Starting phenix.real_space_refine on Wed Feb 14 03:12:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8r_33057/02_2024/7x8r_33057_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8r_33057/02_2024/7x8r_33057.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8r_33057/02_2024/7x8r_33057_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8r_33057/02_2024/7x8r_33057_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8r_33057/02_2024/7x8r_33057_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8r_33057/02_2024/7x8r_33057.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8r_33057/02_2024/7x8r_33057.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8r_33057/02_2024/7x8r_33057_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8r_33057/02_2024/7x8r_33057_neut_updated.pdb" } resolution = 2.61 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= 0.143 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 5414 2.51 5 N 1470 2.21 5 O 1558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "N PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 41": "OE1" <-> "OE2" Residue "R TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 364": "OE1" <-> "OE2" Residue "R GLU 408": "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: 8493 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1940 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 2 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: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} 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: 299, 2568 Unusual residues: {'BYI': 1} Classifications: {'peptide': 298, 'undetermined': 1} Link IDs: {'PTRANS': 6, 'TRANS': 291, None: 1} Not linked: pdbres="GLU R 423 " pdbres="BYI R 601 " Chain breaks: 3 Time building chain proxies: 4.67, per 1000 atoms: 0.55 Number of scatterers: 8493 At special positions: 0 Unit cell: (79.254, 98.532, 155.295, 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 1558 8.00 N 1470 7.00 C 5414 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: 3.26 Conformation dependent library (CDL) restraints added in 1.5 seconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1982 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 10 sheets defined 41.0% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.648A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 53 through 62 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.567A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) 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: 3.531A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 390 removed outlier: 4.014A pdb=" N ILE A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A 374 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 378 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN A 384 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 388 " --> pdb=" O ARG A 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.809A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 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 138 through 169 Processing helix chain 'R' and resid 175 through 207 removed outlier: 3.708A pdb=" N LYS R 202 " --> pdb=" O ASP R 198 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 222 Processing helix chain 'R' and resid 224 through 255 Processing helix chain 'R' and resid 264 through 274 removed outlier: 3.516A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLY R 273 " --> pdb=" O TYR R 269 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP R 274 " --> pdb=" O VAL R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 291 removed outlier: 3.698A pdb=" N VAL R 281 " --> pdb=" O LEU R 278 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL R 282 " --> pdb=" O LEU R 279 " (cutoff:3.500A) Proline residue: R 283 - end of helix removed outlier: 3.916A pdb=" N ILE R 286 " --> pdb=" O PRO R 283 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR R 291 " --> pdb=" O LYS R 288 " (cutoff:3.500A) 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: 4.180A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 360 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 367 Processing helix chain 'R' and resid 379 through 403 removed outlier: 4.348A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 422 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 6.980A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.796A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.943A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.183A 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: 6.659A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.998A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.354A 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: 6.673A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.258A 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: 6.395A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 327 through 330 removed outlier: 6.841A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.901A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1110 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: 2.21 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1371 1.31 - 1.43: 2474 1.43 - 1.56: 4758 1.56 - 1.68: 4 1.68 - 1.81: 71 Bond restraints: 8678 Sorted by residual: bond pdb=" C20 BYI R 601 " pdb=" C38 BYI R 601 " ideal model delta sigma weight residual 0.000 1.549 -1.549 2.00e-02 2.50e+03 6.00e+03 bond pdb=" C21 BYI R 601 " pdb=" C22 BYI R 601 " ideal model delta sigma weight residual 0.153 1.591 -1.438 2.00e-02 2.50e+03 5.17e+03 bond pdb=" C29 BYI R 601 " pdb=" O28 BYI R 601 " ideal model delta sigma weight residual 1.678 1.412 0.266 2.00e-02 2.50e+03 1.76e+02 bond pdb=" C23 BYI R 601 " pdb=" C24 BYI R 601 " ideal model delta sigma weight residual 1.611 1.393 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C26 BYI R 601 " pdb=" C27 BYI R 601 " ideal model delta sigma weight residual 1.600 1.391 0.209 2.00e-02 2.50e+03 1.09e+02 ... (remaining 8673 not shown) Histogram of bond angle deviations from ideal: 87.23 - 98.10: 5 98.10 - 108.98: 520 108.98 - 119.85: 7053 119.85 - 130.73: 4132 130.73 - 141.60: 46 Bond angle restraints: 11756 Sorted by residual: angle pdb=" N ASN A 292 " pdb=" CA ASN A 292 " pdb=" C ASN A 292 " ideal model delta sigma weight residual 111.40 123.55 -12.15 1.22e+00 6.72e-01 9.92e+01 angle pdb=" C18 BYI R 601 " pdb=" C19 BYI R 601 " pdb=" C58 BYI R 601 " ideal model delta sigma weight residual 112.40 141.60 -29.20 3.00e+00 1.11e-01 9.48e+01 angle pdb=" C20 BYI R 601 " pdb=" C19 BYI R 601 " pdb=" C58 BYI R 601 " ideal model delta sigma weight residual 112.64 92.17 20.47 3.00e+00 1.11e-01 4.66e+01 angle pdb=" C19 BYI R 601 " pdb=" C20 BYI R 601 " pdb=" N41 BYI R 601 " ideal model delta sigma weight residual 111.10 123.07 -11.97 3.00e+00 1.11e-01 1.59e+01 angle pdb=" C ILE R 147 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " ideal model delta sigma weight residual 121.14 115.07 6.07 1.75e+00 3.27e-01 1.20e+01 ... (remaining 11751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4629 17.91 - 35.82: 390 35.82 - 53.73: 67 53.73 - 71.64: 13 71.64 - 89.56: 14 Dihedral angle restraints: 5113 sinusoidal: 2049 harmonic: 3064 Sorted by residual: dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 160.27 19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 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 -86.00 -116.40 30.40 1 1.00e+01 1.00e-02 1.32e+01 ... (remaining 5110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.424: 1292 0.424 - 0.847: 2 0.847 - 1.271: 0 1.271 - 1.695: 0 1.695 - 2.118: 1 Chirality restraints: 1295 Sorted by residual: chirality pdb=" C21 BYI R 601 " pdb=" C18 BYI R 601 " pdb=" C20 BYI R 601 " pdb=" C22 BYI R 601 " both_signs ideal model delta sigma weight residual False 0.27 2.39 -2.12 2.00e-01 2.50e+01 1.12e+02 chirality pdb=" C19 BYI R 601 " pdb=" C18 BYI R 601 " pdb=" C20 BYI R 601 " pdb=" C58 BYI R 601 " both_signs ideal model delta sigma weight residual False -2.76 -2.19 -0.56 2.00e-01 2.50e+01 7.94e+00 chirality pdb=" CA ASN A 292 " pdb=" N ASN A 292 " pdb=" C ASN A 292 " pdb=" CB ASN A 292 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.75e+00 ... (remaining 1292 not shown) Planarity restraints: 1490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C19 BYI R 601 " -0.016 2.00e-02 2.50e+03 1.34e-02 4.07e+00 pdb=" C58 BYI R 601 " 0.035 2.00e-02 2.50e+03 pdb=" C59 BYI R 601 " -0.003 2.00e-02 2.50e+03 pdb=" C60 BYI R 601 " 0.001 2.00e-02 2.50e+03 pdb=" C61 BYI R 601 " 0.002 2.00e-02 2.50e+03 pdb=" C62 BYI R 601 " -0.001 2.00e-02 2.50e+03 pdb=" C63 BYI R 601 " -0.011 2.00e-02 2.50e+03 pdb=" O64 BYI R 601 " -0.003 2.00e-02 2.50e+03 pdb=" O72 BYI R 601 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 74 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C SER B 74 " -0.032 2.00e-02 2.50e+03 pdb=" O SER B 74 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN B 75 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO B 236 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.024 5.00e-02 4.00e+02 ... (remaining 1487 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 691 2.74 - 3.28: 8519 3.28 - 3.82: 14608 3.82 - 4.36: 17922 4.36 - 4.90: 30264 Nonbonded interactions: 72004 Sorted by model distance: nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.201 2.440 nonbonded pdb=" ND1 HIS R 171 " pdb=" OE2 GLU R 412 " model vdw 2.212 2.520 nonbonded pdb=" OD1 ASN A 23 " pdb=" N LYS B 89 " model vdw 2.239 2.520 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.242 2.440 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.267 2.440 ... (remaining 71999 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: 0.790 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: 4.020 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 24.880 Find NCS groups from input model: 0.210 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:13.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 0.025 1.549 8678 Z= 0.962 Angle : 0.732 29.204 11756 Z= 0.359 Chirality : 0.077 2.118 1295 Planarity : 0.004 0.044 1490 Dihedral : 14.293 89.556 3122 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: 0.83 (0.26), residues: 1031 helix: 1.61 (0.25), residues: 423 sheet: 0.47 (0.33), residues: 231 loop : -0.57 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.012 0.002 HIS A 357 PHE 0.017 0.002 PHE B 151 TYR 0.024 0.002 TYR B 59 ARG 0.006 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.882 Fit side-chains REVERT: A 370 GLU cc_start: 0.7557 (pm20) cc_final: 0.7334 (pm20) REVERT: R 418 GLU cc_start: 0.6225 (mm-30) cc_final: 0.5942 (mm-30) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 1.5456 time to fit residues: 195.0165 Evaluate side-chains 92 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 0.0980 chunk 52 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN N 31 ASN R 240 ASN R 394 GLN R 410 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 8678 Z= 0.207 Angle : 0.676 25.058 11756 Z= 0.313 Chirality : 0.042 0.267 1295 Planarity : 0.004 0.042 1490 Dihedral : 6.324 84.583 1166 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.76 % Allowed : 9.25 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.26), residues: 1031 helix: 1.91 (0.25), residues: 424 sheet: 0.52 (0.32), residues: 229 loop : -0.54 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.015 0.001 PHE B 151 TYR 0.030 0.001 TYR R 148 ARG 0.005 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 1.040 Fit side-chains REVERT: A 347 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7179 (ptp90) REVERT: B 217 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7317 (pp-130) REVERT: B 270 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7519 (pp) REVERT: R 170 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.6614 (tpt170) REVERT: R 418 GLU cc_start: 0.6252 (mm-30) cc_final: 0.5914 (mm-30) outliers start: 16 outliers final: 3 residues processed: 110 average time/residue: 1.4718 time to fit residues: 171.1958 Evaluate side-chains 105 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 204 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 ASN R 240 ASN R 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.143 8678 Z= 0.339 Angle : 0.721 23.574 11756 Z= 0.347 Chirality : 0.046 0.277 1295 Planarity : 0.004 0.044 1490 Dihedral : 6.636 87.118 1166 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.20 % Allowed : 11.89 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: 0.96 (0.26), residues: 1031 helix: 1.83 (0.25), residues: 424 sheet: 0.46 (0.33), residues: 231 loop : -0.59 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.013 0.002 HIS A 357 PHE 0.020 0.002 PHE B 151 TYR 0.018 0.002 TYR R 402 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 1.062 Fit side-chains REVERT: A 299 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7161 (pt0) REVERT: A 347 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7266 (ptp90) REVERT: B 134 ARG cc_start: 0.6892 (ptp-110) cc_final: 0.6613 (mtm110) REVERT: B 217 MET cc_start: 0.7699 (pmm) cc_final: 0.7380 (pp-130) REVERT: B 270 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7676 (pp) REVERT: R 418 GLU cc_start: 0.6200 (mm-30) cc_final: 0.5918 (mm-30) outliers start: 20 outliers final: 6 residues processed: 110 average time/residue: 1.5410 time to fit residues: 178.4920 Evaluate side-chains 105 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 204 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 394 GLN R 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.143 8678 Z= 0.249 Angle : 0.656 23.264 11756 Z= 0.313 Chirality : 0.043 0.252 1295 Planarity : 0.004 0.044 1490 Dihedral : 6.452 87.357 1166 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.42 % Allowed : 13.66 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1031 helix: 1.96 (0.25), residues: 424 sheet: 0.49 (0.32), residues: 230 loop : -0.57 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.018 0.001 PHE B 151 TYR 0.015 0.001 TYR R 402 ARG 0.005 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 0.898 Fit side-chains REVERT: A 392 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7165 (mt-10) REVERT: B 134 ARG cc_start: 0.6950 (ptp-110) cc_final: 0.6698 (mtm110) REVERT: B 217 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7378 (pp-130) REVERT: B 270 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7690 (pp) REVERT: R 170 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.6750 (tpt170) REVERT: R 418 GLU cc_start: 0.6196 (mm-30) cc_final: 0.5911 (mm-30) outliers start: 22 outliers final: 6 residues processed: 109 average time/residue: 1.4985 time to fit residues: 171.9694 Evaluate side-chains 105 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 204 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.5980 chunk 73 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 0.0670 chunk 88 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 ASN R 180 HIS R 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 8678 Z= 0.203 Angle : 0.621 23.201 11756 Z= 0.294 Chirality : 0.042 0.247 1295 Planarity : 0.003 0.044 1490 Dihedral : 6.179 88.424 1166 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.31 % Allowed : 15.53 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.26), residues: 1031 helix: 2.09 (0.26), residues: 424 sheet: 0.40 (0.32), residues: 232 loop : -0.54 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 47 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE B 151 TYR 0.015 0.001 TYR R 148 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 1.011 Fit side-chains REVERT: A 314 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: A 390 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: B 134 ARG cc_start: 0.6817 (ptp-110) cc_final: 0.6585 (mtm110) REVERT: B 217 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7374 (pp-130) REVERT: B 270 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7643 (pp) REVERT: R 170 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.6945 (tpt170) REVERT: R 412 GLU cc_start: 0.6859 (tp30) cc_final: 0.6311 (tp30) REVERT: R 418 GLU cc_start: 0.6190 (mm-30) cc_final: 0.5914 (mm-30) outliers start: 21 outliers final: 8 residues processed: 111 average time/residue: 1.5251 time to fit residues: 178.2975 Evaluate side-chains 110 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 204 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 8678 Z= 0.301 Angle : 0.671 23.089 11756 Z= 0.324 Chirality : 0.044 0.258 1295 Planarity : 0.004 0.043 1490 Dihedral : 6.294 89.412 1166 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.42 % Allowed : 16.30 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.26), residues: 1031 helix: 1.99 (0.25), residues: 424 sheet: 0.39 (0.32), residues: 231 loop : -0.57 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.009 0.002 HIS A 357 PHE 0.020 0.002 PHE B 151 TYR 0.016 0.002 TYR R 402 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 1.023 Fit side-chains REVERT: A 392 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: B 134 ARG cc_start: 0.6848 (ptp-110) cc_final: 0.6633 (mtm110) REVERT: B 217 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7479 (pmm) REVERT: B 270 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7778 (pp) REVERT: R 170 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.6854 (tpt170) REVERT: R 412 GLU cc_start: 0.6892 (tp30) cc_final: 0.6316 (tp30) REVERT: R 418 GLU cc_start: 0.6215 (mm-30) cc_final: 0.5937 (mm-30) outliers start: 22 outliers final: 9 residues processed: 108 average time/residue: 1.5574 time to fit residues: 177.1743 Evaluate side-chains 110 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 307 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 83 optimal weight: 20.0000 chunk 98 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 394 GLN R 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.137 8678 Z= 0.301 Angle : 0.667 23.060 11756 Z= 0.322 Chirality : 0.044 0.261 1295 Planarity : 0.004 0.044 1490 Dihedral : 6.205 87.649 1166 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.53 % Allowed : 16.85 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1031 helix: 1.94 (0.25), residues: 423 sheet: 0.38 (0.32), residues: 231 loop : -0.56 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.008 0.002 HIS A 357 PHE 0.020 0.002 PHE B 151 TYR 0.017 0.002 TYR R 402 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 0.985 Fit side-chains REVERT: A 347 ARG cc_start: 0.7766 (ptp-110) cc_final: 0.7564 (ptp-110) REVERT: A 392 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7194 (mt-10) REVERT: B 134 ARG cc_start: 0.6841 (ptp-110) cc_final: 0.6635 (mtm110) REVERT: B 217 MET cc_start: 0.7759 (pmm) cc_final: 0.7477 (pmm) REVERT: B 270 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7777 (pp) REVERT: R 170 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.6845 (tpt170) REVERT: R 227 ARG cc_start: 0.7724 (mpp80) cc_final: 0.7413 (mpp80) REVERT: R 412 GLU cc_start: 0.6846 (tp30) cc_final: 0.6257 (tp30) REVERT: R 418 GLU cc_start: 0.6219 (mm-30) cc_final: 0.5939 (mm-30) outliers start: 23 outliers final: 11 residues processed: 111 average time/residue: 1.5757 time to fit residues: 184.5273 Evaluate side-chains 109 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 391 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 5.9990 chunk 62 optimal weight: 0.0870 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.136 8678 Z= 0.274 Angle : 0.651 23.027 11756 Z= 0.314 Chirality : 0.044 0.270 1295 Planarity : 0.004 0.044 1490 Dihedral : 6.089 85.266 1166 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.09 % Allowed : 17.51 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1031 helix: 1.95 (0.25), residues: 423 sheet: 0.38 (0.32), residues: 231 loop : -0.55 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.019 0.001 PHE B 151 TYR 0.016 0.002 TYR R 402 ARG 0.003 0.000 ARG R 419 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 0.948 Fit side-chains REVERT: A 392 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7182 (mt-10) REVERT: B 217 MET cc_start: 0.7745 (pmm) cc_final: 0.7539 (pmm) REVERT: B 270 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7781 (pp) REVERT: R 170 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.6833 (tpt170) REVERT: R 227 ARG cc_start: 0.7653 (mpp80) cc_final: 0.7320 (mpp80) REVERT: R 412 GLU cc_start: 0.6844 (tp30) cc_final: 0.6399 (tp30) REVERT: R 418 GLU cc_start: 0.6214 (mm-30) cc_final: 0.5929 (mm-30) outliers start: 19 outliers final: 11 residues processed: 109 average time/residue: 1.5782 time to fit residues: 181.0810 Evaluate side-chains 111 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 391 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 60 optimal weight: 0.3980 chunk 96 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 394 GLN R 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 8678 Z= 0.221 Angle : 0.630 23.031 11756 Z= 0.302 Chirality : 0.042 0.274 1295 Planarity : 0.004 0.045 1490 Dihedral : 5.978 83.824 1166 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.42 % Allowed : 17.73 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1031 helix: 2.05 (0.26), residues: 423 sheet: 0.40 (0.32), residues: 230 loop : -0.53 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 47 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE B 151 TYR 0.013 0.001 TYR R 402 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 101 time to evaluate : 1.182 Fit side-chains REVERT: A 392 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7161 (mt-10) REVERT: B 217 MET cc_start: 0.7786 (pmm) cc_final: 0.7570 (pmm) REVERT: B 270 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7760 (pp) REVERT: R 170 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6941 (tpt170) REVERT: R 412 GLU cc_start: 0.6550 (tp30) cc_final: 0.6114 (tp30) REVERT: R 418 GLU cc_start: 0.6190 (mm-30) cc_final: 0.5909 (mm-30) outliers start: 22 outliers final: 9 residues processed: 114 average time/residue: 1.4957 time to fit residues: 179.7011 Evaluate side-chains 113 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 391 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 394 GLN R 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.136 8678 Z= 0.266 Angle : 0.652 22.980 11756 Z= 0.314 Chirality : 0.043 0.278 1295 Planarity : 0.004 0.055 1490 Dihedral : 6.010 81.799 1166 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.32 % Allowed : 18.83 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1031 helix: 2.01 (0.25), residues: 423 sheet: 0.38 (0.32), residues: 231 loop : -0.54 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.018 0.001 PHE B 151 TYR 0.015 0.002 TYR R 402 ARG 0.014 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 1.048 Fit side-chains REVERT: A 392 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7129 (mt-10) REVERT: B 134 ARG cc_start: 0.6827 (ptp-110) cc_final: 0.6539 (mtm110) REVERT: B 217 MET cc_start: 0.7734 (pmm) cc_final: 0.7510 (pmm) REVERT: B 270 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.7783 (pp) REVERT: R 170 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.6777 (tpt170) REVERT: R 412 GLU cc_start: 0.6518 (tp30) cc_final: 0.6055 (tp30) REVERT: R 418 GLU cc_start: 0.6202 (mm-30) cc_final: 0.5919 (mm-30) outliers start: 12 outliers final: 8 residues processed: 109 average time/residue: 1.5224 time to fit residues: 174.7838 Evaluate side-chains 111 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 391 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 394 GLN R 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.195610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.146969 restraints weight = 8755.494| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.88 r_work: 0.3353 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 8678 Z= 0.238 Angle : 0.637 22.973 11756 Z= 0.305 Chirality : 0.043 0.283 1295 Planarity : 0.004 0.049 1490 Dihedral : 5.911 79.375 1166 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.32 % Allowed : 18.72 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.26), residues: 1031 helix: 2.05 (0.26), residues: 423 sheet: 0.44 (0.32), residues: 229 loop : -0.54 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.017 0.001 PHE B 151 TYR 0.014 0.001 TYR R 402 ARG 0.012 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3489.48 seconds wall clock time: 62 minutes 57.97 seconds (3777.97 seconds total)