Starting phenix.real_space_refine on Wed Feb 14 03:02:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8s_33058/02_2024/7x8s_33058_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8s_33058/02_2024/7x8s_33058.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8s_33058/02_2024/7x8s_33058_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8s_33058/02_2024/7x8s_33058_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8s_33058/02_2024/7x8s_33058_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8s_33058/02_2024/7x8s_33058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8s_33058/02_2024/7x8s_33058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8s_33058/02_2024/7x8s_33058_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8s_33058/02_2024/7x8s_33058_neut_updated.pdb" } resolution = 3.09 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= -0.001 sd= 0.089 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 51 5.16 5 C 5408 2.51 5 N 1468 2.21 5 O 1553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 322": "OE1" <-> "OE2" Residue "N TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 41": "OE1" <-> "OE2" Residue "R ARG 299": "NH1" <-> "NH2" Residue "R GLU 412": "OE1" <-> "OE2" Residue "R GLU 418": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8480 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1933 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 228} Unresolved chain links: 1 Chain breaks: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2568 Unusual residues: {'WB2': 1} Classifications: {'peptide': 299, 'undetermined': 1} Link IDs: {'PTRANS': 5, 'TRANS': 293, None: 1} Not linked: pdbres="GLU R 423 " pdbres="WB2 R 501 " Chain breaks: 3 Time building chain proxies: 4.89, per 1000 atoms: 0.58 Number of scatterers: 8480 At special positions: 0 Unit cell: (77.112, 96.39, 154.224, 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 51 16.00 O 1553 8.00 N 1468 7.00 C 5408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.8 seconds 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 10 sheets defined 39.0% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 13 through 37 Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 235 through 238 Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.690A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.557A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 30 through 47 removed outlier: 5.317A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 33 through 51 Processing helix chain 'R' and resid 139 through 163 Processing helix chain 'R' and resid 175 through 207 Processing helix chain 'R' and resid 214 through 221 Processing helix chain 'R' and resid 224 through 241 Processing helix chain 'R' and resid 243 through 255 Processing helix chain 'R' and resid 262 through 289 removed outlier: 3.653A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Proline residue: R 277 - end of helix Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 303 through 337 removed outlier: 4.174A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 3.794A pdb=" N ALA R 337 " --> pdb=" O SER R 333 " (cutoff:3.500A) Processing helix chain 'R' and resid 345 through 360 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 366 Processing helix chain 'R' and resid 379 through 403 removed outlier: 4.338A pdb=" N LYS R 383 " --> pdb=" O ARG R 380 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU R 384 " --> pdb=" O PHE R 381 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU R 388 " --> pdb=" O PHE R 385 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER R 392 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY R 395 " --> pdb=" O SER R 392 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU R 401 " --> pdb=" O VAL R 398 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR R 402 " --> pdb=" O ALA R 399 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS R 403 " --> pdb=" O ILE R 400 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 420 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 362 removed outlier: 7.773A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.934A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.170A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.810A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.108A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.850A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.546A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 308 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.796A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.550A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.854A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1029 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: 2.55 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1372 1.31 - 1.44: 2470 1.44 - 1.56: 4743 1.56 - 1.69: 8 1.69 - 1.81: 71 Bond restraints: 8664 Sorted by residual: bond pdb=" C16 WB2 R 501 " pdb=" N15 WB2 R 501 " ideal model delta sigma weight residual 0.000 1.482 -1.482 2.00e-02 2.50e+03 5.49e+03 bond pdb=" C12 WB2 R 501 " pdb=" C13 WB2 R 501 " ideal model delta sigma weight residual 2.182 1.560 0.622 2.00e-02 2.50e+03 9.68e+02 bond pdb=" C16 WB2 R 501 " pdb=" C56 WB2 R 501 " ideal model delta sigma weight residual 1.228 1.585 -0.357 2.00e-02 2.50e+03 3.19e+02 bond pdb=" C20 WB2 R 501 " pdb=" C37 WB2 R 501 " ideal model delta sigma weight residual 1.312 1.626 -0.314 2.00e-02 2.50e+03 2.46e+02 bond pdb=" C13 WB2 R 501 " pdb=" N15 WB2 R 501 " ideal model delta sigma weight residual 1.665 1.394 0.271 2.00e-02 2.50e+03 1.84e+02 ... (remaining 8659 not shown) Histogram of bond angle deviations from ideal: 88.11 - 97.29: 5 97.29 - 106.47: 167 106.47 - 115.65: 5288 115.65 - 124.83: 6107 124.83 - 134.01: 169 Bond angle restraints: 11736 Sorted by residual: angle pdb=" C62 WB2 R 501 " pdb=" C59 WB2 R 501 " pdb=" O60 WB2 R 501 " ideal model delta sigma weight residual 91.75 119.49 -27.74 3.00e+00 1.11e-01 8.55e+01 angle pdb=" C58 WB2 R 501 " pdb=" C59 WB2 R 501 " pdb=" O60 WB2 R 501 " ideal model delta sigma weight residual 141.46 121.21 20.25 3.00e+00 1.11e-01 4.55e+01 angle pdb=" N LEU R 379 " pdb=" CA LEU R 379 " pdb=" C LEU R 379 " ideal model delta sigma weight residual 112.89 106.51 6.38 1.24e+00 6.50e-01 2.65e+01 angle pdb=" C22 WB2 R 501 " pdb=" C23 WB2 R 501 " pdb=" O24 WB2 R 501 " ideal model delta sigma weight residual 107.63 121.45 -13.82 3.00e+00 1.11e-01 2.12e+01 angle pdb=" C16 WB2 R 501 " pdb=" C56 WB2 R 501 " pdb=" C57 WB2 R 501 " ideal model delta sigma weight residual 107.67 121.08 -13.41 3.00e+00 1.11e-01 2.00e+01 ... (remaining 11731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 4978 35.86 - 71.73: 113 71.73 - 107.59: 9 107.59 - 143.45: 2 143.45 - 179.31: 1 Dihedral angle restraints: 5103 sinusoidal: 2040 harmonic: 3063 Sorted by residual: dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 10.39 82.61 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -150.71 64.71 1 1.00e+01 1.00e-02 5.50e+01 dihedral pdb=" C33 WB2 R 501 " pdb=" C30 WB2 R 501 " pdb=" C32 WB2 R 501 " pdb=" O29 WB2 R 501 " ideal model delta sinusoidal sigma weight residual 137.88 -42.81 -179.31 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.297: 1292 1.297 - 2.594: 0 2.594 - 3.890: 0 3.890 - 5.187: 0 5.187 - 6.484: 3 Chirality restraints: 1295 Sorted by residual: chirality pdb=" C37 WB2 R 501 " pdb=" C20 WB2 R 501 " pdb=" C38 WB2 R 501 " pdb=" C56 WB2 R 501 " both_signs ideal model delta sigma weight residual False -2.86 3.62 -6.48 2.00e-01 2.50e+01 1.05e+03 chirality pdb=" C20 WB2 R 501 " pdb=" C16 WB2 R 501 " pdb=" C21 WB2 R 501 " pdb=" C37 WB2 R 501 " both_signs ideal model delta sigma weight residual False 2.64 -3.11 5.75 2.00e-01 2.50e+01 8.26e+02 chirality pdb=" C56 WB2 R 501 " pdb=" C16 WB2 R 501 " pdb=" C37 WB2 R 501 " pdb=" C57 WB2 R 501 " both_signs ideal model delta sigma weight residual False 2.58 -2.98 5.55 2.00e-01 2.50e+01 7.71e+02 ... (remaining 1292 not shown) Planarity restraints: 1489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO B 236 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.014 2.00e-02 2.50e+03 1.13e-02 2.53e+00 pdb=" CG TYR B 59 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 280 " -0.012 2.00e-02 2.50e+03 1.20e-02 2.51e+00 pdb=" CG PHE R 280 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE R 280 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE R 280 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE R 280 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE R 280 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE R 280 " -0.000 2.00e-02 2.50e+03 ... (remaining 1486 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 253 2.70 - 3.25: 8366 3.25 - 3.80: 13597 3.80 - 4.35: 17299 4.35 - 4.90: 29633 Nonbonded interactions: 69148 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.155 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.192 2.440 nonbonded pdb=" ND2 ASN B 155 " pdb=" OD1 ASP B 170 " model vdw 2.198 2.520 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.202 2.440 nonbonded pdb=" OG SER B 67 " pdb=" OD1 ASP B 323 " model vdw 2.208 2.440 ... (remaining 69143 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.010 Extract box with map and model: 4.050 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.670 Find NCS groups from input model: 0.270 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 1.482 8664 Z= 1.515 Angle : 0.808 27.739 11736 Z= 0.363 Chirality : 0.289 6.484 1295 Planarity : 0.003 0.048 1489 Dihedral : 16.187 179.315 3114 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.39 % Favored : 96.51 % Rotamer: Outliers : 0.22 % Allowed : 0.55 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.27), residues: 1032 helix: 1.33 (0.27), residues: 418 sheet: -0.51 (0.34), residues: 215 loop : -0.90 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 417 HIS 0.008 0.001 HIS R 171 PHE 0.027 0.001 PHE R 280 TYR 0.028 0.001 TYR B 59 ARG 0.008 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 250 SER cc_start: 0.8843 (m) cc_final: 0.8581 (m) REVERT: R 145 TYR cc_start: 0.7805 (t80) cc_final: 0.7414 (t80) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.2116 time to fit residues: 47.9321 Evaluate side-chains 149 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 30.0000 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.0357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.147 8664 Z= 0.355 Angle : 1.081 35.573 11736 Z= 0.447 Chirality : 0.164 3.975 1295 Planarity : 0.004 0.048 1489 Dihedral : 9.752 178.904 1171 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.66 % Allowed : 7.64 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.27), residues: 1032 helix: 1.37 (0.27), residues: 416 sheet: -0.48 (0.35), residues: 215 loop : -0.90 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP N 36 HIS 0.005 0.001 HIS B 91 PHE 0.019 0.002 PHE R 280 TYR 0.018 0.001 TYR R 148 ARG 0.011 0.000 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 149 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 250 SER cc_start: 0.8833 (m) cc_final: 0.8585 (m) REVERT: R 145 TYR cc_start: 0.7824 (t80) cc_final: 0.7417 (t80) REVERT: R 204 MET cc_start: 0.7334 (mtp) cc_final: 0.6608 (mtp) outliers start: 6 outliers final: 5 residues processed: 153 average time/residue: 0.2271 time to fit residues: 47.1134 Evaluate side-chains 149 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 357 ILE Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.0399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.147 8664 Z= 0.355 Angle : 1.081 35.573 11736 Z= 0.447 Chirality : 0.164 3.975 1295 Planarity : 0.004 0.048 1489 Dihedral : 9.754 178.904 1171 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.55 % Allowed : 8.08 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.27), residues: 1032 helix: 1.37 (0.27), residues: 416 sheet: -0.48 (0.35), residues: 215 loop : -0.90 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP N 36 HIS 0.005 0.001 HIS B 91 PHE 0.019 0.002 PHE R 280 TYR 0.018 0.001 TYR R 148 ARG 0.011 0.000 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 250 SER cc_start: 0.8833 (m) cc_final: 0.8585 (m) REVERT: R 145 TYR cc_start: 0.7818 (t80) cc_final: 0.7417 (t80) REVERT: R 204 MET cc_start: 0.7338 (mtp) cc_final: 0.6607 (mtp) outliers start: 5 outliers final: 5 residues processed: 147 average time/residue: 0.2219 time to fit residues: 44.4869 Evaluate side-chains 149 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 357 ILE Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 48 optimal weight: 0.2980 chunk 10 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 26 optimal weight: 20.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.0399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.147 8664 Z= 0.355 Angle : 1.081 35.573 11736 Z= 0.447 Chirality : 0.164 3.975 1295 Planarity : 0.004 0.048 1489 Dihedral : 9.755 178.904 1171 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.55 % Allowed : 8.08 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.27), residues: 1032 helix: 1.37 (0.27), residues: 416 sheet: -0.48 (0.35), residues: 215 loop : -0.90 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP N 36 HIS 0.005 0.001 HIS B 91 PHE 0.019 0.002 PHE R 280 TYR 0.018 0.001 TYR R 148 ARG 0.011 0.000 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 250 SER cc_start: 0.8834 (m) cc_final: 0.8585 (m) REVERT: R 145 TYR cc_start: 0.7818 (t80) cc_final: 0.7417 (t80) REVERT: R 204 MET cc_start: 0.7338 (mtp) cc_final: 0.6607 (mtp) outliers start: 5 outliers final: 5 residues processed: 147 average time/residue: 0.2162 time to fit residues: 43.4933 Evaluate side-chains 149 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 357 ILE Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 25 optimal weight: 20.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.0399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.146 8664 Z= 0.355 Angle : 1.081 35.571 11736 Z= 0.447 Chirality : 0.164 3.974 1295 Planarity : 0.004 0.048 1489 Dihedral : 9.736 178.904 1171 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.55 % Allowed : 8.08 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.27), residues: 1032 helix: 1.37 (0.27), residues: 416 sheet: -0.48 (0.35), residues: 215 loop : -0.90 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP N 36 HIS 0.005 0.001 HIS B 91 PHE 0.019 0.002 PHE R 280 TYR 0.018 0.001 TYR R 148 ARG 0.011 0.000 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 250 SER cc_start: 0.8834 (m) cc_final: 0.8586 (m) REVERT: R 145 TYR cc_start: 0.7818 (t80) cc_final: 0.7417 (t80) REVERT: R 204 MET cc_start: 0.7338 (mtp) cc_final: 0.6607 (mtp) outliers start: 5 outliers final: 5 residues processed: 147 average time/residue: 0.2136 time to fit residues: 42.9226 Evaluate side-chains 149 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 357 ILE Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 0.0980 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.0399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.141 8664 Z= 0.349 Angle : 1.077 35.539 11736 Z= 0.445 Chirality : 0.164 3.962 1295 Planarity : 0.004 0.048 1489 Dihedral : 9.774 178.915 1171 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.55 % Allowed : 8.08 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.27), residues: 1032 helix: 1.37 (0.27), residues: 416 sheet: -0.48 (0.35), residues: 215 loop : -0.90 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP N 36 HIS 0.005 0.001 HIS B 91 PHE 0.019 0.001 PHE R 280 TYR 0.018 0.001 TYR R 148 ARG 0.012 0.000 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 250 SER cc_start: 0.8833 (m) cc_final: 0.8585 (m) REVERT: R 145 TYR cc_start: 0.7818 (t80) cc_final: 0.7417 (t80) REVERT: R 204 MET cc_start: 0.7336 (mtp) cc_final: 0.6607 (mtp) outliers start: 5 outliers final: 5 residues processed: 147 average time/residue: 0.2186 time to fit residues: 43.9900 Evaluate side-chains 149 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 357 ILE Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 60 optimal weight: 0.0470 chunk 45 optimal weight: 0.0980 chunk 61 optimal weight: 0.9980 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.0588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8664 Z= 0.211 Angle : 0.934 38.187 11736 Z= 0.391 Chirality : 0.161 3.875 1295 Planarity : 0.004 0.070 1489 Dihedral : 9.637 172.209 1171 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.00 % Allowed : 8.53 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.27), residues: 1032 helix: 1.64 (0.27), residues: 416 sheet: -0.35 (0.35), residues: 213 loop : -0.86 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 36 HIS 0.010 0.001 HIS R 363 PHE 0.015 0.002 PHE R 367 TYR 0.017 0.001 TYR R 148 ARG 0.008 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 1.063 Fit side-chains REVERT: A 250 SER cc_start: 0.8780 (m) cc_final: 0.8547 (m) REVERT: A 368 ASP cc_start: 0.6640 (OUTLIER) cc_final: 0.6234 (t0) REVERT: R 145 TYR cc_start: 0.7788 (t80) cc_final: 0.7371 (t80) REVERT: R 233 MET cc_start: 0.6103 (tpp) cc_final: 0.5832 (tpt) outliers start: 9 outliers final: 6 residues processed: 149 average time/residue: 0.2279 time to fit residues: 46.3010 Evaluate side-chains 147 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 357 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 8664 Z= 0.217 Angle : 0.928 37.927 11736 Z= 0.389 Chirality : 0.159 3.883 1295 Planarity : 0.004 0.069 1489 Dihedral : 9.655 172.763 1171 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.00 % Allowed : 9.97 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.27), residues: 1032 helix: 1.62 (0.27), residues: 416 sheet: -0.35 (0.35), residues: 213 loop : -0.85 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.009 0.001 HIS R 363 PHE 0.023 0.001 PHE R 367 TYR 0.018 0.001 TYR R 148 ARG 0.011 0.000 ARG R 299 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 141 time to evaluate : 0.969 Fit side-chains REVERT: A 250 SER cc_start: 0.8737 (m) cc_final: 0.8530 (m) REVERT: A 368 ASP cc_start: 0.6697 (OUTLIER) cc_final: 0.6252 (t0) REVERT: R 145 TYR cc_start: 0.7795 (t80) cc_final: 0.7421 (t80) REVERT: R 233 MET cc_start: 0.6241 (tpp) cc_final: 0.5979 (tpt) outliers start: 9 outliers final: 7 residues processed: 145 average time/residue: 0.2019 time to fit residues: 41.0206 Evaluate side-chains 148 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 140 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 357 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 0.1980 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 0.3980 chunk 60 optimal weight: 0.3980 chunk 97 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 8664 Z= 0.217 Angle : 0.928 37.926 11736 Z= 0.389 Chirality : 0.159 3.883 1295 Planarity : 0.004 0.069 1489 Dihedral : 9.654 172.764 1171 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.89 % Allowed : 10.41 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.27), residues: 1032 helix: 1.62 (0.27), residues: 416 sheet: -0.35 (0.35), residues: 213 loop : -0.85 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.009 0.001 HIS R 363 PHE 0.023 0.001 PHE R 367 TYR 0.018 0.001 TYR R 148 ARG 0.011 0.000 ARG R 299 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 140 time to evaluate : 0.943 Fit side-chains REVERT: A 250 SER cc_start: 0.8739 (m) cc_final: 0.8530 (m) REVERT: A 368 ASP cc_start: 0.6692 (OUTLIER) cc_final: 0.6252 (t0) REVERT: R 145 TYR cc_start: 0.7795 (t80) cc_final: 0.7421 (t80) REVERT: R 233 MET cc_start: 0.6240 (tpp) cc_final: 0.5979 (tpt) outliers start: 8 outliers final: 7 residues processed: 143 average time/residue: 0.1998 time to fit residues: 40.1059 Evaluate side-chains 148 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 140 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 357 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 87 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8664 Z= 0.211 Angle : 0.925 36.156 11736 Z= 0.385 Chirality : 0.157 3.907 1295 Planarity : 0.005 0.126 1489 Dihedral : 9.709 173.846 1171 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.00 % Allowed : 10.41 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.27), residues: 1032 helix: 1.62 (0.27), residues: 416 sheet: -0.40 (0.35), residues: 215 loop : -0.83 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.009 0.001 HIS R 363 PHE 0.028 0.001 PHE R 367 TYR 0.017 0.001 TYR R 148 ARG 0.014 0.000 ARG R 299 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 0.980 Fit side-chains REVERT: A 250 SER cc_start: 0.8745 (m) cc_final: 0.8532 (m) REVERT: A 368 ASP cc_start: 0.6696 (OUTLIER) cc_final: 0.6338 (t0) REVERT: G 44 HIS cc_start: 0.6533 (t-90) cc_final: 0.6254 (t-90) REVERT: R 145 TYR cc_start: 0.7855 (t80) cc_final: 0.7470 (t80) REVERT: R 233 MET cc_start: 0.6183 (tpp) cc_final: 0.5923 (tpt) outliers start: 9 outliers final: 7 residues processed: 147 average time/residue: 0.2076 time to fit residues: 42.1410 Evaluate side-chains 150 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 357 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 12 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.206785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.154746 restraints weight = 9281.642| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.86 r_work: 0.3391 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8664 Z= 0.228 Angle : 0.920 35.080 11736 Z= 0.384 Chirality : 0.157 3.975 1295 Planarity : 0.004 0.079 1489 Dihedral : 9.709 173.841 1171 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.00 % Allowed : 10.63 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.27), residues: 1032 helix: 1.60 (0.27), residues: 417 sheet: -0.42 (0.35), residues: 215 loop : -0.83 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.011 0.001 HIS R 363 PHE 0.017 0.001 PHE R 367 TYR 0.017 0.001 TYR R 148 ARG 0.006 0.000 ARG A 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2018.40 seconds wall clock time: 37 minutes 19.13 seconds (2239.13 seconds total)