Starting phenix.real_space_refine on Fri Feb 16 20:38:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xz5_33525/02_2024/7xz5_33525_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xz5_33525/02_2024/7xz5_33525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xz5_33525/02_2024/7xz5_33525.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xz5_33525/02_2024/7xz5_33525.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xz5_33525/02_2024/7xz5_33525_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xz5_33525/02_2024/7xz5_33525_neut_trim_updated.pdb" } resolution = 3.1 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= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 56 5.16 5 C 5243 2.51 5 N 1433 2.21 5 O 1534 1.98 5 H 8189 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 228": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 265": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 317": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 333": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 336": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 342": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 373": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 374": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 380": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 385": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 389": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 134": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 150": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 214": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 219": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 251": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 304": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 314": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 98": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 71": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 81": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 103": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 112": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 287": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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: 16456 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3910 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5108 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 885 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1909 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 4644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4644 Unusual residues: {'LSC': 1} Classifications: {'peptide': 292, 'undetermined': 1} Link IDs: {'PTRANS': 9, 'TRANS': 282, None: 1} Not linked: pdbres="VAL R 300 " pdbres="LSC R 401 " Chain breaks: 1 Time building chain proxies: 7.76, per 1000 atoms: 0.47 Number of scatterers: 16456 At special positions: 0 Unit cell: (100.674, 99.603, 116.739, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 1 15.00 O 1534 8.00 N 1433 7.00 C 5243 6.00 H 8189 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 155 " distance=2.04 Simple disulfide: pdb=" SG CYS R 251 " - pdb=" SG CYS R 254 " distance=2.05 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: 12.96 Conformation dependent library (CDL) restraints added in 1.7 seconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 10 sheets defined 39.4% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.67 Creating SS restraints... Processing helix chain 'A' and resid 10 through 38 Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 350 removed outlier: 4.112A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 390 removed outlier: 3.739A pdb=" N ILE A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.824A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 2 through 35 removed outlier: 4.035A pdb=" N ILE R 10 " --> pdb=" O SER R 6 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 65 removed outlier: 3.651A pdb=" N LEU R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU R 62 " --> pdb=" O ILE R 58 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR R 63 " --> pdb=" O SER R 59 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ASP R 64 " --> pdb=" O GLY R 60 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN R 65 " --> pdb=" O LEU R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 108 removed outlier: 4.184A pdb=" N THR R 76 " --> pdb=" O THR R 73 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS R 78 " --> pdb=" O LYS R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 116 removed outlier: 3.550A pdb=" N LEU R 114 " --> pdb=" O PRO R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 142 Proline residue: R 140 - end of helix Processing helix chain 'R' and resid 163 through 171 Processing helix chain 'R' and resid 174 through 209 Processing helix chain 'R' and resid 222 through 250 removed outlier: 3.932A pdb=" N VAL R 229 " --> pdb=" O ARG R 225 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU R 236 " --> pdb=" O GLY R 232 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TRP R 238 " --> pdb=" O PHE R 234 " (cutoff:3.500A) Proline residue: R 240 - end of helix Processing helix chain 'R' and resid 256 through 260 removed outlier: 3.694A pdb=" N LEU R 260 " --> pdb=" O TYR R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 278 removed outlier: 4.251A pdb=" N GLY R 268 " --> pdb=" O LEU R 264 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN R 271 " --> pdb=" O LEU R 267 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER R 272 " --> pdb=" O GLY R 268 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU R 273 " --> pdb=" O VAL R 269 " (cutoff:3.500A) Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 284 through 298 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.441A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.001A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.973A 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: 6.473A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.289A 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 151 removed outlier: 6.566A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 202 removed outlier: 3.570A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.460A 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: 6.356A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.453A 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: 6.427A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.561A 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: 3.614A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.287A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1014 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: 5.78 Time building geometry restraints manager: 13.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6948 1.03 - 1.23: 1279 1.23 - 1.42: 3757 1.42 - 1.62: 4552 1.62 - 1.82: 81 Bond restraints: 16617 Sorted by residual: bond pdb=" ND1 HIS R 162 " pdb=" CE1 HIS R 162 " ideal model delta sigma weight residual 1.321 1.233 0.088 1.00e-02 1.00e+04 7.67e+01 bond pdb=" CE1 HIS R 164 " pdb=" NE2 HIS R 164 " ideal model delta sigma weight residual 1.321 1.233 0.088 1.00e-02 1.00e+04 7.66e+01 bond pdb=" CD2 HIS R 164 " pdb=" NE2 HIS R 164 " ideal model delta sigma weight residual 1.374 1.287 0.087 1.10e-02 8.26e+03 6.29e+01 bond pdb=" CZ ARG R 103 " pdb=" NH2 ARG R 103 " ideal model delta sigma weight residual 1.330 1.230 0.100 1.30e-02 5.92e+03 5.86e+01 bond pdb=" CZ ARG R 81 " pdb=" NH2 ARG R 81 " ideal model delta sigma weight residual 1.330 1.231 0.099 1.30e-02 5.92e+03 5.82e+01 ... (remaining 16612 not shown) Histogram of bond angle deviations from ideal: 96.14 - 104.24: 299 104.24 - 112.33: 18182 112.33 - 120.42: 6719 120.42 - 128.51: 4609 128.51 - 136.60: 88 Bond angle restraints: 29897 Sorted by residual: angle pdb=" N PRO N 100 " pdb=" CA PRO N 100 " pdb=" C PRO N 100 " ideal model delta sigma weight residual 113.78 127.83 -14.05 1.62e+00 3.81e-01 7.52e+01 angle pdb=" C21 LSC R 401 " pdb=" C22 LSC R 401 " pdb=" O23 LSC R 401 " ideal model delta sigma weight residual 108.44 133.71 -25.27 3.00e+00 1.11e-01 7.10e+01 angle pdb=" C LEU R 267 " pdb=" N GLY R 268 " pdb=" CA GLY R 268 " ideal model delta sigma weight residual 119.94 128.10 -8.16 1.11e+00 8.12e-01 5.41e+01 angle pdb=" CA PHE R 181 " pdb=" CB PHE R 181 " pdb=" CG PHE R 181 " ideal model delta sigma weight residual 113.80 121.13 -7.33 1.00e+00 1.00e+00 5.37e+01 angle pdb=" C ALA R 159 " pdb=" N VAL R 160 " pdb=" CA VAL R 160 " ideal model delta sigma weight residual 121.97 134.89 -12.92 1.80e+00 3.09e-01 5.15e+01 ... (remaining 29892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.91: 7516 27.91 - 55.82: 271 55.82 - 83.73: 49 83.73 - 111.64: 6 111.64 - 139.55: 2 Dihedral angle restraints: 7844 sinusoidal: 4233 harmonic: 3611 Sorted by residual: dihedral pdb=" C TYR R 185 " pdb=" N TYR R 185 " pdb=" CA TYR R 185 " pdb=" CB TYR R 185 " ideal model delta harmonic sigma weight residual -122.60 -134.73 12.13 0 2.50e+00 1.60e-01 2.35e+01 dihedral pdb=" C PHE R 138 " pdb=" N PHE R 138 " pdb=" CA PHE R 138 " pdb=" CB PHE R 138 " ideal model delta harmonic sigma weight residual -122.60 -134.28 11.68 0 2.50e+00 1.60e-01 2.18e+01 dihedral pdb=" C GLU R 261 " pdb=" N GLU R 261 " pdb=" CA GLU R 261 " pdb=" CB GLU R 261 " ideal model delta harmonic sigma weight residual -122.60 -134.20 11.60 0 2.50e+00 1.60e-01 2.15e+01 ... (remaining 7841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 1100 0.140 - 0.281: 10 0.281 - 0.421: 16 0.421 - 0.562: 102 0.562 - 0.702: 61 Chirality restraints: 1289 Sorted by residual: chirality pdb=" CG LEU R 139 " pdb=" CB LEU R 139 " pdb=" CD1 LEU R 139 " pdb=" CD2 LEU R 139 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CG LEU R 167 " pdb=" CB LEU R 167 " pdb=" CD1 LEU R 167 " pdb=" CD2 LEU R 167 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CG LEU R 77 " pdb=" CB LEU R 77 " pdb=" CD1 LEU R 77 " pdb=" CD2 LEU R 77 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.21e+01 ... (remaining 1286 not shown) Planarity restraints: 2465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN R 65 " -0.097 2.00e-02 2.50e+03 1.06e-01 1.67e+02 pdb=" CD GLN R 65 " 0.007 2.00e-02 2.50e+03 pdb=" OE1 GLN R 65 " 0.093 2.00e-02 2.50e+03 pdb=" NE2 GLN R 65 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN R 65 " 0.155 2.00e-02 2.50e+03 pdb="HE22 GLN R 65 " -0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 265 " -0.090 2.00e-02 2.50e+03 3.75e-02 5.63e+01 pdb=" CG TRP R 265 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP R 265 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP R 265 " 0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP R 265 " 0.045 2.00e-02 2.50e+03 pdb=" CE2 TRP R 265 " 0.019 2.00e-02 2.50e+03 pdb=" CE3 TRP R 265 " 0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 265 " -0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 265 " 0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP R 265 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP R 265 " -0.013 2.00e-02 2.50e+03 pdb=" HE1 TRP R 265 " 0.048 2.00e-02 2.50e+03 pdb=" HE3 TRP R 265 " 0.027 2.00e-02 2.50e+03 pdb=" HZ2 TRP R 265 " -0.073 2.00e-02 2.50e+03 pdb=" HZ3 TRP R 265 " 0.005 2.00e-02 2.50e+03 pdb=" HH2 TRP R 265 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 234 " 0.038 2.00e-02 2.50e+03 4.13e-02 5.13e+01 pdb=" CG PHE R 234 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE R 234 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE R 234 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE R 234 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE R 234 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE R 234 " 0.029 2.00e-02 2.50e+03 pdb=" HD1 PHE R 234 " -0.088 2.00e-02 2.50e+03 pdb=" HD2 PHE R 234 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 PHE R 234 " 0.026 2.00e-02 2.50e+03 pdb=" HE2 PHE R 234 " -0.081 2.00e-02 2.50e+03 pdb=" HZ PHE R 234 " 0.031 2.00e-02 2.50e+03 ... (remaining 2462 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 928 2.19 - 2.79: 33000 2.79 - 3.40: 45185 3.40 - 4.00: 59109 4.00 - 4.60: 91945 Nonbonded interactions: 230167 Sorted by model distance: nonbonded pdb=" H PHE B 235 " pdb=" O ALA B 240 " model vdw 1.590 1.850 nonbonded pdb=" OD1 ASP B 153 " pdb=" H ASN B 155 " model vdw 1.606 1.850 nonbonded pdb=" H GLN R 148 " pdb=" O VAL R 160 " model vdw 1.624 1.850 nonbonded pdb=" HG SER B 147 " pdb=" O VAL B 187 " model vdw 1.634 1.850 nonbonded pdb=" O ALA R 235 " pdb=" HG1 THR R 239 " model vdw 1.634 1.850 ... (remaining 230162 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: 0.490 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: 0.260 Extract box with map and model: 2.750 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 54.740 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 : 0.020 0.129 8428 Z= 1.295 Angle : 1.553 25.271 11401 Z= 1.011 Chirality : 0.210 0.702 1289 Planarity : 0.005 0.066 1450 Dihedral : 14.345 139.551 3062 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 8.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.26), residues: 1036 helix: 1.59 (0.25), residues: 422 sheet: 1.31 (0.37), residues: 202 loop : 0.04 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP R 265 HIS 0.003 0.001 HIS B 91 PHE 0.036 0.004 PHE R 234 TYR 0.054 0.004 TYR R 257 ARG 0.011 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 263 TYR cc_start: 0.6750 (m-80) cc_final: 0.6415 (m-10) REVERT: R 298 LYS cc_start: 0.6378 (ttmm) cc_final: 0.5945 (mptt) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.5671 time to fit residues: 125.4417 Evaluate side-chains 133 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8428 Z= 0.200 Angle : 0.508 4.671 11401 Z= 0.282 Chirality : 0.040 0.144 1289 Planarity : 0.004 0.033 1450 Dihedral : 7.219 94.510 1169 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.34 % Allowed : 5.50 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.27), residues: 1036 helix: 2.04 (0.26), residues: 413 sheet: 0.96 (0.38), residues: 196 loop : 0.15 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 297 HIS 0.010 0.001 HIS R 255 PHE 0.019 0.002 PHE N 108 TYR 0.012 0.001 TYR A 37 ARG 0.002 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 MET cc_start: 0.7678 (mtp) cc_final: 0.7417 (mtm) REVERT: R 263 TYR cc_start: 0.6569 (m-80) cc_final: 0.6331 (m-10) REVERT: R 298 LYS cc_start: 0.6304 (ttmm) cc_final: 0.5942 (mptt) outliers start: 3 outliers final: 3 residues processed: 144 average time/residue: 0.5622 time to fit residues: 105.2094 Evaluate side-chains 137 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 134 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 266 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8428 Z= 0.256 Angle : 0.519 6.247 11401 Z= 0.287 Chirality : 0.040 0.139 1289 Planarity : 0.005 0.047 1450 Dihedral : 6.843 85.549 1169 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.35 % Allowed : 6.62 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.27), residues: 1036 helix: 1.66 (0.26), residues: 418 sheet: 0.74 (0.37), residues: 206 loop : 0.16 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.008 0.002 HIS A 357 PHE 0.019 0.002 PHE N 108 TYR 0.012 0.002 TYR A 339 ARG 0.003 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7733 (mmm-85) cc_final: 0.7429 (mtm-85) REVERT: G 21 MET cc_start: 0.7714 (mtp) cc_final: 0.7429 (mtm) REVERT: N 106 ASP cc_start: 0.6108 (t0) cc_final: 0.5901 (t0) REVERT: R 298 LYS cc_start: 0.6616 (ttmm) cc_final: 0.6287 (mptt) outliers start: 12 outliers final: 7 residues processed: 149 average time/residue: 0.6000 time to fit residues: 115.5886 Evaluate side-chains 142 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 135 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 274 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 8428 Z= 0.411 Angle : 0.602 7.912 11401 Z= 0.332 Chirality : 0.043 0.150 1289 Planarity : 0.006 0.075 1450 Dihedral : 7.019 79.523 1169 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.36 % Allowed : 8.64 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1036 helix: 1.19 (0.26), residues: 412 sheet: 0.50 (0.34), residues: 227 loop : -0.11 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.011 0.002 HIS A 357 PHE 0.024 0.002 PHE N 108 TYR 0.015 0.002 TYR A 37 ARG 0.005 0.001 ARG R 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7776 (mmm-85) cc_final: 0.7368 (mtt-85) REVERT: A 248 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8349 (p) REVERT: G 21 MET cc_start: 0.7776 (mtp) cc_final: 0.7498 (mtm) outliers start: 21 outliers final: 14 residues processed: 144 average time/residue: 0.5797 time to fit residues: 108.1838 Evaluate side-chains 139 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 239 THR Chi-restraints excluded: chain R residue 265 TRP Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 274 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8428 Z= 0.268 Angle : 0.530 7.133 11401 Z= 0.290 Chirality : 0.040 0.138 1289 Planarity : 0.004 0.047 1450 Dihedral : 6.634 81.628 1169 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.91 % Allowed : 10.10 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.27), residues: 1036 helix: 1.21 (0.26), residues: 416 sheet: 0.49 (0.34), residues: 222 loop : -0.18 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.013 0.002 PHE N 108 TYR 0.013 0.002 TYR A 37 ARG 0.003 0.000 ARG R 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.6849 (ttm) cc_final: 0.6411 (tmm) REVERT: G 21 MET cc_start: 0.7693 (mtp) cc_final: 0.7428 (mtm) REVERT: R 82 MET cc_start: 0.7471 (tpp) cc_final: 0.7172 (tpp) REVERT: R 179 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7419 (mp) outliers start: 17 outliers final: 15 residues processed: 137 average time/residue: 0.5779 time to fit residues: 101.4693 Evaluate side-chains 137 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 265 TRP Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 274 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8428 Z= 0.235 Angle : 0.512 6.799 11401 Z= 0.279 Chirality : 0.039 0.140 1289 Planarity : 0.004 0.043 1450 Dihedral : 6.376 80.611 1169 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.24 % Allowed : 10.44 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.27), residues: 1036 helix: 1.29 (0.26), residues: 413 sheet: 0.48 (0.35), residues: 222 loop : -0.18 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.014 0.001 PHE N 108 TYR 0.012 0.001 TYR A 37 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 VAL cc_start: 0.8712 (OUTLIER) cc_final: 0.8356 (p) REVERT: A 386 MET cc_start: 0.6842 (ttm) cc_final: 0.6411 (tmm) REVERT: B 327 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8505 (p) REVERT: G 21 MET cc_start: 0.7707 (mtp) cc_final: 0.7435 (mtm) REVERT: R 82 MET cc_start: 0.7401 (tpp) cc_final: 0.7134 (tpp) REVERT: R 179 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7380 (mp) outliers start: 20 outliers final: 16 residues processed: 139 average time/residue: 0.5679 time to fit residues: 101.6396 Evaluate side-chains 142 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 265 TRP Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 274 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 0.0030 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8428 Z= 0.141 Angle : 0.462 5.003 11401 Z= 0.250 Chirality : 0.038 0.131 1289 Planarity : 0.004 0.035 1450 Dihedral : 6.028 79.648 1169 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.12 % Allowed : 11.90 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.27), residues: 1036 helix: 1.53 (0.27), residues: 414 sheet: 0.67 (0.35), residues: 215 loop : -0.11 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.010 0.001 PHE N 108 TYR 0.010 0.001 TYR A 37 ARG 0.003 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8348 (p) REVERT: A 386 MET cc_start: 0.6791 (ttm) cc_final: 0.6382 (tmm) REVERT: B 188 MET cc_start: 0.8405 (mmm) cc_final: 0.8127 (mmm) REVERT: G 21 MET cc_start: 0.7713 (mtp) cc_final: 0.7440 (mtm) REVERT: R 82 MET cc_start: 0.7270 (tpp) cc_final: 0.6965 (tpp) REVERT: R 225 ARG cc_start: 0.7200 (ttp80) cc_final: 0.6995 (ttp-110) outliers start: 10 outliers final: 8 residues processed: 138 average time/residue: 0.5755 time to fit residues: 102.4091 Evaluate side-chains 133 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 265 TRP Chi-restraints excluded: chain R residue 266 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8428 Z= 0.257 Angle : 0.515 6.251 11401 Z= 0.280 Chirality : 0.040 0.139 1289 Planarity : 0.004 0.047 1450 Dihedral : 6.196 73.586 1169 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.35 % Allowed : 12.01 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.27), residues: 1036 helix: 1.40 (0.27), residues: 410 sheet: 0.47 (0.34), residues: 224 loop : -0.21 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.019 0.002 PHE N 108 TYR 0.013 0.001 TYR R 185 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8364 (p) REVERT: B 327 VAL cc_start: 0.8729 (OUTLIER) cc_final: 0.8487 (p) REVERT: G 21 MET cc_start: 0.7778 (mtp) cc_final: 0.7504 (mtm) REVERT: R 82 MET cc_start: 0.7403 (tpp) cc_final: 0.7127 (tpp) REVERT: R 179 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7380 (mp) REVERT: R 225 ARG cc_start: 0.7294 (ttp80) cc_final: 0.7087 (ttp-110) outliers start: 12 outliers final: 8 residues processed: 136 average time/residue: 0.5850 time to fit residues: 102.5384 Evaluate side-chains 135 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 265 TRP Chi-restraints excluded: chain R residue 266 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8428 Z= 0.170 Angle : 0.476 5.529 11401 Z= 0.257 Chirality : 0.039 0.135 1289 Planarity : 0.004 0.035 1450 Dihedral : 6.024 75.364 1169 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.23 % Allowed : 12.68 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.27), residues: 1036 helix: 1.45 (0.27), residues: 416 sheet: 0.52 (0.35), residues: 220 loop : -0.16 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE N 108 TYR 0.011 0.001 TYR A 37 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8320 (p) REVERT: B 188 MET cc_start: 0.8427 (mmm) cc_final: 0.8144 (mmm) REVERT: G 21 MET cc_start: 0.7705 (mtp) cc_final: 0.7431 (mtm) REVERT: R 82 MET cc_start: 0.7307 (tpp) cc_final: 0.7085 (tpp) REVERT: R 225 ARG cc_start: 0.7246 (ttp80) cc_final: 0.7013 (ttp-110) outliers start: 11 outliers final: 10 residues processed: 134 average time/residue: 0.6017 time to fit residues: 103.8053 Evaluate side-chains 134 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 265 TRP Chi-restraints excluded: chain R residue 266 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8428 Z= 0.257 Angle : 0.516 6.462 11401 Z= 0.280 Chirality : 0.040 0.139 1289 Planarity : 0.004 0.048 1450 Dihedral : 6.170 69.941 1169 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.46 % Allowed : 12.23 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1036 helix: 1.38 (0.27), residues: 412 sheet: 0.43 (0.35), residues: 224 loop : -0.21 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.019 0.001 PHE N 108 TYR 0.013 0.001 TYR A 37 ARG 0.005 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8358 (p) REVERT: G 21 MET cc_start: 0.7775 (mtp) cc_final: 0.7505 (mtm) REVERT: R 82 MET cc_start: 0.7349 (tpp) cc_final: 0.7106 (tpp) REVERT: R 225 ARG cc_start: 0.7302 (ttp80) cc_final: 0.7048 (ttp-110) outliers start: 13 outliers final: 11 residues processed: 134 average time/residue: 0.5929 time to fit residues: 102.1635 Evaluate side-chains 136 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 265 TRP Chi-restraints excluded: chain R residue 266 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 10 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 54 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.148779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.111355 restraints weight = 28229.905| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.09 r_work: 0.3114 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8428 Z= 0.134 Angle : 0.462 4.881 11401 Z= 0.249 Chirality : 0.038 0.134 1289 Planarity : 0.004 0.036 1450 Dihedral : 5.917 75.484 1169 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.90 % Allowed : 12.91 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.27), residues: 1036 helix: 1.58 (0.27), residues: 415 sheet: 0.66 (0.35), residues: 215 loop : -0.10 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.002 0.001 HIS A 357 PHE 0.010 0.001 PHE R 181 TYR 0.010 0.001 TYR A 37 ARG 0.003 0.000 ARG G 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4173.70 seconds wall clock time: 74 minutes 26.59 seconds (4466.59 seconds total)