight: 0.9990 chunk 182 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 140 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 overall best weight: 0.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN C 330 ASN ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 GLN H 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18343 Z= 0.178 Angle : 0.640 10.912 24746 Z= 0.297 Chirality : 0.040 0.222 2840 Planarity : 0.003 0.044 3163 Dihedral : 6.468 95.723 2629 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.37 % Favored : 92.97 % Rotamer: Outliers : 2.64 % Allowed : 21.36 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.17), residues: 2277 helix: -0.26 (0.16), residues: 1068 sheet: -1.70 (0.30), residues: 300 loop : -2.06 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS H 294 PHE 0.018 0.001 PHE E 126 TYR 0.020 0.001 TYR E 301 ARG 0.011 0.000 ARG C 303 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 272 time to evaluate : 1.954 Fit side-chains REVERT: A 243 MET cc_start: 0.7189 (ttt) cc_final: 0.6907 (tmm) REVERT: A 292 ILE cc_start: 0.6959 (tp) cc_final: 0.6690 (mm) REVERT: B 128 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6259 (pt0) REVERT: B 250 ARG cc_start: 0.6967 (ttp-110) cc_final: 0.6572 (ttm110) REVERT: B 258 GLU cc_start: 0.7002 (tt0) cc_final: 0.6703 (pt0) REVERT: C 94 GLN cc_start: 0.7093 (pp30) cc_final: 0.6570 (mt0) REVERT: C 202 GLN cc_start: 0.7613 (tp-100) cc_final: 0.6736 (mm-40) REVERT: C 205 TYR cc_start: 0.8167 (m-10) cc_final: 0.7858 (m-10) REVERT: C 242 GLN cc_start: 0.7232 (mm110) cc_final: 0.6888 (mm-40) REVERT: C 315 TYR cc_start: 0.7512 (t80) cc_final: 0.6906 (t80) REVERT: D 211 MET cc_start: 0.7472 (mmm) cc_final: 0.7006 (mtp) REVERT: D 249 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7528 (mm) REVERT: D 250 ARG cc_start: 0.7522 (tpt170) cc_final: 0.7289 (ttt-90) REVERT: E 94 GLN cc_start: 0.6742 (mt0) cc_final: 0.6376 (mp10) REVERT: E 136 ILE cc_start: 0.7779 (pt) cc_final: 0.6868 (mm) REVERT: E 143 THR cc_start: 0.7728 (OUTLIER) cc_final: 0.7300 (p) REVERT: F 43 GLU cc_start: 0.7245 (mp0) cc_final: 0.6840 (mp0) REVERT: F 64 LYS cc_start: 0.8032 (mmmt) cc_final: 0.7672 (mtpp) REVERT: F 124 GLU cc_start: 0.7265 (tt0) cc_final: 0.6721 (tt0) REVERT: G 118 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7004 (pt0) REVERT: G 130 ARG cc_start: 0.7241 (mtt90) cc_final: 0.6712 (mmm160) REVERT: G 163 GLU cc_start: 0.5910 (tp30) cc_final: 0.5306 (pt0) REVERT: H 100 ILE cc_start: 0.7612 (mm) cc_final: 0.7210 (mm) REVERT: H 118 GLU cc_start: 0.7333 (tt0) cc_final: 0.6387 (tt0) REVERT: H 250 ARG cc_start: 0.7413 (ttp-110) cc_final: 0.7170 (ttp-110) outliers start: 49 outliers final: 41 residues processed: 303 average time/residue: 0.3143 time to fit residues: 143.4516 Evaluate side-chains 313 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 268 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 292 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 182 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 187 optimal weight: 0.8980 chunk 23 optimal weight: 0.0670 chunk 33 optimal weight: 6.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN D 23 GLN ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.190847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.140083 restraints weight = 18423.647| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.73 r_work: 0.3456 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18343 Z= 0.187 Angle : 0.642 11.204 24746 Z= 0.298 Chirality : 0.041 0.231 2840 Planarity : 0.003 0.043 3163 Dihedral : 6.319 89.524 2629 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.61 % Allowed : 6.10 % Favored : 93.28 % Rotamer: Outliers : 2.54 % Allowed : 21.63 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.17), residues: 2277 helix: -0.26 (0.16), residues: 1068 sheet: -1.65 (0.30), residues: 300 loop : -2.05 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS H 294 PHE 0.015 0.001 PHE G 126 TYR 0.014 0.001 TYR H 315 ARG 0.010 0.000 ARG G 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4309.57 seconds wall clock time: 78 minutes 27.08 seconds (4707.08 seconds total)