Starting phenix.real_space_refine on Wed Feb 14 06:02:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7exd_31371/02_2024/7exd_31371_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7exd_31371/02_2024/7exd_31371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7exd_31371/02_2024/7exd_31371.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7exd_31371/02_2024/7exd_31371.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7exd_31371/02_2024/7exd_31371_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7exd_31371/02_2024/7exd_31371_neut_updated.pdb" } resolution = 3.4 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= 0.002 sd= 0.033 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: 5 Type Number sf(0) Gaussians S 60 5.16 5 C 5574 2.51 5 N 1491 2.21 5 O 1621 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "E ARG 160": "NH1" <-> "NH2" Residue "E GLU 234": "OE1" <-> "OE2" Residue "R ARG 19": "NH1" <-> "NH2" Residue "R ARG 52": "NH1" <-> "NH2" Residue "R ARG 86": "NH1" <-> "NH2" Residue "R ARG 123": "NH1" <-> "NH2" Residue "R ARG 133": "NH1" <-> "NH2" Residue "R ARG 135": "NH1" <-> "NH2" Residue "R ARG 162": "NH1" <-> "NH2" Residue "R ARG 206": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8749 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1766 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "G" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 447 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2196 Unusual residues: {'05X': 1} Classifications: {'peptide': 272, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 262, None: 1} Not linked: pdbres="LEU R 361 " pdbres="05X R 501 " Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Time building chain proxies: 4.78, per 1000 atoms: 0.55 Number of scatterers: 8749 At special positions: 0 Unit cell: (114.48, 128.52, 112.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 F 3 9.00 O 1621 8.00 N 1491 7.00 C 5574 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 172 " distance=2.03 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: 3.09 Conformation dependent library (CDL) restraints added in 1.7 seconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 12 sheets defined 34.7% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 9 through 32 removed outlier: 3.650A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.489A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.638A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'R' and resid 20 through 50 removed outlier: 4.000A pdb=" N VAL R 26 " --> pdb=" O SER R 22 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU R 33 " --> pdb=" O THR R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 75 removed outlier: 4.324A pdb=" N LEU R 61 " --> pdb=" O ALA R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 85 Processing helix chain 'R' and resid 93 through 126 removed outlier: 3.737A pdb=" N ASP R 97 " --> pdb=" O GLN R 93 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ILE R 98 " --> pdb=" O VAL R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 134 No H-bonds generated for 'chain 'R' and resid 131 through 134' Processing helix chain 'R' and resid 137 through 153 Processing helix chain 'R' and resid 157 through 162 removed outlier: 3.707A pdb=" N TRP R 161 " --> pdb=" O PRO R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 169 No H-bonds generated for 'chain 'R' and resid 167 through 169' Processing helix chain 'R' and resid 179 through 212 removed outlier: 3.725A pdb=" N ALA R 189 " --> pdb=" O SER R 185 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ILE R 192 " --> pdb=" O GLY R 188 " (cutoff:3.500A) Proline residue: R 193 - end of helix Processing helix chain 'R' and resid 286 through 318 removed outlier: 3.765A pdb=" N LYS R 290 " --> pdb=" O THR R 286 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE R 302 " --> pdb=" O ILE R 298 " (cutoff:3.500A) Proline residue: R 308 - end of helix removed outlier: 3.536A pdb=" N ASN R 317 " --> pdb=" O GLU R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 326 through 346 removed outlier: 3.927A pdb=" N ASN R 339 " --> pdb=" O LEU R 335 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER R 340 " --> pdb=" O GLY R 336 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU R 341 " --> pdb=" O TYR R 337 " (cutoff:3.500A) Proline residue: R 344 - end of helix Processing helix chain 'R' and resid 352 through 360 removed outlier: 3.772A pdb=" N GLN R 359 " --> pdb=" O LYS R 355 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS R 360 " --> pdb=" O LYS R 356 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.604A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.082A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.772A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 123 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 150 removed outlier: 6.809A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.561A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.582A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.469A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.805A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.163A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.777A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.521A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL E 226 " --> pdb=" O GLN E 179 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1074 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: 2.73 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1409 1.31 - 1.44: 2455 1.44 - 1.57: 4979 1.57 - 1.69: 0 1.69 - 1.82: 86 Bond restraints: 8929 Sorted by residual: bond pdb=" C17 05X R 501 " pdb=" N16 05X R 501 " ideal model delta sigma weight residual 1.360 1.457 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C12 05X R 501 " pdb=" N16 05X R 501 " ideal model delta sigma weight residual 1.396 1.455 -0.059 2.00e-02 2.50e+03 8.64e+00 bond pdb=" N PHE R 310 " pdb=" CA PHE R 310 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.63e+00 bond pdb=" N TYR R 212 " pdb=" CA TYR R 212 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.45e+00 bond pdb=" C5 05X R 501 " pdb=" C8 05X R 501 " ideal model delta sigma weight residual 1.506 1.551 -0.045 2.00e-02 2.50e+03 5.06e+00 ... (remaining 8924 not shown) Histogram of bond angle deviations from ideal: 100.61 - 107.28: 234 107.28 - 113.96: 5065 113.96 - 120.63: 3614 120.63 - 127.30: 3095 127.30 - 133.97: 89 Bond angle restraints: 12097 Sorted by residual: angle pdb=" N ARG R 287 " pdb=" CA ARG R 287 " pdb=" C ARG R 287 " ideal model delta sigma weight residual 113.41 105.04 8.37 1.22e+00 6.72e-01 4.71e+01 angle pdb=" N LYS R 175 " pdb=" CA LYS R 175 " pdb=" C LYS R 175 " ideal model delta sigma weight residual 108.52 102.20 6.32 1.63e+00 3.76e-01 1.50e+01 angle pdb=" N ILE R 104 " pdb=" CA ILE R 104 " pdb=" C ILE R 104 " ideal model delta sigma weight residual 110.42 114.02 -3.60 9.60e-01 1.09e+00 1.40e+01 angle pdb=" CA PHE R 310 " pdb=" C PHE R 310 " pdb=" O PHE R 310 " ideal model delta sigma weight residual 120.42 117.03 3.39 1.06e+00 8.90e-01 1.02e+01 angle pdb=" C ARG R 287 " pdb=" N GLU R 288 " pdb=" CA GLU R 288 " ideal model delta sigma weight residual 120.28 116.35 3.93 1.34e+00 5.57e-01 8.60e+00 ... (remaining 12092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 4802 16.13 - 32.26: 411 32.26 - 48.39: 66 48.39 - 64.52: 21 64.52 - 80.65: 8 Dihedral angle restraints: 5308 sinusoidal: 2060 harmonic: 3248 Sorted by residual: dihedral pdb=" CA HIS R 178 " pdb=" C HIS R 178 " pdb=" N ILE R 179 " pdb=" CA ILE R 179 " ideal model delta harmonic sigma weight residual 180.00 -162.24 -17.76 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA PHE R 153 " pdb=" C PHE R 153 " pdb=" N ILE R 154 " pdb=" CA ILE R 154 " ideal model delta harmonic sigma weight residual 180.00 162.90 17.10 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CB CYS R 96 " pdb=" SG CYS R 96 " pdb=" SG CYS R 172 " pdb=" CB CYS R 172 " ideal model delta sinusoidal sigma weight residual 93.00 119.54 -26.54 1 1.00e+01 1.00e-02 1.01e+01 ... (remaining 5305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1085 0.041 - 0.082: 204 0.082 - 0.123: 87 0.123 - 0.164: 6 0.164 - 0.205: 2 Chirality restraints: 1384 Sorted by residual: chirality pdb=" CA LYS R 175 " pdb=" N LYS R 175 " pdb=" C LYS R 175 " pdb=" CB LYS R 175 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ARG R 287 " pdb=" N ARG R 287 " pdb=" C ARG R 287 " pdb=" CB ARG R 287 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1381 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 286 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C THR R 286 " -0.052 2.00e-02 2.50e+03 pdb=" O THR R 286 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG R 287 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO R 157 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO R 158 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO R 158 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 158 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO G 53 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " -0.024 5.00e-02 4.00e+02 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 169 2.67 - 3.23: 8839 3.23 - 3.79: 13436 3.79 - 4.34: 18360 4.34 - 4.90: 30227 Nonbonded interactions: 71031 Sorted by model distance: nonbonded pdb=" NH1 ARG B 22 " pdb=" OD1 ASP B 258 " model vdw 2.114 2.520 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.146 2.440 nonbonded pdb=" NH1 ARG B 96 " pdb=" OE2 GLU B 138 " model vdw 2.184 2.520 nonbonded pdb=" OD1 ASP A 272 " pdb=" N LEU A 273 " model vdw 2.204 2.520 nonbonded pdb=" ND1 HIS G 44 " pdb=" OE2 GLU G 47 " model vdw 2.233 2.520 ... (remaining 71026 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.150 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 25.710 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 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 0.097 8929 Z= 0.189 Angle : 0.518 8.371 12097 Z= 0.296 Chirality : 0.039 0.205 1384 Planarity : 0.003 0.047 1518 Dihedral : 12.790 80.645 3201 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.53 % Allowed : 0.21 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.95 (0.27), residues: 1100 helix: 2.45 (0.29), residues: 366 sheet: 1.17 (0.31), residues: 277 loop : 0.51 (0.33), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 334 HIS 0.003 0.001 HIS R 113 PHE 0.011 0.001 PHE R 302 TYR 0.010 0.001 TYR R 191 ARG 0.014 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 325 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8294 (tppp) cc_final: 0.7903 (tppp) REVERT: A 191 PHE cc_start: 0.7739 (t80) cc_final: 0.7461 (t80) REVERT: A 222 ILE cc_start: 0.8234 (mt) cc_final: 0.7970 (mt) REVERT: A 271 LYS cc_start: 0.7797 (ptmt) cc_final: 0.7482 (ptmt) REVERT: A 289 GLU cc_start: 0.7970 (mp0) cc_final: 0.7770 (mp0) REVERT: A 308 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7275 (mt-10) REVERT: A 336 PHE cc_start: 0.8204 (t80) cc_final: 0.7693 (t80) REVERT: A 351 CYS cc_start: 0.7512 (t) cc_final: 0.7257 (t) REVERT: B 134 ARG cc_start: 0.7568 (ptt180) cc_final: 0.7322 (ptp90) REVERT: B 153 ASP cc_start: 0.7124 (t0) cc_final: 0.6883 (t70) REVERT: B 188 MET cc_start: 0.6135 (mmp) cc_final: 0.5674 (mmt) REVERT: B 205 ASP cc_start: 0.7284 (p0) cc_final: 0.7055 (p0) REVERT: B 232 ILE cc_start: 0.8430 (tt) cc_final: 0.8230 (tt) REVERT: G 21 MET cc_start: 0.7212 (tmm) cc_final: 0.6739 (tmm) REVERT: E 59 TYR cc_start: 0.7769 (m-80) cc_final: 0.7473 (m-10) REVERT: E 191 ARG cc_start: 0.7527 (mmt90) cc_final: 0.7284 (mmt90) REVERT: R 77 MET cc_start: 0.7414 (mtp) cc_final: 0.7198 (mtp) REVERT: R 126 THR cc_start: 0.7044 (t) cc_final: 0.6805 (t) REVERT: R 176 HIS cc_start: 0.7094 (t70) cc_final: 0.6714 (t70) REVERT: R 290 LYS cc_start: 0.8248 (tmtt) cc_final: 0.7994 (tmtt) outliers start: 5 outliers final: 2 residues processed: 328 average time/residue: 0.2306 time to fit residues: 99.8274 Evaluate side-chains 294 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 292 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 354 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 230 ASN ** R 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8929 Z= 0.220 Angle : 0.562 6.994 12097 Z= 0.293 Chirality : 0.044 0.147 1384 Planarity : 0.004 0.059 1518 Dihedral : 5.095 54.316 1227 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.17 % Allowed : 11.21 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.53 (0.27), residues: 1100 helix: 1.92 (0.28), residues: 370 sheet: 0.73 (0.30), residues: 291 loop : 0.59 (0.34), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 211 HIS 0.007 0.001 HIS R 213 PHE 0.018 0.002 PHE A 259 TYR 0.024 0.002 TYR R 347 ARG 0.005 0.001 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 296 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8314 (tppp) cc_final: 0.7857 (tppp) REVERT: A 33 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7209 (mt-10) REVERT: A 34 VAL cc_start: 0.8062 (t) cc_final: 0.7852 (t) REVERT: A 219 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8191 (p) REVERT: A 271 LYS cc_start: 0.7784 (ptmt) cc_final: 0.7453 (ptmt) REVERT: A 275 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6924 (mm-30) REVERT: A 297 GLU cc_start: 0.7569 (mp0) cc_final: 0.7366 (mp0) REVERT: A 342 VAL cc_start: 0.7815 (t) cc_final: 0.7607 (t) REVERT: A 354 PHE cc_start: 0.5356 (OUTLIER) cc_final: 0.4238 (t80) REVERT: B 52 ARG cc_start: 0.7303 (ptp90) cc_final: 0.7045 (ptp90) REVERT: B 114 CYS cc_start: 0.7502 (p) cc_final: 0.7254 (p) REVERT: B 134 ARG cc_start: 0.7600 (ptt180) cc_final: 0.7290 (ptp90) REVERT: B 170 ASP cc_start: 0.7503 (t0) cc_final: 0.7117 (t0) REVERT: B 186 ASP cc_start: 0.7394 (p0) cc_final: 0.6966 (p0) REVERT: B 188 MET cc_start: 0.6176 (mmp) cc_final: 0.5858 (mmt) REVERT: B 205 ASP cc_start: 0.7180 (p0) cc_final: 0.6950 (p0) REVERT: B 247 ASP cc_start: 0.7535 (p0) cc_final: 0.7292 (p0) REVERT: B 249 THR cc_start: 0.7826 (p) cc_final: 0.7558 (p) REVERT: B 258 ASP cc_start: 0.6765 (t0) cc_final: 0.6239 (t0) REVERT: B 259 GLN cc_start: 0.7496 (pp30) cc_final: 0.6968 (pp30) REVERT: B 273 ILE cc_start: 0.8056 (mp) cc_final: 0.7850 (mp) REVERT: G 21 MET cc_start: 0.7250 (tmm) cc_final: 0.6823 (tmm) REVERT: G 22 GLU cc_start: 0.7964 (tt0) cc_final: 0.7752 (tt0) REVERT: E 34 MET cc_start: 0.7421 (mmm) cc_final: 0.6893 (mmm) REVERT: E 59 TYR cc_start: 0.7767 (m-80) cc_final: 0.7426 (m-80) REVERT: E 99 SER cc_start: 0.8039 (t) cc_final: 0.7631 (p) REVERT: E 228 TYR cc_start: 0.8028 (m-10) cc_final: 0.7778 (m-10) REVERT: R 77 MET cc_start: 0.7517 (mtp) cc_final: 0.7003 (mtp) REVERT: R 175 LYS cc_start: 0.7974 (tptp) cc_final: 0.7757 (tppp) REVERT: R 176 HIS cc_start: 0.7192 (t70) cc_final: 0.6767 (t70) outliers start: 30 outliers final: 25 residues processed: 306 average time/residue: 0.2357 time to fit residues: 94.8917 Evaluate side-chains 326 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 299 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 23 LYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 287 ARG Chi-restraints excluded: chain R residue 310 PHE Chi-restraints excluded: chain R residue 325 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 62 HIS B 230 ASN G 18 GLN E 186 GLN ** R 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8929 Z= 0.197 Angle : 0.531 6.033 12097 Z= 0.277 Chirality : 0.042 0.148 1384 Planarity : 0.004 0.066 1518 Dihedral : 5.055 54.569 1227 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.70 % Allowed : 15.64 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.20 (0.26), residues: 1100 helix: 1.60 (0.27), residues: 375 sheet: 0.65 (0.31), residues: 279 loop : 0.34 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.005 0.001 HIS R 213 PHE 0.013 0.002 PHE R 302 TYR 0.020 0.002 TYR E 228 ARG 0.006 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 297 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8353 (tppp) cc_final: 0.7898 (tppp) REVERT: A 33 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7286 (mt-10) REVERT: A 212 ILE cc_start: 0.8659 (tp) cc_final: 0.8309 (tp) REVERT: A 271 LYS cc_start: 0.7796 (ptmt) cc_final: 0.7428 (ptmt) REVERT: A 275 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6941 (mm-30) REVERT: A 339 VAL cc_start: 0.8457 (t) cc_final: 0.8154 (m) REVERT: B 50 THR cc_start: 0.8065 (m) cc_final: 0.7328 (t) REVERT: B 83 ASP cc_start: 0.7257 (t0) cc_final: 0.6825 (t0) REVERT: B 134 ARG cc_start: 0.7582 (ptt180) cc_final: 0.7313 (ptp90) REVERT: B 186 ASP cc_start: 0.7370 (p0) cc_final: 0.7089 (p0) REVERT: B 188 MET cc_start: 0.6325 (mmp) cc_final: 0.6028 (mmt) REVERT: B 205 ASP cc_start: 0.7169 (p0) cc_final: 0.6934 (p0) REVERT: B 233 CYS cc_start: 0.7854 (t) cc_final: 0.7523 (t) REVERT: B 258 ASP cc_start: 0.6985 (t0) cc_final: 0.6094 (t0) REVERT: B 259 GLN cc_start: 0.7558 (pp30) cc_final: 0.7052 (pp30) REVERT: B 296 VAL cc_start: 0.8150 (t) cc_final: 0.7725 (m) REVERT: G 21 MET cc_start: 0.7263 (tmm) cc_final: 0.6820 (tmm) REVERT: G 22 GLU cc_start: 0.7954 (tt0) cc_final: 0.7720 (tt0) REVERT: E 34 MET cc_start: 0.7444 (mmm) cc_final: 0.6904 (mmm) REVERT: E 99 SER cc_start: 0.8016 (t) cc_final: 0.7676 (p) REVERT: E 186 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7102 (pt0) REVERT: E 228 TYR cc_start: 0.8072 (m-10) cc_final: 0.7759 (m-80) REVERT: R 53 LYS cc_start: 0.7842 (tppp) cc_final: 0.7525 (tppp) REVERT: R 77 MET cc_start: 0.7417 (mtp) cc_final: 0.7096 (mtp) REVERT: R 143 MET cc_start: 0.7836 (tpp) cc_final: 0.7481 (tpp) REVERT: R 175 LYS cc_start: 0.8004 (tptp) cc_final: 0.7798 (tppp) REVERT: R 186 THR cc_start: 0.7489 (OUTLIER) cc_final: 0.7281 (m) REVERT: R 191 TYR cc_start: 0.7894 (m-80) cc_final: 0.7646 (m-80) REVERT: R 290 LYS cc_start: 0.7831 (tmtt) cc_final: 0.7552 (tmtt) outliers start: 35 outliers final: 27 residues processed: 308 average time/residue: 0.2338 time to fit residues: 94.6925 Evaluate side-chains 333 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 304 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain R residue 23 LYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 138 LYS Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 287 ARG Chi-restraints excluded: chain R residue 310 PHE Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 340 SER Chi-restraints excluded: chain R residue 342 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 66 optimal weight: 0.0470 chunk 99 optimal weight: 0.0570 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 0.0050 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.6012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8929 Z= 0.174 Angle : 0.518 5.841 12097 Z= 0.271 Chirality : 0.041 0.134 1384 Planarity : 0.004 0.069 1518 Dihedral : 4.672 54.508 1225 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.59 % Allowed : 16.70 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.07 (0.26), residues: 1100 helix: 1.53 (0.27), residues: 375 sheet: 0.49 (0.30), residues: 281 loop : 0.29 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.005 0.001 HIS R 213 PHE 0.022 0.001 PHE R 190 TYR 0.017 0.002 TYR E 101 ARG 0.006 0.001 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 296 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8376 (tppp) cc_final: 0.7867 (tppp) REVERT: A 212 ILE cc_start: 0.8675 (tp) cc_final: 0.8330 (tp) REVERT: A 218 VAL cc_start: 0.8568 (t) cc_final: 0.8262 (p) REVERT: A 222 ILE cc_start: 0.8357 (mt) cc_final: 0.8147 (mt) REVERT: A 262 THR cc_start: 0.8241 (m) cc_final: 0.7760 (p) REVERT: A 271 LYS cc_start: 0.7785 (ptmt) cc_final: 0.7408 (ptmt) REVERT: A 275 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7084 (mm-30) REVERT: B 50 THR cc_start: 0.8099 (m) cc_final: 0.7599 (t) REVERT: B 68 ARG cc_start: 0.7781 (ttt180) cc_final: 0.7490 (ttt-90) REVERT: B 83 ASP cc_start: 0.7267 (t0) cc_final: 0.6580 (t0) REVERT: B 134 ARG cc_start: 0.7564 (ptt180) cc_final: 0.7321 (ptp90) REVERT: B 155 ASN cc_start: 0.7868 (t0) cc_final: 0.7618 (t0) REVERT: B 186 ASP cc_start: 0.7322 (p0) cc_final: 0.6978 (p0) REVERT: B 188 MET cc_start: 0.6472 (mmp) cc_final: 0.6077 (mmt) REVERT: B 205 ASP cc_start: 0.7170 (p0) cc_final: 0.6943 (p0) REVERT: B 233 CYS cc_start: 0.7762 (t) cc_final: 0.7506 (t) REVERT: B 258 ASP cc_start: 0.6898 (t0) cc_final: 0.6268 (t0) REVERT: B 259 GLN cc_start: 0.7607 (pp30) cc_final: 0.7090 (pp30) REVERT: B 294 CYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6651 (m) REVERT: B 296 VAL cc_start: 0.8181 (t) cc_final: 0.7786 (m) REVERT: G 21 MET cc_start: 0.7296 (tmm) cc_final: 0.6869 (tmm) REVERT: E 34 MET cc_start: 0.7428 (mmm) cc_final: 0.6892 (mmm) REVERT: E 99 SER cc_start: 0.8021 (t) cc_final: 0.7684 (p) REVERT: E 228 TYR cc_start: 0.8046 (m-10) cc_final: 0.7767 (m-80) REVERT: R 23 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8116 (mmmm) REVERT: R 53 LYS cc_start: 0.7901 (tppp) cc_final: 0.7574 (tppp) REVERT: R 143 MET cc_start: 0.7788 (tpp) cc_final: 0.7499 (tpp) REVERT: R 154 ILE cc_start: 0.8393 (tp) cc_final: 0.8189 (tp) REVERT: R 175 LYS cc_start: 0.8043 (tptp) cc_final: 0.7841 (tppp) REVERT: R 191 TYR cc_start: 0.8023 (m-80) cc_final: 0.7724 (m-80) REVERT: R 290 LYS cc_start: 0.8004 (tmtt) cc_final: 0.7673 (tmtt) outliers start: 34 outliers final: 24 residues processed: 301 average time/residue: 0.2441 time to fit residues: 97.0729 Evaluate side-chains 318 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 292 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 23 LYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain R residue 138 LYS Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 287 ARG Chi-restraints excluded: chain R residue 310 PHE Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 340 SER Chi-restraints excluded: chain R residue 342 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 0.0170 chunk 72 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 94 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 88 ASN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8929 Z= 0.169 Angle : 0.514 7.205 12097 Z= 0.269 Chirality : 0.041 0.142 1384 Planarity : 0.004 0.071 1518 Dihedral : 4.443 55.537 1222 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.59 % Allowed : 18.71 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.99 (0.26), residues: 1100 helix: 1.54 (0.27), residues: 375 sheet: 0.36 (0.30), residues: 282 loop : 0.24 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS R 213 PHE 0.018 0.001 PHE R 190 TYR 0.018 0.002 TYR E 101 ARG 0.005 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 299 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8365 (tppp) cc_final: 0.7889 (tppp) REVERT: A 212 ILE cc_start: 0.8706 (tp) cc_final: 0.8399 (tp) REVERT: A 218 VAL cc_start: 0.8635 (t) cc_final: 0.8328 (p) REVERT: A 222 ILE cc_start: 0.8351 (mt) cc_final: 0.8118 (mt) REVERT: A 262 THR cc_start: 0.8240 (m) cc_final: 0.7761 (p) REVERT: A 271 LYS cc_start: 0.7788 (ptmt) cc_final: 0.7554 (ptmt) REVERT: A 308 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7154 (mt-10) REVERT: B 50 THR cc_start: 0.8130 (m) cc_final: 0.7622 (t) REVERT: B 134 ARG cc_start: 0.7547 (ptt180) cc_final: 0.7271 (ptp90) REVERT: B 155 ASN cc_start: 0.7838 (t0) cc_final: 0.7604 (t0) REVERT: B 186 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6861 (p0) REVERT: B 188 MET cc_start: 0.6582 (mmp) cc_final: 0.6174 (mmt) REVERT: B 205 ASP cc_start: 0.7230 (p0) cc_final: 0.7025 (p0) REVERT: B 233 CYS cc_start: 0.7735 (t) cc_final: 0.7478 (t) REVERT: B 239 ASN cc_start: 0.7889 (m-40) cc_final: 0.7582 (m-40) REVERT: B 259 GLN cc_start: 0.7652 (pp30) cc_final: 0.7050 (pp30) REVERT: B 294 CYS cc_start: 0.6883 (OUTLIER) cc_final: 0.6630 (m) REVERT: B 296 VAL cc_start: 0.8198 (t) cc_final: 0.7835 (m) REVERT: G 21 MET cc_start: 0.7247 (tmm) cc_final: 0.6919 (tmm) REVERT: E 34 MET cc_start: 0.7425 (mmm) cc_final: 0.6873 (mmm) REVERT: E 59 TYR cc_start: 0.7684 (m-10) cc_final: 0.7482 (m-10) REVERT: E 91 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.8251 (t) REVERT: E 99 SER cc_start: 0.8000 (t) cc_final: 0.7698 (p) REVERT: E 228 TYR cc_start: 0.8021 (m-10) cc_final: 0.7754 (m-80) REVERT: R 23 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8110 (mmmm) REVERT: R 53 LYS cc_start: 0.7902 (tppp) cc_final: 0.7556 (tppp) REVERT: R 77 MET cc_start: 0.7466 (mtp) cc_final: 0.7115 (mtp) REVERT: R 143 MET cc_start: 0.7774 (tpp) cc_final: 0.7492 (tpp) REVERT: R 154 ILE cc_start: 0.8316 (tp) cc_final: 0.8114 (tp) REVERT: R 290 LYS cc_start: 0.8102 (tmtt) cc_final: 0.7769 (tmtt) outliers start: 34 outliers final: 22 residues processed: 310 average time/residue: 0.2339 time to fit residues: 95.8243 Evaluate side-chains 320 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 294 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 23 LYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 340 SER Chi-restraints excluded: chain R residue 342 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 0.0980 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN E 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8929 Z= 0.193 Angle : 0.531 6.202 12097 Z= 0.276 Chirality : 0.042 0.163 1384 Planarity : 0.004 0.073 1518 Dihedral : 4.511 56.461 1222 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.28 % Allowed : 20.93 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.90 (0.26), residues: 1100 helix: 1.51 (0.27), residues: 376 sheet: 0.26 (0.30), residues: 288 loop : 0.17 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 211 HIS 0.005 0.001 HIS R 213 PHE 0.024 0.001 PHE R 190 TYR 0.023 0.002 TYR E 101 ARG 0.008 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 301 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8364 (tppp) cc_final: 0.7887 (tppp) REVERT: A 212 ILE cc_start: 0.8709 (tp) cc_final: 0.8409 (tp) REVERT: A 222 ILE cc_start: 0.8332 (mt) cc_final: 0.8097 (mt) REVERT: A 271 LYS cc_start: 0.7806 (ptmt) cc_final: 0.7543 (ptmt) REVERT: A 308 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7484 (mt-10) REVERT: B 50 THR cc_start: 0.8153 (m) cc_final: 0.7605 (t) REVERT: B 134 ARG cc_start: 0.7487 (ptt180) cc_final: 0.7253 (ptp90) REVERT: B 186 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6796 (p0) REVERT: B 188 MET cc_start: 0.6739 (mmp) cc_final: 0.6323 (mmt) REVERT: B 205 ASP cc_start: 0.7256 (p0) cc_final: 0.7021 (p0) REVERT: B 233 CYS cc_start: 0.7757 (t) cc_final: 0.7543 (t) REVERT: B 239 ASN cc_start: 0.7930 (m-40) cc_final: 0.7595 (m-40) REVERT: B 259 GLN cc_start: 0.7689 (pp30) cc_final: 0.7054 (pp30) REVERT: B 294 CYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6647 (m) REVERT: B 296 VAL cc_start: 0.8193 (t) cc_final: 0.7849 (m) REVERT: B 323 ASP cc_start: 0.7791 (p0) cc_final: 0.7358 (p0) REVERT: B 325 MET cc_start: 0.7373 (tpp) cc_final: 0.7045 (tpp) REVERT: G 21 MET cc_start: 0.7215 (tmm) cc_final: 0.6866 (tmm) REVERT: E 34 MET cc_start: 0.7409 (mmm) cc_final: 0.6869 (mmm) REVERT: E 91 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8275 (t) REVERT: E 99 SER cc_start: 0.7948 (t) cc_final: 0.7691 (p) REVERT: E 186 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7197 (pt0) REVERT: E 228 TYR cc_start: 0.8047 (m-10) cc_final: 0.7800 (m-80) REVERT: R 23 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8115 (mmmm) REVERT: R 53 LYS cc_start: 0.7885 (tppp) cc_final: 0.7464 (tppp) REVERT: R 143 MET cc_start: 0.7806 (tpp) cc_final: 0.7513 (tpp) REVERT: R 186 THR cc_start: 0.7552 (m) cc_final: 0.7337 (m) REVERT: R 290 LYS cc_start: 0.8141 (tmtt) cc_final: 0.7819 (tmtt) outliers start: 31 outliers final: 23 residues processed: 312 average time/residue: 0.2275 time to fit residues: 93.6163 Evaluate side-chains 325 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 297 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 23 LYS Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 310 PHE Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 340 SER Chi-restraints excluded: chain R residue 342 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8929 Z= 0.198 Angle : 0.545 6.587 12097 Z= 0.282 Chirality : 0.042 0.154 1384 Planarity : 0.004 0.073 1518 Dihedral : 4.555 57.237 1222 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.12 % Allowed : 20.93 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.84 (0.26), residues: 1100 helix: 1.49 (0.27), residues: 378 sheet: 0.23 (0.30), residues: 287 loop : 0.10 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.004 0.001 HIS R 213 PHE 0.021 0.001 PHE R 190 TYR 0.025 0.002 TYR E 101 ARG 0.006 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 295 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8384 (tppp) cc_final: 0.7904 (tppp) REVERT: A 212 ILE cc_start: 0.8718 (tp) cc_final: 0.8443 (tp) REVERT: A 222 ILE cc_start: 0.8325 (mt) cc_final: 0.8102 (mt) REVERT: A 271 LYS cc_start: 0.7824 (ptmt) cc_final: 0.7502 (ptmt) REVERT: A 308 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7261 (mt-10) REVERT: B 50 THR cc_start: 0.8131 (m) cc_final: 0.7621 (t) REVERT: B 134 ARG cc_start: 0.7472 (ptt180) cc_final: 0.7248 (ptp90) REVERT: B 186 ASP cc_start: 0.7171 (OUTLIER) cc_final: 0.6813 (p0) REVERT: B 188 MET cc_start: 0.6787 (mmp) cc_final: 0.6362 (mmt) REVERT: B 205 ASP cc_start: 0.7259 (p0) cc_final: 0.7007 (p0) REVERT: B 233 CYS cc_start: 0.7746 (t) cc_final: 0.7514 (t) REVERT: B 239 ASN cc_start: 0.7981 (m-40) cc_final: 0.7711 (m-40) REVERT: B 259 GLN cc_start: 0.7708 (pp30) cc_final: 0.7022 (pp30) REVERT: B 296 VAL cc_start: 0.8192 (t) cc_final: 0.7863 (m) REVERT: B 323 ASP cc_start: 0.7795 (p0) cc_final: 0.7358 (p0) REVERT: B 325 MET cc_start: 0.7371 (tpp) cc_final: 0.7055 (tpp) REVERT: G 21 MET cc_start: 0.7213 (tmm) cc_final: 0.6870 (tmm) REVERT: E 12 VAL cc_start: 0.7292 (OUTLIER) cc_final: 0.7090 (m) REVERT: E 34 MET cc_start: 0.7402 (mmm) cc_final: 0.6842 (mmm) REVERT: E 60 TYR cc_start: 0.8088 (m-80) cc_final: 0.7793 (m-80) REVERT: E 90 ASP cc_start: 0.7462 (m-30) cc_final: 0.7205 (m-30) REVERT: E 91 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8287 (t) REVERT: E 99 SER cc_start: 0.7981 (t) cc_final: 0.7742 (p) REVERT: E 228 TYR cc_start: 0.8081 (m-10) cc_final: 0.7857 (m-80) REVERT: R 23 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8122 (mmmm) REVERT: R 53 LYS cc_start: 0.7880 (tppp) cc_final: 0.7440 (tppp) REVERT: R 143 MET cc_start: 0.7781 (tpp) cc_final: 0.7485 (tpp) REVERT: R 186 THR cc_start: 0.7631 (OUTLIER) cc_final: 0.7428 (m) REVERT: R 290 LYS cc_start: 0.8157 (tmtt) cc_final: 0.7820 (tmtt) outliers start: 39 outliers final: 28 residues processed: 312 average time/residue: 0.2540 time to fit residues: 104.9819 Evaluate side-chains 324 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 291 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 23 LYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 287 ARG Chi-restraints excluded: chain R residue 310 PHE Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 340 SER Chi-restraints excluded: chain R residue 342 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8929 Z= 0.211 Angle : 0.555 7.696 12097 Z= 0.287 Chirality : 0.042 0.154 1384 Planarity : 0.004 0.074 1518 Dihedral : 4.626 58.394 1222 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.02 % Allowed : 21.14 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.83 (0.26), residues: 1100 helix: 1.58 (0.27), residues: 370 sheet: 0.11 (0.30), residues: 288 loop : 0.11 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.004 0.001 HIS R 213 PHE 0.019 0.001 PHE R 190 TYR 0.024 0.002 TYR E 101 ARG 0.006 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 292 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8403 (tppp) cc_final: 0.7830 (tppp) REVERT: A 33 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7214 (mt-10) REVERT: A 212 ILE cc_start: 0.8718 (tp) cc_final: 0.8478 (tp) REVERT: A 222 ILE cc_start: 0.8313 (mt) cc_final: 0.8096 (mt) REVERT: A 271 LYS cc_start: 0.7787 (ptmt) cc_final: 0.7472 (ptmt) REVERT: A 275 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7005 (mm-30) REVERT: A 296 TYR cc_start: 0.7901 (t80) cc_final: 0.6702 (t80) REVERT: A 308 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7240 (mt-10) REVERT: B 50 THR cc_start: 0.8168 (m) cc_final: 0.7653 (t) REVERT: B 134 ARG cc_start: 0.7470 (ptt180) cc_final: 0.7152 (ptp90) REVERT: B 186 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6826 (p0) REVERT: B 188 MET cc_start: 0.6821 (mmp) cc_final: 0.6389 (mmt) REVERT: B 205 ASP cc_start: 0.7244 (p0) cc_final: 0.7001 (p0) REVERT: B 233 CYS cc_start: 0.7741 (t) cc_final: 0.7486 (t) REVERT: B 239 ASN cc_start: 0.7992 (m-40) cc_final: 0.7612 (m-40) REVERT: B 259 GLN cc_start: 0.7762 (pp30) cc_final: 0.7056 (pp30) REVERT: B 296 VAL cc_start: 0.8222 (t) cc_final: 0.7906 (m) REVERT: B 323 ASP cc_start: 0.7798 (p0) cc_final: 0.7359 (p0) REVERT: B 325 MET cc_start: 0.7381 (tpp) cc_final: 0.7058 (tpp) REVERT: G 21 MET cc_start: 0.7218 (tmm) cc_final: 0.6868 (tmm) REVERT: E 34 MET cc_start: 0.7375 (mmm) cc_final: 0.6837 (mmm) REVERT: E 90 ASP cc_start: 0.7519 (m-30) cc_final: 0.7288 (m-30) REVERT: E 91 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8298 (t) REVERT: E 99 SER cc_start: 0.7976 (t) cc_final: 0.7774 (p) REVERT: E 228 TYR cc_start: 0.8095 (m-10) cc_final: 0.7882 (m-80) REVERT: R 23 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8134 (mmmm) REVERT: R 53 LYS cc_start: 0.7871 (tppp) cc_final: 0.7432 (tppp) REVERT: R 143 MET cc_start: 0.7773 (tpp) cc_final: 0.7477 (tpp) REVERT: R 290 LYS cc_start: 0.8194 (tmtt) cc_final: 0.7848 (tmtt) outliers start: 38 outliers final: 27 residues processed: 310 average time/residue: 0.2377 time to fit residues: 97.0445 Evaluate side-chains 314 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 284 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 23 LYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 287 ARG Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 340 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 58 optimal weight: 0.1980 chunk 42 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 63 optimal weight: 0.0870 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8929 Z= 0.163 Angle : 0.548 7.694 12097 Z= 0.282 Chirality : 0.042 0.165 1384 Planarity : 0.004 0.074 1518 Dihedral : 4.638 58.716 1222 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.17 % Allowed : 22.52 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.80 (0.26), residues: 1100 helix: 1.59 (0.28), residues: 370 sheet: 0.14 (0.30), residues: 284 loop : 0.03 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.005 0.001 HIS R 213 PHE 0.025 0.001 PHE R 190 TYR 0.023 0.001 TYR E 101 ARG 0.009 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 300 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8374 (tppp) cc_final: 0.7905 (tppp) REVERT: A 212 ILE cc_start: 0.8718 (tp) cc_final: 0.8465 (tp) REVERT: A 218 VAL cc_start: 0.8664 (t) cc_final: 0.8360 (p) REVERT: A 222 ILE cc_start: 0.8306 (mt) cc_final: 0.8091 (mt) REVERT: A 271 LYS cc_start: 0.7806 (ptmt) cc_final: 0.7527 (ptmt) REVERT: A 275 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7065 (mm-30) REVERT: A 296 TYR cc_start: 0.7856 (t80) cc_final: 0.6751 (t80) REVERT: A 308 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7227 (mt-10) REVERT: B 50 THR cc_start: 0.8142 (m) cc_final: 0.7610 (t) REVERT: B 165 THR cc_start: 0.7864 (p) cc_final: 0.7509 (m) REVERT: B 180 PHE cc_start: 0.8049 (m-80) cc_final: 0.7729 (m-80) REVERT: B 186 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6838 (p0) REVERT: B 188 MET cc_start: 0.6867 (mmp) cc_final: 0.6380 (mmt) REVERT: B 205 ASP cc_start: 0.7235 (p0) cc_final: 0.6974 (p0) REVERT: B 233 CYS cc_start: 0.7864 (t) cc_final: 0.7641 (t) REVERT: B 239 ASN cc_start: 0.7899 (m-40) cc_final: 0.7687 (p0) REVERT: B 259 GLN cc_start: 0.7762 (pp30) cc_final: 0.7085 (pp30) REVERT: B 289 TYR cc_start: 0.7992 (m-80) cc_final: 0.7160 (m-80) REVERT: B 294 CYS cc_start: 0.6824 (OUTLIER) cc_final: 0.6535 (m) REVERT: B 296 VAL cc_start: 0.8217 (t) cc_final: 0.7903 (m) REVERT: B 323 ASP cc_start: 0.7790 (p0) cc_final: 0.7355 (p0) REVERT: B 325 MET cc_start: 0.7358 (tpp) cc_final: 0.7045 (tpp) REVERT: G 21 MET cc_start: 0.7215 (tmm) cc_final: 0.6868 (tmm) REVERT: E 34 MET cc_start: 0.7347 (mmm) cc_final: 0.6831 (mmm) REVERT: E 53 SER cc_start: 0.8563 (t) cc_final: 0.8247 (p) REVERT: E 72 ARG cc_start: 0.8055 (ptm160) cc_final: 0.7826 (ptm160) REVERT: E 90 ASP cc_start: 0.7532 (m-30) cc_final: 0.7249 (m-30) REVERT: E 91 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8270 (t) REVERT: E 99 SER cc_start: 0.7923 (t) cc_final: 0.7608 (p) REVERT: E 228 TYR cc_start: 0.8065 (m-10) cc_final: 0.7833 (m-80) REVERT: R 23 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8128 (mmmm) REVERT: R 143 MET cc_start: 0.7760 (tpp) cc_final: 0.7452 (tpp) REVERT: R 287 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.7036 (ptm160) REVERT: R 290 LYS cc_start: 0.8224 (tmtt) cc_final: 0.7854 (tmtt) REVERT: R 355 LYS cc_start: 0.8092 (mttm) cc_final: 0.7655 (mttm) outliers start: 30 outliers final: 22 residues processed: 312 average time/residue: 0.2336 time to fit residues: 96.7959 Evaluate side-chains 323 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 296 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 23 LYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 287 ARG Chi-restraints excluded: chain R residue 340 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.6980 chunk 71 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 8 optimal weight: 0.0670 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8929 Z= 0.195 Angle : 0.557 8.236 12097 Z= 0.289 Chirality : 0.043 0.156 1384 Planarity : 0.004 0.075 1518 Dihedral : 4.687 59.977 1222 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.96 % Allowed : 23.26 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.75 (0.26), residues: 1100 helix: 1.53 (0.27), residues: 371 sheet: 0.03 (0.30), residues: 287 loop : 0.08 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.004 0.001 HIS R 213 PHE 0.023 0.002 PHE R 190 TYR 0.018 0.002 TYR E 101 ARG 0.010 0.001 ARG E 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 301 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8387 (tppp) cc_final: 0.7803 (tppp) REVERT: A 33 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7218 (mt-10) REVERT: A 212 ILE cc_start: 0.8720 (tp) cc_final: 0.8476 (tp) REVERT: A 271 LYS cc_start: 0.7836 (ptmt) cc_final: 0.7494 (ptmt) REVERT: A 275 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7065 (mm-30) REVERT: A 296 TYR cc_start: 0.7874 (t80) cc_final: 0.6779 (t80) REVERT: A 308 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7213 (mt-10) REVERT: A 315 ASP cc_start: 0.7636 (p0) cc_final: 0.7379 (p0) REVERT: A 336 PHE cc_start: 0.8392 (t80) cc_final: 0.8146 (t80) REVERT: B 50 THR cc_start: 0.8154 (m) cc_final: 0.7644 (t) REVERT: B 134 ARG cc_start: 0.7520 (ptt180) cc_final: 0.7167 (ptp90) REVERT: B 165 THR cc_start: 0.7901 (p) cc_final: 0.7512 (m) REVERT: B 170 ASP cc_start: 0.7571 (t0) cc_final: 0.7284 (t0) REVERT: B 180 PHE cc_start: 0.8051 (m-80) cc_final: 0.7708 (m-80) REVERT: B 186 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6851 (p0) REVERT: B 188 MET cc_start: 0.6798 (mmp) cc_final: 0.6352 (mmt) REVERT: B 205 ASP cc_start: 0.7225 (p0) cc_final: 0.6957 (p0) REVERT: B 233 CYS cc_start: 0.7745 (t) cc_final: 0.7503 (t) REVERT: B 259 GLN cc_start: 0.7851 (pp30) cc_final: 0.7199 (pp30) REVERT: B 289 TYR cc_start: 0.7978 (m-80) cc_final: 0.7038 (m-80) REVERT: B 296 VAL cc_start: 0.8234 (t) cc_final: 0.7902 (m) REVERT: B 323 ASP cc_start: 0.7803 (p0) cc_final: 0.7351 (p0) REVERT: B 325 MET cc_start: 0.7388 (tpp) cc_final: 0.7063 (tpp) REVERT: G 21 MET cc_start: 0.7214 (tmm) cc_final: 0.6853 (tmm) REVERT: E 34 MET cc_start: 0.7371 (mmm) cc_final: 0.6849 (mmm) REVERT: E 53 SER cc_start: 0.8560 (t) cc_final: 0.8247 (p) REVERT: E 60 TYR cc_start: 0.8094 (m-80) cc_final: 0.7825 (m-80) REVERT: E 72 ARG cc_start: 0.8067 (ptm160) cc_final: 0.7854 (ptm160) REVERT: E 90 ASP cc_start: 0.7575 (m-30) cc_final: 0.7302 (m-30) REVERT: E 91 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8274 (t) REVERT: E 99 SER cc_start: 0.7950 (t) cc_final: 0.7636 (p) REVERT: E 138 ILE cc_start: 0.8436 (mm) cc_final: 0.8022 (mm) REVERT: R 23 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8137 (mmmm) REVERT: R 143 MET cc_start: 0.7768 (tpp) cc_final: 0.7470 (tpp) REVERT: R 287 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.7068 (ptm160) REVERT: R 290 LYS cc_start: 0.8233 (tmtt) cc_final: 0.7867 (tmtt) REVERT: R 355 LYS cc_start: 0.8097 (mttm) cc_final: 0.7664 (mttm) outliers start: 28 outliers final: 22 residues processed: 311 average time/residue: 0.2226 time to fit residues: 91.9974 Evaluate side-chains 324 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 298 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 23 LYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 287 ARG Chi-restraints excluded: chain R residue 340 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.0170 chunk 86 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 88 optimal weight: 0.0770 chunk 10 optimal weight: 0.0670 chunk 15 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 overall best weight: 0.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.133628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.119289 restraints weight = 13587.282| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.44 r_work: 0.3458 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8929 Z= 0.149 Angle : 0.547 8.169 12097 Z= 0.282 Chirality : 0.043 0.195 1384 Planarity : 0.004 0.073 1518 Dihedral : 4.570 59.765 1222 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.96 % Allowed : 23.26 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.78 (0.26), residues: 1100 helix: 1.55 (0.28), residues: 370 sheet: 0.18 (0.30), residues: 275 loop : 0.01 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS R 213 PHE 0.023 0.001 PHE R 190 TYR 0.016 0.001 TYR E 101 ARG 0.009 0.001 ARG E 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2595.38 seconds wall clock time: 47 minutes 26.59 seconds (2846.59 seconds total)