Starting phenix.real_space_refine on Wed Feb 14 20:34:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbj_22117/02_2024/6xbj_22117_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbj_22117/02_2024/6xbj_22117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbj_22117/02_2024/6xbj_22117.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbj_22117/02_2024/6xbj_22117.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbj_22117/02_2024/6xbj_22117_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbj_22117/02_2024/6xbj_22117_updated.pdb" } resolution = 3.88 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 76 5.16 5 C 6481 2.51 5 N 1735 2.21 5 O 1906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 74": "NH1" <-> "NH2" Residue "R ASP 95": "OD1" <-> "OD2" Residue "R ASP 97": "OD1" <-> "OD2" Residue "R GLU 100": "OE1" <-> "OE2" Residue "R ARG 113": "NH1" <-> "NH2" Residue "R GLU 135": "OE1" <-> "OE2" Residue "R ARG 144": "NH1" <-> "NH2" Residue "R GLU 158": "OE1" <-> "OE2" Residue "R ASP 165": "OD1" <-> "OD2" Residue "R PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 224": "OE1" <-> "OE2" Residue "R ASP 255": "OD1" <-> "OD2" Residue "R PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 290": "NH1" <-> "NH2" Residue "R ARG 291": "NH1" <-> "NH2" Residue "R ARG 296": "NH1" <-> "NH2" Residue "R GLU 305": "OE1" <-> "OE2" Residue "R TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 384": "NH1" <-> "NH2" Residue "R TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 482": "NH1" <-> "NH2" Residue "A ASP 9": "OD1" <-> "OD2" Residue "A ARG 32": "NH1" <-> "NH2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "S TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 73": "OD1" <-> "OD2" Residue "S TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10198 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 3658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3658 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 21, 'TRANS': 443} Chain breaks: 1 Chain: "A" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1736 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "S" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.87, per 1000 atoms: 0.58 Number of scatterers: 10198 At special positions: 0 Unit cell: (109.956, 124.117, 163.268, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 76 16.00 O 1906 8.00 N 1735 7.00 C 6481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS R 64 " - pdb=" SG CYS R 178 " distance=2.03 Simple disulfide: pdb=" SG CYS R 70 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 127 " distance=2.03 Simple disulfide: pdb=" SG CYS R 118 " - pdb=" SG CYS R 154 " distance=2.03 Simple disulfide: pdb=" SG CYS R 147 " - pdb=" SG CYS R 169 " distance=2.03 Simple disulfide: pdb=" SG CYS R 193 " - pdb=" SG CYS R 213 " distance=2.03 Simple disulfide: pdb=" SG CYS R 217 " - pdb=" SG CYS R 295 " distance=2.03 Simple disulfide: pdb=" SG CYS R 314 " - pdb=" SG CYS R 390 " distance=2.03 Simple disulfide: pdb=" SG CYS R 490 " - pdb=" SG CYS R 507 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.06 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.02 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: 3.98 Conformation dependent library (CDL) restraints added in 2.0 seconds 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 15 sheets defined 32.6% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'R' and resid 99 through 113 removed outlier: 4.092A pdb=" N GLY R 111 " --> pdb=" O VAL R 107 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU R 112 " --> pdb=" O LEU R 108 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ARG R 113 " --> pdb=" O TRP R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 129 removed outlier: 4.384A pdb=" N VAL R 121 " --> pdb=" O ARG R 117 " (cutoff:3.500A) Proline residue: R 124 - end of helix Processing helix chain 'R' and resid 144 through 150 removed outlier: 3.741A pdb=" N THR R 150 " --> pdb=" O LEU R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 160 Processing helix chain 'R' and resid 182 through 184 No H-bonds generated for 'chain 'R' and resid 182 through 184' Processing helix chain 'R' and resid 203 through 205 No H-bonds generated for 'chain 'R' and resid 203 through 205' Processing helix chain 'R' and resid 224 through 254 Processing helix chain 'R' and resid 262 through 281 Processing helix chain 'R' and resid 289 through 293 Processing helix chain 'R' and resid 315 through 345 removed outlier: 3.730A pdb=" N ALA R 345 " --> pdb=" O THR R 341 " (cutoff:3.500A) Processing helix chain 'R' and resid 352 through 355 removed outlier: 3.895A pdb=" N GLY R 355 " --> pdb=" O PRO R 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 352 through 355' Processing helix chain 'R' and resid 357 through 377 Proline residue: R 368 - end of helix Processing helix chain 'R' and resid 397 through 428 Proline residue: R 407 - end of helix Processing helix chain 'R' and resid 439 through 493 removed outlier: 3.568A pdb=" N LYS R 444 " --> pdb=" O LYS R 440 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE R 455 " --> pdb=" O ARG R 451 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE R 460 " --> pdb=" O GLY R 456 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL R 463 " --> pdb=" O ALA R 459 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR R 466 " --> pdb=" O PHE R 462 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP R 473 " --> pdb=" O CYS R 469 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN R 476 " --> pdb=" O TYR R 472 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ALA R 478 " --> pdb=" O PHE R 474 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU R 479 " --> pdb=" O PHE R 475 " (cutoff:3.500A) Processing helix chain 'R' and resid 515 through 533 removed outlier: 3.656A pdb=" N MET R 532 " --> pdb=" O THR R 528 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER R 533 " --> pdb=" O GLY R 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 31 removed outlier: 4.021A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 215 removed outlier: 5.639A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 277 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 308 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.178A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing sheet with id= A, first strand: chain 'R' and resid 197 through 199 Processing sheet with id= B, first strand: chain 'A' and resid 220 through 224 removed outlier: 3.968A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 265 through 268 removed outlier: 6.638A pdb=" N TYR A 320 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU A 268 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N HIS A 322 " --> pdb=" O LEU A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 49 through 52 removed outlier: 3.854A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.117A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 111 through 113 removed outlier: 3.846A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 148 through 153 removed outlier: 3.575A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 220 through 223 removed outlier: 3.680A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.471A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 296 through 298 removed outlier: 3.564A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.843A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.656A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.631A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'S' and resid 143 through 147 removed outlier: 3.642A pdb=" N ILE S 145 " --> pdb=" O LEU S 202 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR S 201 " --> pdb=" O SER S 194 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'S' and resid 214 through 216 removed outlier: 3.587A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1125 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: 2.61 Time building geometry restraints manager: 4.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1984 1.33 - 1.46: 2601 1.46 - 1.58: 5737 1.58 - 1.70: 0 1.70 - 1.82: 105 Bond restraints: 10427 Sorted by residual: bond pdb=" N VAL S 64 " pdb=" CA VAL S 64 " ideal model delta sigma weight residual 1.455 1.498 -0.042 1.04e-02 9.25e+03 1.66e+01 bond pdb=" N VAL B 90 " pdb=" CA VAL B 90 " ideal model delta sigma weight residual 1.452 1.497 -0.045 1.18e-02 7.18e+03 1.46e+01 bond pdb=" N VAL R 404 " pdb=" CA VAL R 404 " ideal model delta sigma weight residual 1.452 1.497 -0.044 1.18e-02 7.18e+03 1.42e+01 bond pdb=" N LEU R 367 " pdb=" CA LEU R 367 " ideal model delta sigma weight residual 1.461 1.495 -0.034 9.20e-03 1.18e+04 1.39e+01 bond pdb=" N GLY B 185 " pdb=" CA GLY B 185 " ideal model delta sigma weight residual 1.445 1.478 -0.034 9.20e-03 1.18e+04 1.33e+01 ... (remaining 10422 not shown) Histogram of bond angle deviations from ideal: 99.47 - 106.52: 258 106.52 - 113.56: 5350 113.56 - 120.60: 4801 120.60 - 127.65: 3639 127.65 - 134.69: 86 Bond angle restraints: 14134 Sorted by residual: angle pdb=" C TYR S 223 " pdb=" CA TYR S 223 " pdb=" CB TYR S 223 " ideal model delta sigma weight residual 110.34 101.08 9.26 1.30e+00 5.92e-01 5.07e+01 angle pdb=" C GLN R 216 " pdb=" N CYS R 217 " pdb=" CA CYS R 217 " ideal model delta sigma weight residual 120.28 127.65 -7.37 1.34e+00 5.57e-01 3.03e+01 angle pdb=" C GLU R 194 " pdb=" N VAL R 195 " pdb=" CA VAL R 195 " ideal model delta sigma weight residual 120.43 125.32 -4.89 9.60e-01 1.09e+00 2.60e+01 angle pdb=" C GLY R 415 " pdb=" N GLY R 416 " pdb=" CA GLY R 416 " ideal model delta sigma weight residual 119.99 125.40 -5.41 1.13e+00 7.83e-01 2.29e+01 angle pdb=" C PHE A 259 " pdb=" N THR A 260 " pdb=" CA THR A 260 " ideal model delta sigma weight residual 120.38 126.90 -6.52 1.37e+00 5.33e-01 2.26e+01 ... (remaining 14129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.29: 5928 25.29 - 50.58: 278 50.58 - 75.87: 19 75.87 - 101.16: 0 101.16 - 126.45: 1 Dihedral angle restraints: 6226 sinusoidal: 2479 harmonic: 3747 Sorted by residual: dihedral pdb=" CA TYR S 223 " pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CA PRO S 224 " ideal model delta harmonic sigma weight residual 180.00 53.55 126.45 0 5.00e+00 4.00e-02 6.40e+02 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 159.74 -66.74 1 1.00e+01 1.00e-02 5.81e+01 dihedral pdb=" CB CYS R 217 " pdb=" SG CYS R 217 " pdb=" SG CYS R 295 " pdb=" CB CYS R 295 " ideal model delta sinusoidal sigma weight residual -86.00 -137.69 51.69 1 1.00e+01 1.00e-02 3.65e+01 ... (remaining 6223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 720 0.057 - 0.115: 587 0.115 - 0.172: 244 0.172 - 0.229: 20 0.229 - 0.286: 1 Chirality restraints: 1572 Sorted by residual: chirality pdb=" C13 CLR R 701 " pdb=" C12 CLR R 701 " pdb=" C14 CLR R 701 " pdb=" C17 CLR R 701 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C14 CLR R 701 " pdb=" C13 CLR R 701 " pdb=" C15 CLR R 701 " pdb=" C8 CLR R 701 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA TYR R 262 " pdb=" N TYR R 262 " pdb=" C TYR R 262 " pdb=" CB TYR R 262 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1569 not shown) Planarity restraints: 1801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR S 223 " 0.052 5.00e-02 4.00e+02 7.89e-02 9.95e+00 pdb=" N PRO S 224 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO S 224 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO S 224 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 121 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.89e+00 pdb=" C CYS B 121 " -0.049 2.00e-02 2.50e+03 pdb=" O CYS B 121 " 0.018 2.00e-02 2.50e+03 pdb=" N SER B 122 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 259 " 0.010 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C PHE A 259 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE A 259 " 0.014 2.00e-02 2.50e+03 pdb=" N THR A 260 " 0.013 2.00e-02 2.50e+03 ... (remaining 1798 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 322 2.71 - 3.26: 10036 3.26 - 3.81: 15312 3.81 - 4.35: 19638 4.35 - 4.90: 33024 Nonbonded interactions: 78332 Sorted by model distance: nonbonded pdb=" O MET R 525 " pdb=" OG1 THR R 528 " model vdw 2.168 2.440 nonbonded pdb=" O ILE R 375 " pdb=" O VAL R 378 " model vdw 2.184 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.314 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.334 2.440 nonbonded pdb=" OG1 THR B 65 " pdb=" O PRO B 107 " model vdw 2.342 2.440 ... (remaining 78327 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.290 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.040 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 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 : 0.014 0.060 10427 Z= 0.902 Angle : 1.762 9.259 14134 Z= 1.293 Chirality : 0.082 0.286 1572 Planarity : 0.004 0.079 1801 Dihedral : 13.702 126.448 3782 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.36 % Allowed : 5.99 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % 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: -4.02 (0.19), residues: 1283 helix: -1.62 (0.22), residues: 411 sheet: -3.57 (0.28), residues: 216 loop : -3.08 (0.20), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 163 HIS 0.008 0.002 HIS B 54 PHE 0.019 0.003 PHE A 334 TYR 0.024 0.003 TYR S 103 ARG 0.006 0.001 ARG S 179 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 287 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 74 ARG cc_start: 0.7136 (mmm-85) cc_final: 0.6766 (tpt90) REVERT: R 237 PHE cc_start: 0.7163 (t80) cc_final: 0.6641 (t80) REVERT: R 261 ARG cc_start: 0.5099 (ptt-90) cc_final: 0.4857 (ptt-90) REVERT: R 301 MET cc_start: 0.8609 (ptp) cc_final: 0.8054 (ptp) REVERT: R 339 TRP cc_start: 0.7367 (m-10) cc_final: 0.6973 (m-10) REVERT: R 381 VAL cc_start: 0.6174 (OUTLIER) cc_final: 0.5743 (p) REVERT: R 397 TYR cc_start: 0.7588 (p90) cc_final: 0.7375 (p90) REVERT: R 424 MET cc_start: 0.8881 (mtm) cc_final: 0.8570 (mtm) REVERT: R 439 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7703 (tp30) REVERT: R 473 ASP cc_start: 0.8618 (t0) cc_final: 0.8351 (t0) REVERT: R 475 PHE cc_start: 0.5459 (m-80) cc_final: 0.4983 (m-10) REVERT: R 480 TRP cc_start: 0.7432 (m-10) cc_final: 0.7113 (m-90) REVERT: R 482 ARG cc_start: 0.7839 (tmm-80) cc_final: 0.7398 (mpt180) REVERT: R 486 ASP cc_start: 0.8086 (m-30) cc_final: 0.7376 (m-30) REVERT: R 526 PHE cc_start: 0.7629 (m-10) cc_final: 0.7420 (m-80) REVERT: R 532 MET cc_start: 0.7814 (mmt) cc_final: 0.7546 (mmt) REVERT: A 8 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7953 (mt-10) REVERT: A 200 ASP cc_start: 0.7996 (p0) cc_final: 0.7552 (t0) REVERT: A 242 ARG cc_start: 0.7558 (mmm-85) cc_final: 0.6900 (mmt180) REVERT: A 243 MET cc_start: 0.7368 (tpp) cc_final: 0.7048 (tpp) REVERT: A 275 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8335 (tt0) REVERT: A 277 LYS cc_start: 0.8117 (tptt) cc_final: 0.7812 (tppt) REVERT: A 302 TYR cc_start: 0.7625 (t80) cc_final: 0.7194 (t80) REVERT: B 20 ASP cc_start: 0.8974 (t0) cc_final: 0.8771 (t0) REVERT: B 36 ASN cc_start: 0.8418 (t0) cc_final: 0.8186 (t0) REVERT: B 37 ILE cc_start: 0.8993 (tp) cc_final: 0.8644 (tp) REVERT: B 95 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7484 (pp) REVERT: B 138 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7381 (pp20) REVERT: B 188 MET cc_start: 0.8194 (mmm) cc_final: 0.7953 (mmm) REVERT: B 189 SER cc_start: 0.8613 (t) cc_final: 0.8298 (t) REVERT: B 215 GLU cc_start: 0.8196 (mp0) cc_final: 0.7445 (mp0) REVERT: B 217 MET cc_start: 0.7107 (ptp) cc_final: 0.6887 (ptp) REVERT: B 228 ASP cc_start: 0.7689 (m-30) cc_final: 0.6515 (m-30) REVERT: B 260 GLU cc_start: 0.8671 (tt0) cc_final: 0.8138 (tt0) REVERT: B 284 LEU cc_start: 0.7605 (pt) cc_final: 0.7235 (pt) REVERT: B 295 ASN cc_start: 0.8514 (m-40) cc_final: 0.8136 (m-40) REVERT: B 297 TRP cc_start: 0.8319 (m100) cc_final: 0.7691 (m100) REVERT: B 325 MET cc_start: 0.8160 (mmm) cc_final: 0.7791 (tpt) REVERT: B 339 TRP cc_start: 0.8243 (m100) cc_final: 0.7772 (m100) REVERT: G 18 GLN cc_start: 0.6855 (tm-30) cc_final: 0.6006 (tm-30) REVERT: G 21 MET cc_start: 0.7900 (ttp) cc_final: 0.7507 (tmm) REVERT: G 38 MET cc_start: 0.7914 (tmm) cc_final: 0.7574 (tpp) REVERT: G 42 GLU cc_start: 0.8250 (tm-30) cc_final: 0.8038 (pp20) REVERT: G 48 ASP cc_start: 0.6960 (t70) cc_final: 0.6748 (t0) REVERT: S 3 GLN cc_start: 0.7014 (tp40) cc_final: 0.6485 (tt0) REVERT: S 87 ARG cc_start: 0.7143 (mtp180) cc_final: 0.6915 (mtt90) REVERT: S 89 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8714 (mm-30) REVERT: S 125 ASP cc_start: 0.8072 (p0) cc_final: 0.7789 (p0) REVERT: S 141 GLU cc_start: 0.7343 (mp0) cc_final: 0.6794 (mp0) REVERT: S 180 MET cc_start: 0.8477 (ptm) cc_final: 0.7595 (ptm) REVERT: S 208 GLU cc_start: 0.8370 (pt0) cc_final: 0.7778 (pm20) REVERT: S 211 ASP cc_start: 0.8641 (t0) cc_final: 0.8156 (t0) outliers start: 4 outliers final: 0 residues processed: 291 average time/residue: 0.2650 time to fit residues: 103.1592 Evaluate side-chains 208 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 206 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain B residue 95 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 99 GLN R 114 ASN R 136 ASN R 180 ASN ** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 433 HIS R 511 ASN A 213 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 340 ASN S 167 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10427 Z= 0.205 Angle : 0.620 11.684 14134 Z= 0.314 Chirality : 0.041 0.210 1572 Planarity : 0.004 0.071 1801 Dihedral : 6.229 72.000 1478 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.99 % Allowed : 12.79 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.22), residues: 1283 helix: 0.37 (0.25), residues: 430 sheet: -3.04 (0.28), residues: 255 loop : -2.42 (0.22), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 163 HIS 0.006 0.001 HIS S 35 PHE 0.011 0.001 PHE R 318 TYR 0.014 0.001 TYR S 50 ARG 0.005 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 232 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 159 ARG cc_start: 0.7325 (ttm-80) cc_final: 0.6908 (ttt-90) REVERT: R 237 PHE cc_start: 0.7081 (t80) cc_final: 0.6577 (t80) REVERT: R 301 MET cc_start: 0.8438 (ptp) cc_final: 0.7990 (ptp) REVERT: R 339 TRP cc_start: 0.7394 (m-10) cc_final: 0.6836 (m-90) REVERT: R 381 VAL cc_start: 0.5793 (OUTLIER) cc_final: 0.5569 (p) REVERT: R 397 TYR cc_start: 0.7662 (p90) cc_final: 0.7413 (p90) REVERT: R 473 ASP cc_start: 0.8747 (t0) cc_final: 0.8533 (t0) REVERT: R 475 PHE cc_start: 0.5502 (m-80) cc_final: 0.4985 (m-10) REVERT: R 480 TRP cc_start: 0.7238 (m-10) cc_final: 0.6972 (m-10) REVERT: R 481 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7420 (tp30) REVERT: R 485 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8401 (ptm-80) REVERT: A 8 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8126 (mt-10) REVERT: A 53 MET cc_start: 0.7424 (mmt) cc_final: 0.7200 (mmm) REVERT: A 200 ASP cc_start: 0.7969 (p0) cc_final: 0.7295 (t0) REVERT: A 205 ARG cc_start: 0.8157 (mtm-85) cc_final: 0.7333 (tpp-160) REVERT: A 275 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8278 (tt0) REVERT: A 313 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6739 (ptp90) REVERT: A 327 THR cc_start: 0.6434 (OUTLIER) cc_final: 0.5875 (t) REVERT: B 36 ASN cc_start: 0.8327 (t0) cc_final: 0.8120 (t0) REVERT: B 37 ILE cc_start: 0.8930 (tp) cc_final: 0.8708 (tp) REVERT: B 59 TYR cc_start: 0.7833 (m-10) cc_final: 0.7390 (m-80) REVERT: B 95 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7196 (pp) REVERT: B 138 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7377 (pp20) REVERT: B 215 GLU cc_start: 0.7770 (mp0) cc_final: 0.7390 (mp0) REVERT: B 217 MET cc_start: 0.6830 (ptp) cc_final: 0.6611 (ptt) REVERT: B 228 ASP cc_start: 0.7724 (m-30) cc_final: 0.6652 (m-30) REVERT: B 297 TRP cc_start: 0.8620 (m100) cc_final: 0.7911 (m-10) REVERT: B 339 TRP cc_start: 0.7709 (m100) cc_final: 0.7381 (m100) REVERT: G 18 GLN cc_start: 0.6849 (tm-30) cc_final: 0.6126 (tm-30) REVERT: G 21 MET cc_start: 0.7889 (ttp) cc_final: 0.7550 (tmm) REVERT: G 48 ASP cc_start: 0.7177 (t70) cc_final: 0.6746 (t0) REVERT: S 3 GLN cc_start: 0.6612 (tp40) cc_final: 0.5901 (tt0) REVERT: S 87 ARG cc_start: 0.7138 (mtp180) cc_final: 0.6885 (mtt90) REVERT: S 125 ASP cc_start: 0.8018 (p0) cc_final: 0.7732 (p0) REVERT: S 141 GLU cc_start: 0.7325 (mp0) cc_final: 0.6831 (mp0) REVERT: S 166 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8177 (tt) REVERT: S 180 MET cc_start: 0.8259 (ptm) cc_final: 0.7560 (ptm) REVERT: S 208 GLU cc_start: 0.8486 (pt0) cc_final: 0.7877 (pm20) REVERT: S 211 ASP cc_start: 0.8673 (t0) cc_final: 0.8113 (t0) outliers start: 33 outliers final: 12 residues processed: 253 average time/residue: 0.2596 time to fit residues: 89.8830 Evaluate side-chains 216 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 198 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 470 HIS Chi-restraints excluded: chain R residue 485 ARG Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN B 91 HIS B 237 ASN G 44 HIS G 59 ASN S 167 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 10427 Z= 0.531 Angle : 0.743 12.597 14134 Z= 0.379 Chirality : 0.046 0.212 1572 Planarity : 0.005 0.066 1801 Dihedral : 6.254 61.035 1478 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.99 % Allowed : 14.88 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.22), residues: 1283 helix: 0.57 (0.24), residues: 429 sheet: -3.10 (0.27), residues: 265 loop : -2.36 (0.23), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 82 HIS 0.012 0.001 HIS A 188 PHE 0.023 0.002 PHE B 241 TYR 0.020 0.002 TYR S 50 ARG 0.005 0.001 ARG R 261 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 196 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 ARG cc_start: 0.7036 (mmm-85) cc_final: 0.6600 (tpt90) REVERT: R 237 PHE cc_start: 0.7000 (OUTLIER) cc_final: 0.6498 (t80) REVERT: R 301 MET cc_start: 0.8406 (ptp) cc_final: 0.8102 (ptp) REVERT: R 339 TRP cc_start: 0.7490 (m-10) cc_final: 0.6853 (m-90) REVERT: R 481 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7498 (tp30) REVERT: A 14 GLU cc_start: 0.7342 (tm-30) cc_final: 0.7077 (tm-30) REVERT: A 205 ARG cc_start: 0.8324 (mtm-85) cc_final: 0.7579 (tpp-160) REVERT: A 313 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6736 (ptp90) REVERT: A 327 THR cc_start: 0.6463 (OUTLIER) cc_final: 0.5872 (t) REVERT: B 138 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7380 (pp20) REVERT: B 211 TRP cc_start: 0.8558 (m100) cc_final: 0.8344 (m100) REVERT: B 215 GLU cc_start: 0.7548 (mp0) cc_final: 0.7179 (mp0) REVERT: B 228 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.6843 (m-30) REVERT: B 297 TRP cc_start: 0.8624 (m100) cc_final: 0.7958 (m100) REVERT: G 18 GLN cc_start: 0.6738 (tm-30) cc_final: 0.6005 (tm-30) REVERT: G 21 MET cc_start: 0.7944 (ttp) cc_final: 0.7638 (tmm) REVERT: G 48 ASP cc_start: 0.6986 (t70) cc_final: 0.6396 (t70) REVERT: S 87 ARG cc_start: 0.7128 (mtp180) cc_final: 0.6912 (mtt90) REVERT: S 141 GLU cc_start: 0.7333 (mp0) cc_final: 0.6871 (mp0) REVERT: S 166 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8173 (tt) REVERT: S 180 MET cc_start: 0.8226 (ptm) cc_final: 0.7839 (ptm) REVERT: S 208 GLU cc_start: 0.8459 (pt0) cc_final: 0.7870 (pm20) REVERT: S 211 ASP cc_start: 0.8767 (t0) cc_final: 0.8174 (t0) outliers start: 55 outliers final: 39 residues processed: 239 average time/residue: 0.2371 time to fit residues: 78.3807 Evaluate side-chains 227 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 183 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 MET Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 241 THR Chi-restraints excluded: chain R residue 314 CYS Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 448 THR Chi-restraints excluded: chain R residue 458 LEU Chi-restraints excluded: chain R residue 469 CYS Chi-restraints excluded: chain R residue 470 HIS Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 149 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN S 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10427 Z= 0.215 Angle : 0.609 10.344 14134 Z= 0.303 Chirality : 0.041 0.157 1572 Planarity : 0.004 0.060 1801 Dihedral : 5.902 57.238 1478 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.63 % Allowed : 17.88 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.23), residues: 1283 helix: 1.05 (0.25), residues: 430 sheet: -2.63 (0.30), residues: 238 loop : -2.26 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 119 HIS 0.007 0.001 HIS S 35 PHE 0.011 0.001 PHE R 252 TYR 0.014 0.001 TYR R 472 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 202 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 237 PHE cc_start: 0.7002 (OUTLIER) cc_final: 0.6436 (t80) REVERT: R 301 MET cc_start: 0.8433 (ptp) cc_final: 0.8116 (ptp) REVERT: R 339 TRP cc_start: 0.7389 (m-10) cc_final: 0.6821 (m-90) REVERT: R 381 VAL cc_start: 0.6597 (OUTLIER) cc_final: 0.6376 (p) REVERT: R 397 TYR cc_start: 0.7636 (p90) cc_final: 0.7397 (p90) REVERT: A 205 ARG cc_start: 0.8263 (mtm-85) cc_final: 0.7475 (tpp-160) REVERT: A 313 ARG cc_start: 0.7275 (ptp90) cc_final: 0.6831 (ptp90) REVERT: A 327 THR cc_start: 0.6447 (OUTLIER) cc_final: 0.5857 (t) REVERT: B 36 ASN cc_start: 0.8351 (t0) cc_final: 0.8121 (t0) REVERT: B 59 TYR cc_start: 0.8014 (m-80) cc_final: 0.7464 (m-80) REVERT: B 82 TRP cc_start: 0.8687 (m100) cc_final: 0.8349 (m100) REVERT: B 138 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7407 (pp20) REVERT: B 215 GLU cc_start: 0.7760 (mp0) cc_final: 0.7400 (mp0) REVERT: B 228 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7055 (p0) REVERT: B 297 TRP cc_start: 0.8675 (m100) cc_final: 0.8095 (m100) REVERT: B 339 TRP cc_start: 0.7515 (m100) cc_final: 0.7136 (m100) REVERT: G 18 GLN cc_start: 0.6863 (tm-30) cc_final: 0.6162 (tm-30) REVERT: G 21 MET cc_start: 0.7905 (ttp) cc_final: 0.7597 (tmm) REVERT: G 48 ASP cc_start: 0.6997 (t70) cc_final: 0.6672 (t0) REVERT: S 22 CYS cc_start: 0.6231 (OUTLIER) cc_final: 0.5850 (t) REVERT: S 82 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7415 (mm-40) REVERT: S 87 ARG cc_start: 0.7132 (mtp180) cc_final: 0.6915 (mtt90) REVERT: S 141 GLU cc_start: 0.7341 (mp0) cc_final: 0.6906 (mp0) REVERT: S 166 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8133 (tt) REVERT: S 180 MET cc_start: 0.8194 (ptm) cc_final: 0.7634 (ptm) REVERT: S 208 GLU cc_start: 0.8513 (pt0) cc_final: 0.7891 (pm20) REVERT: S 211 ASP cc_start: 0.8696 (t0) cc_final: 0.8263 (t0) REVERT: S 222 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7932 (mm-30) REVERT: S 235 LEU cc_start: 0.8031 (tt) cc_final: 0.7812 (mt) outliers start: 51 outliers final: 33 residues processed: 236 average time/residue: 0.2219 time to fit residues: 72.8044 Evaluate side-chains 230 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 191 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 131 MET Chi-restraints excluded: chain R residue 145 THR Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 314 CYS Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 378 VAL Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 469 CYS Chi-restraints excluded: chain R residue 470 HIS Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 105 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 63 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6224 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10427 Z= 0.174 Angle : 0.586 12.219 14134 Z= 0.288 Chirality : 0.040 0.166 1572 Planarity : 0.004 0.061 1801 Dihedral : 5.402 53.467 1478 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.90 % Allowed : 17.97 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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 (0.23), residues: 1283 helix: 1.31 (0.25), residues: 422 sheet: -2.43 (0.31), residues: 240 loop : -2.13 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP R 119 HIS 0.006 0.001 HIS S 35 PHE 0.010 0.001 PHE A 223 TYR 0.012 0.001 TYR A 302 ARG 0.005 0.000 ARG R 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 207 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 237 PHE cc_start: 0.6925 (OUTLIER) cc_final: 0.6452 (t80) REVERT: R 257 ARG cc_start: 0.6888 (mmm160) cc_final: 0.6542 (ptp-170) REVERT: R 301 MET cc_start: 0.8420 (ptp) cc_final: 0.8079 (ptp) REVERT: R 339 TRP cc_start: 0.7396 (m-10) cc_final: 0.6794 (m-90) REVERT: R 381 VAL cc_start: 0.6449 (OUTLIER) cc_final: 0.6226 (p) REVERT: R 397 TYR cc_start: 0.7630 (p90) cc_final: 0.7423 (p90) REVERT: R 450 LEU cc_start: 0.7620 (tp) cc_final: 0.7237 (mt) REVERT: A 205 ARG cc_start: 0.8253 (mtm-85) cc_final: 0.7473 (tpp-160) REVERT: A 313 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6867 (ptp90) REVERT: A 327 THR cc_start: 0.6474 (OUTLIER) cc_final: 0.5901 (t) REVERT: B 10 GLU cc_start: 0.8862 (tp30) cc_final: 0.8210 (mp0) REVERT: B 36 ASN cc_start: 0.8380 (t0) cc_final: 0.8126 (t0) REVERT: B 59 TYR cc_start: 0.7986 (m-80) cc_final: 0.7446 (m-80) REVERT: B 138 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7421 (pp20) REVERT: B 215 GLU cc_start: 0.7900 (mp0) cc_final: 0.7514 (mp0) REVERT: B 228 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7117 (p0) REVERT: B 297 TRP cc_start: 0.8599 (m100) cc_final: 0.8104 (m100) REVERT: G 18 GLN cc_start: 0.6755 (tm-30) cc_final: 0.5951 (tm-30) REVERT: G 21 MET cc_start: 0.7840 (ttp) cc_final: 0.7578 (tmm) REVERT: G 48 ASP cc_start: 0.7014 (t70) cc_final: 0.6589 (t0) REVERT: S 22 CYS cc_start: 0.6152 (OUTLIER) cc_final: 0.5835 (t) REVERT: S 82 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7704 (mp10) REVERT: S 141 GLU cc_start: 0.7278 (mp0) cc_final: 0.6842 (mp0) REVERT: S 166 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8200 (tt) REVERT: S 180 MET cc_start: 0.8153 (ptm) cc_final: 0.7628 (ptm) REVERT: S 208 GLU cc_start: 0.8576 (pt0) cc_final: 0.7976 (pm20) REVERT: S 211 ASP cc_start: 0.8632 (t0) cc_final: 0.8360 (t0) REVERT: S 222 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7815 (mm-30) outliers start: 54 outliers final: 30 residues processed: 241 average time/residue: 0.2207 time to fit residues: 74.4619 Evaluate side-chains 228 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 191 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 131 MET Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 314 CYS Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 378 VAL Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 469 CYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 72 optimal weight: 0.1980 chunk 30 optimal weight: 0.5980 chunk 123 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6232 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10427 Z= 0.196 Angle : 0.592 14.005 14134 Z= 0.290 Chirality : 0.040 0.150 1572 Planarity : 0.004 0.059 1801 Dihedral : 5.201 51.750 1478 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.72 % Allowed : 18.51 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -1.29 (0.23), residues: 1283 helix: 1.48 (0.25), residues: 427 sheet: -2.25 (0.31), residues: 240 loop : -1.99 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.010 0.001 PHE A 223 TYR 0.016 0.001 TYR R 472 ARG 0.005 0.000 ARG R 261 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 195 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 237 PHE cc_start: 0.6964 (OUTLIER) cc_final: 0.6499 (t80) REVERT: R 257 ARG cc_start: 0.6934 (mmm160) cc_final: 0.6566 (ptp-170) REVERT: R 339 TRP cc_start: 0.7406 (m-10) cc_final: 0.6784 (m-90) REVERT: R 381 VAL cc_start: 0.6337 (OUTLIER) cc_final: 0.5884 (p) REVERT: R 397 TYR cc_start: 0.7632 (p90) cc_final: 0.7419 (p90) REVERT: R 475 PHE cc_start: 0.5354 (OUTLIER) cc_final: 0.5087 (m-80) REVERT: A 205 ARG cc_start: 0.8266 (mtm-85) cc_final: 0.7480 (tpp-160) REVERT: A 327 THR cc_start: 0.6488 (OUTLIER) cc_final: 0.5923 (t) REVERT: B 10 GLU cc_start: 0.8849 (tp30) cc_final: 0.8209 (mp0) REVERT: B 36 ASN cc_start: 0.8409 (t0) cc_final: 0.8102 (t0) REVERT: B 59 TYR cc_start: 0.8002 (m-80) cc_final: 0.7513 (m-80) REVERT: B 82 TRP cc_start: 0.8503 (m100) cc_final: 0.8266 (m100) REVERT: B 215 GLU cc_start: 0.7902 (mp0) cc_final: 0.7502 (mp0) REVERT: B 228 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7183 (p0) REVERT: B 297 TRP cc_start: 0.8591 (m100) cc_final: 0.8103 (m100) REVERT: G 18 GLN cc_start: 0.6785 (tm-30) cc_final: 0.6215 (tm-30) REVERT: G 21 MET cc_start: 0.7817 (ttp) cc_final: 0.7589 (tmm) REVERT: G 48 ASP cc_start: 0.7046 (t70) cc_final: 0.6620 (t0) REVERT: S 22 CYS cc_start: 0.6231 (OUTLIER) cc_final: 0.5855 (t) REVERT: S 82 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7810 (mp10) REVERT: S 141 GLU cc_start: 0.7267 (mp0) cc_final: 0.6853 (mp0) REVERT: S 166 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8168 (tt) REVERT: S 180 MET cc_start: 0.8152 (ptm) cc_final: 0.7632 (ptm) REVERT: S 208 GLU cc_start: 0.8598 (pt0) cc_final: 0.7967 (pm20) REVERT: S 211 ASP cc_start: 0.8733 (t0) cc_final: 0.8413 (t0) REVERT: S 223 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7615 (t80) outliers start: 52 outliers final: 36 residues processed: 229 average time/residue: 0.2101 time to fit residues: 68.1208 Evaluate side-chains 230 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 186 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 131 MET Chi-restraints excluded: chain R residue 145 THR Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 314 CYS Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 378 VAL Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 458 LEU Chi-restraints excluded: chain R residue 469 CYS Chi-restraints excluded: chain R residue 475 PHE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 149 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 3.9990 chunk 13 optimal weight: 0.0670 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 0.0970 chunk 69 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10427 Z= 0.174 Angle : 0.595 13.134 14134 Z= 0.290 Chirality : 0.040 0.145 1572 Planarity : 0.004 0.110 1801 Dihedral : 5.048 49.340 1478 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.90 % Allowed : 19.15 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -1.17 (0.24), residues: 1283 helix: 1.61 (0.26), residues: 426 sheet: -2.15 (0.31), residues: 240 loop : -1.96 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.009 0.001 PHE A 223 TYR 0.019 0.001 TYR A 302 ARG 0.003 0.000 ARG R 485 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 201 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 237 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.6551 (t80) REVERT: R 257 ARG cc_start: 0.6862 (mmm160) cc_final: 0.6515 (ptp-170) REVERT: R 301 MET cc_start: 0.8225 (ptp) cc_final: 0.8017 (ptp) REVERT: R 305 GLU cc_start: 0.6001 (tp30) cc_final: 0.5131 (tp30) REVERT: R 339 TRP cc_start: 0.7414 (m-10) cc_final: 0.6779 (m-90) REVERT: R 397 TYR cc_start: 0.7746 (p90) cc_final: 0.7540 (p90) REVERT: R 475 PHE cc_start: 0.5299 (OUTLIER) cc_final: 0.5071 (m-80) REVERT: A 197 LYS cc_start: 0.5779 (mttt) cc_final: 0.5562 (mttm) REVERT: A 205 ARG cc_start: 0.8262 (mtm-85) cc_final: 0.7997 (tpp80) REVERT: A 310 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7421 (mm) REVERT: A 327 THR cc_start: 0.6442 (OUTLIER) cc_final: 0.5873 (t) REVERT: B 10 GLU cc_start: 0.8842 (tp30) cc_final: 0.8241 (mp0) REVERT: B 36 ASN cc_start: 0.8435 (t0) cc_final: 0.8127 (t0) REVERT: B 59 TYR cc_start: 0.7976 (m-80) cc_final: 0.7486 (m-80) REVERT: B 215 GLU cc_start: 0.7877 (mp0) cc_final: 0.7483 (mp0) REVERT: B 228 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7171 (p0) REVERT: B 297 TRP cc_start: 0.8553 (m100) cc_final: 0.8087 (m100) REVERT: G 18 GLN cc_start: 0.6757 (tm-30) cc_final: 0.6222 (tm-30) REVERT: G 21 MET cc_start: 0.7781 (ttp) cc_final: 0.7546 (tmm) REVERT: G 48 ASP cc_start: 0.7012 (t70) cc_final: 0.6555 (t0) REVERT: S 141 GLU cc_start: 0.7220 (mp0) cc_final: 0.6800 (mp0) REVERT: S 166 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8184 (tt) REVERT: S 180 MET cc_start: 0.8128 (ptm) cc_final: 0.7572 (ptm) REVERT: S 208 GLU cc_start: 0.8623 (pt0) cc_final: 0.7989 (pm20) REVERT: S 211 ASP cc_start: 0.8651 (t0) cc_final: 0.8446 (t0) REVERT: S 223 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7661 (t80) outliers start: 54 outliers final: 32 residues processed: 234 average time/residue: 0.2294 time to fit residues: 76.8089 Evaluate side-chains 228 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 189 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 131 MET Chi-restraints excluded: chain R residue 145 THR Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 314 CYS Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 378 VAL Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 458 LEU Chi-restraints excluded: chain R residue 469 CYS Chi-restraints excluded: chain R residue 475 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 149 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 chunk 24 optimal weight: 0.4980 chunk 23 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 60 optimal weight: 0.3980 chunk 11 optimal weight: 20.0000 chunk 96 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10427 Z= 0.164 Angle : 0.594 13.202 14134 Z= 0.291 Chirality : 0.040 0.170 1572 Planarity : 0.004 0.107 1801 Dihedral : 4.860 46.427 1477 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.90 % Allowed : 20.60 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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 (0.24), residues: 1283 helix: 1.88 (0.26), residues: 414 sheet: -2.09 (0.30), residues: 263 loop : -1.93 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 82 HIS 0.006 0.001 HIS S 35 PHE 0.009 0.001 PHE S 227 TYR 0.022 0.001 TYR A 302 ARG 0.004 0.000 ARG R 485 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 209 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 237 PHE cc_start: 0.7019 (OUTLIER) cc_final: 0.6577 (t80) REVERT: R 257 ARG cc_start: 0.6861 (mmm160) cc_final: 0.6536 (ptp-170) REVERT: R 301 MET cc_start: 0.8211 (ptp) cc_final: 0.7974 (ptp) REVERT: R 339 TRP cc_start: 0.7353 (m-10) cc_final: 0.6735 (m-90) REVERT: R 397 TYR cc_start: 0.7802 (p90) cc_final: 0.7591 (p90) REVERT: R 450 LEU cc_start: 0.7665 (tp) cc_final: 0.7286 (mt) REVERT: R 475 PHE cc_start: 0.5236 (OUTLIER) cc_final: 0.4986 (m-80) REVERT: A 51 LYS cc_start: 0.9167 (tptt) cc_final: 0.8615 (pttt) REVERT: A 205 ARG cc_start: 0.8311 (mtm-85) cc_final: 0.8021 (tpp80) REVERT: A 310 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7381 (mm) REVERT: A 327 THR cc_start: 0.6451 (OUTLIER) cc_final: 0.5889 (t) REVERT: B 10 GLU cc_start: 0.8841 (tp30) cc_final: 0.8252 (mp0) REVERT: B 36 ASN cc_start: 0.8471 (t0) cc_final: 0.8212 (t0) REVERT: B 59 TYR cc_start: 0.7996 (m-80) cc_final: 0.7555 (m-80) REVERT: B 138 GLU cc_start: 0.7268 (pp20) cc_final: 0.6533 (pp20) REVERT: B 215 GLU cc_start: 0.7908 (mp0) cc_final: 0.7307 (mp0) REVERT: B 228 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7089 (p0) REVERT: B 297 TRP cc_start: 0.8428 (m100) cc_final: 0.7994 (m100) REVERT: G 18 GLN cc_start: 0.6747 (tm-30) cc_final: 0.6219 (tm-30) REVERT: G 21 MET cc_start: 0.7811 (ttp) cc_final: 0.7549 (tmm) REVERT: G 48 ASP cc_start: 0.7041 (t70) cc_final: 0.6535 (t0) REVERT: S 82 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7497 (mp10) REVERT: S 141 GLU cc_start: 0.7195 (mp0) cc_final: 0.6764 (mp0) REVERT: S 166 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8114 (tp) REVERT: S 180 MET cc_start: 0.8105 (ptm) cc_final: 0.7554 (ptm) REVERT: S 208 GLU cc_start: 0.8650 (pt0) cc_final: 0.8023 (pm20) REVERT: S 223 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.7589 (t80) outliers start: 43 outliers final: 29 residues processed: 234 average time/residue: 0.2263 time to fit residues: 74.5665 Evaluate side-chains 227 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 191 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 131 MET Chi-restraints excluded: chain R residue 145 THR Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 314 CYS Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 378 VAL Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 458 LEU Chi-restraints excluded: chain R residue 475 PHE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 149 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN S 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10427 Z= 0.266 Angle : 0.645 14.566 14134 Z= 0.320 Chirality : 0.041 0.160 1572 Planarity : 0.004 0.100 1801 Dihedral : 5.056 47.413 1477 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.17 % Allowed : 21.51 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -1.11 (0.23), residues: 1283 helix: 1.79 (0.25), residues: 426 sheet: -2.11 (0.30), residues: 261 loop : -2.02 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 82 HIS 0.004 0.001 HIS A 188 PHE 0.013 0.001 PHE R 318 TYR 0.018 0.001 TYR A 230 ARG 0.004 0.000 ARG R 485 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 192 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 237 PHE cc_start: 0.7109 (OUTLIER) cc_final: 0.6667 (t80) REVERT: R 257 ARG cc_start: 0.6912 (mmm160) cc_final: 0.6579 (ptp-170) REVERT: R 301 MET cc_start: 0.8196 (ptp) cc_final: 0.7947 (ptp) REVERT: R 339 TRP cc_start: 0.7410 (m-10) cc_final: 0.6965 (m-10) REVERT: R 397 TYR cc_start: 0.7750 (p90) cc_final: 0.7521 (p90) REVERT: R 481 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7647 (tp30) REVERT: A 205 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.7527 (tpp-160) REVERT: A 310 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7364 (mm) REVERT: A 327 THR cc_start: 0.6465 (OUTLIER) cc_final: 0.5908 (t) REVERT: B 10 GLU cc_start: 0.8878 (tp30) cc_final: 0.8265 (mp0) REVERT: B 36 ASN cc_start: 0.8446 (t0) cc_final: 0.8184 (t0) REVERT: B 59 TYR cc_start: 0.8051 (m-80) cc_final: 0.7690 (m-80) REVERT: B 114 CYS cc_start: 0.8275 (t) cc_final: 0.7879 (t) REVERT: B 138 GLU cc_start: 0.7371 (pp20) cc_final: 0.6723 (pp20) REVERT: B 215 GLU cc_start: 0.7978 (mp0) cc_final: 0.7466 (mp0) REVERT: B 228 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7162 (p0) REVERT: B 297 TRP cc_start: 0.8555 (m100) cc_final: 0.8037 (m100) REVERT: G 18 GLN cc_start: 0.6760 (tm-30) cc_final: 0.6237 (tm-30) REVERT: G 21 MET cc_start: 0.7843 (ttp) cc_final: 0.7585 (tmm) REVERT: G 48 ASP cc_start: 0.7050 (t70) cc_final: 0.6552 (t0) REVERT: S 82 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7836 (mm-40) REVERT: S 141 GLU cc_start: 0.7199 (mp0) cc_final: 0.6778 (mp0) REVERT: S 166 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8157 (tt) REVERT: S 180 MET cc_start: 0.8145 (ptm) cc_final: 0.7675 (ptm) REVERT: S 208 GLU cc_start: 0.8602 (pt0) cc_final: 0.7977 (pm20) REVERT: S 223 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7736 (t80) outliers start: 46 outliers final: 36 residues processed: 219 average time/residue: 0.2182 time to fit residues: 67.1412 Evaluate side-chains 227 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 184 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 131 MET Chi-restraints excluded: chain R residue 145 THR Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 378 VAL Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 424 MET Chi-restraints excluded: chain R residue 458 LEU Chi-restraints excluded: chain R residue 469 CYS Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 149 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 101 optimal weight: 0.2980 chunk 10 optimal weight: 0.0980 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 63 HIS ** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN S 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10427 Z= 0.185 Angle : 0.641 15.166 14134 Z= 0.311 Chirality : 0.041 0.162 1572 Planarity : 0.004 0.100 1801 Dihedral : 4.957 45.982 1477 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.81 % Allowed : 22.41 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -1.04 (0.24), residues: 1283 helix: 1.79 (0.25), residues: 426 sheet: -1.99 (0.31), residues: 259 loop : -1.97 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 82 HIS 0.006 0.001 HIS S 35 PHE 0.010 0.001 PHE S 227 TYR 0.019 0.001 TYR A 230 ARG 0.003 0.000 ARG R 485 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 199 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 237 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.6687 (t80) REVERT: R 257 ARG cc_start: 0.6881 (mmm160) cc_final: 0.6548 (ptp-170) REVERT: R 301 MET cc_start: 0.8191 (ptp) cc_final: 0.7937 (ptp) REVERT: R 339 TRP cc_start: 0.7374 (m-10) cc_final: 0.6752 (m-90) REVERT: R 380 GLN cc_start: 0.6593 (mm-40) cc_final: 0.6364 (mm-40) REVERT: R 397 TYR cc_start: 0.7803 (p90) cc_final: 0.7592 (p90) REVERT: R 475 PHE cc_start: 0.5267 (OUTLIER) cc_final: 0.5014 (m-80) REVERT: A 205 ARG cc_start: 0.8280 (mtm-85) cc_final: 0.7483 (tpp-160) REVERT: A 310 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7369 (mm) REVERT: A 327 THR cc_start: 0.6483 (OUTLIER) cc_final: 0.5903 (t) REVERT: B 10 GLU cc_start: 0.8854 (tp30) cc_final: 0.8263 (mp0) REVERT: B 36 ASN cc_start: 0.8449 (t0) cc_final: 0.8186 (t0) REVERT: B 59 TYR cc_start: 0.8025 (m-80) cc_final: 0.7676 (m-80) REVERT: B 114 CYS cc_start: 0.8148 (t) cc_final: 0.7788 (t) REVERT: B 138 GLU cc_start: 0.7297 (pp20) cc_final: 0.6700 (pp20) REVERT: B 215 GLU cc_start: 0.8011 (mp0) cc_final: 0.7506 (mp0) REVERT: B 228 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7066 (p0) REVERT: B 297 TRP cc_start: 0.8501 (m100) cc_final: 0.8011 (m100) REVERT: B 325 MET cc_start: 0.7990 (ttp) cc_final: 0.7174 (tpt) REVERT: G 18 GLN cc_start: 0.6713 (tm-30) cc_final: 0.6194 (tm-30) REVERT: G 21 MET cc_start: 0.7834 (ttp) cc_final: 0.7576 (tmm) REVERT: G 48 ASP cc_start: 0.7038 (t70) cc_final: 0.6498 (t0) REVERT: S 82 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7865 (mm-40) REVERT: S 141 GLU cc_start: 0.7175 (mp0) cc_final: 0.6753 (mp0) REVERT: S 166 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8211 (tt) REVERT: S 180 MET cc_start: 0.8154 (ptm) cc_final: 0.7590 (ptm) REVERT: S 208 GLU cc_start: 0.8627 (pt0) cc_final: 0.8001 (pm20) REVERT: S 223 TYR cc_start: 0.8095 (OUTLIER) cc_final: 0.7636 (t80) outliers start: 42 outliers final: 31 residues processed: 224 average time/residue: 0.2311 time to fit residues: 72.0617 Evaluate side-chains 232 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 193 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 131 MET Chi-restraints excluded: chain R residue 145 THR Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 424 MET Chi-restraints excluded: chain R residue 458 LEU Chi-restraints excluded: chain R residue 475 PHE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 149 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 28 optimal weight: 0.0870 chunk 101 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 104 optimal weight: 0.0670 chunk 12 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.144219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.100073 restraints weight = 16329.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103110 restraints weight = 8748.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105143 restraints weight = 5816.317| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10427 Z= 0.182 Angle : 0.635 15.409 14134 Z= 0.309 Chirality : 0.040 0.158 1572 Planarity : 0.004 0.096 1801 Dihedral : 4.858 45.887 1477 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.54 % Allowed : 22.60 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -1.00 (0.24), residues: 1283 helix: 1.84 (0.26), residues: 421 sheet: -1.89 (0.31), residues: 259 loop : -1.97 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.009 0.001 PHE S 227 TYR 0.018 0.001 TYR A 230 ARG 0.003 0.000 ARG S 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2487.49 seconds wall clock time: 45 minutes 50.77 seconds (2750.77 seconds total)