Starting phenix.real_space_refine on Sun Feb 18 22:07:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7v_20270/02_2024/6p7v_20270.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7v_20270/02_2024/6p7v_20270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7v_20270/02_2024/6p7v_20270.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7v_20270/02_2024/6p7v_20270.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7v_20270/02_2024/6p7v_20270.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7v_20270/02_2024/6p7v_20270.pdb" } resolution = 4.0 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 56 5.16 5 C 7501 2.51 5 N 1906 2.21 5 O 2069 1.98 5 H 11620 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 92": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 158": "OD1" <-> "OD2" Residue "C ARG 225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C ARG 237": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 358": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 374": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 384": "OD1" <-> "OD2" Residue "D ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 301": "OD1" <-> "OD2" Residue "B ARG 313": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 333": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 362": "OD1" <-> "OD2" Residue "B TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 368": "OD1" <-> "OD2" Residue "B GLU 388": "OE1" <-> "OE2" Residue "B GLU 391": "OE1" <-> "OE2" Residue "B ARG 409": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 462": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 505": "OD1" <-> "OD2" Residue "B ARG 508": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 511": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 543": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 575": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 615": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A ARG 333": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 377": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A ARG 409": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 461": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 462": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A ARG 508": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 511": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 543": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 575": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A ASP 609": "OD1" <-> "OD2" Residue "A PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 615": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23152 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 5437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 5437 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2059 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain breaks: 1 Chain: "B" Number of atoms: 7977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 7977 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 14, 'TRANS': 461} Chain breaks: 6 Chain: "A" Number of atoms: 7679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 7679 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 14, 'TRANS': 442} Chain breaks: 6 Time building chain proxies: 9.95, per 1000 atoms: 0.43 Number of scatterers: 23152 At special positions: 0 Unit cell: (96.5055, 112.413, 127.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 O 2069 8.00 N 1906 7.00 C 7501 6.00 H 11620 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 18.41 Conformation dependent library (CDL) restraints added in 2.2 seconds 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2696 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 5 sheets defined 69.5% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 11 through 22 removed outlier: 3.897A pdb=" N ARG C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 100 Processing helix chain 'C' and resid 132 through 140 Processing helix chain 'C' and resid 157 through 170 Processing helix chain 'C' and resid 189 through 195 Processing helix chain 'C' and resid 196 through 201 removed outlier: 4.446A pdb=" N GLU C 199 " --> pdb=" O PRO C 196 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER C 200 " --> pdb=" O CYS C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 303 through 309 Processing helix chain 'C' and resid 327 through 345 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.655A pdb=" N GLU C 372 " --> pdb=" O ARG C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 27 Processing helix chain 'D' and resid 29 through 36 removed outlier: 3.553A pdb=" N GLN D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 95 through 101 Processing helix chain 'D' and resid 105 through 112 Processing helix chain 'D' and resid 115 through 130 Processing helix chain 'D' and resid 131 through 148 removed outlier: 3.718A pdb=" N LEU D 135 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 156 removed outlier: 3.869A pdb=" N ILE D 154 " --> pdb=" O THR D 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 81 Processing helix chain 'B' and resid 100 through 105 removed outlier: 3.512A pdb=" N GLU B 103 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 133 removed outlier: 3.574A pdb=" N ILE B 122 " --> pdb=" O SER B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 Processing helix chain 'B' and resid 145 through 162 Processing helix chain 'B' and resid 181 through 200 Processing helix chain 'B' and resid 202 through 210 removed outlier: 3.675A pdb=" N ILE B 206 " --> pdb=" O PRO B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 218 removed outlier: 3.917A pdb=" N GLU B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 256 Processing helix chain 'B' and resid 261 through 271 removed outlier: 3.564A pdb=" N GLN B 265 " --> pdb=" O VAL B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 279 through 298 removed outlier: 3.541A pdb=" N GLY B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 333 Processing helix chain 'B' and resid 342 through 346 removed outlier: 3.540A pdb=" N ASN B 346 " --> pdb=" O HIS B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 389 Processing helix chain 'B' and resid 394 through 413 Processing helix chain 'B' and resid 418 through 447 Processing helix chain 'B' and resid 451 through 473 Proline residue: B 459 - end of helix Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.711A pdb=" N THR B 479 " --> pdb=" O TYR B 475 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR B 480 " --> pdb=" O PHE B 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 475 through 480' Processing helix chain 'B' and resid 481 through 502 removed outlier: 3.738A pdb=" N VAL B 485 " --> pdb=" O HIS B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 522 removed outlier: 3.524A pdb=" N LEU B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 548 Processing helix chain 'B' and resid 560 through 578 removed outlier: 4.301A pdb=" N GLU B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 618 Processing helix chain 'A' and resid 63 through 81 Processing helix chain 'A' and resid 118 through 133 removed outlier: 3.623A pdb=" N ILE A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 141 Processing helix chain 'A' and resid 145 through 162 Processing helix chain 'A' and resid 181 through 200 Processing helix chain 'A' and resid 202 through 210 removed outlier: 3.767A pdb=" N ILE A 206 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 232 through 256 removed outlier: 3.683A pdb=" N ARG A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 272 removed outlier: 4.122A pdb=" N ASN A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 298 removed outlier: 3.516A pdb=" N GLY A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 333 Processing helix chain 'A' and resid 373 through 390 removed outlier: 3.677A pdb=" N SER A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 413 Processing helix chain 'A' and resid 418 through 447 Processing helix chain 'A' and resid 451 through 473 Proline residue: A 459 - end of helix Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.584A pdb=" N THR A 479 " --> pdb=" O TYR A 475 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 480 " --> pdb=" O PHE A 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 475 through 480' Processing helix chain 'A' and resid 481 through 502 removed outlier: 3.722A pdb=" N VAL A 485 " --> pdb=" O HIS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 522 Processing helix chain 'A' and resid 525 through 548 removed outlier: 3.538A pdb=" N ILE A 529 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 578 removed outlier: 3.821A pdb=" N GLU A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 618 Processing sheet with id=AA1, first strand: chain 'C' and resid 105 through 111 removed outlier: 3.748A pdb=" N VAL C 129 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 178 through 179 removed outlier: 7.091A pdb=" N ILE C 178 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU C 207 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 276 through 277 removed outlier: 6.837A pdb=" N ILE C 276 " --> pdb=" O ILE C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.661A pdb=" N LEU C 365 " --> pdb=" O ILE C 389 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 16 through 21 695 hydrogen bonds defined for protein. 2052 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: 7.90 Time building geometry restraints manager: 19.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 11591 1.02 - 1.22: 33 1.22 - 1.42: 4993 1.42 - 1.62: 6709 1.62 - 1.82: 83 Bond restraints: 23409 Sorted by residual: bond pdb=" CA ASN B 106 " pdb=" CB ASN B 106 " ideal model delta sigma weight residual 1.526 1.471 0.055 1.76e-02 3.23e+03 9.93e+00 bond pdb=" CG1 ILE A 254 " pdb=" CD1 ILE A 254 " ideal model delta sigma weight residual 1.513 1.405 0.108 3.90e-02 6.57e+02 7.67e+00 bond pdb=" CB VAL B 329 " pdb=" CG1 VAL B 329 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 5.05e+00 bond pdb=" CG LEU A 282 " pdb=" CD1 LEU A 282 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.86e+00 bond pdb=" CA ILE B 254 " pdb=" C ILE B 254 " ideal model delta sigma weight residual 1.524 1.499 0.025 1.18e-02 7.18e+03 4.61e+00 ... (remaining 23404 not shown) Histogram of bond angle deviations from ideal: 94.20 - 102.27: 51 102.27 - 110.33: 21666 110.33 - 118.40: 9922 118.40 - 126.46: 10454 126.46 - 134.53: 242 Bond angle restraints: 42335 Sorted by residual: angle pdb=" C GLY A 134 " pdb=" N TRP A 135 " pdb=" CA TRP A 135 " ideal model delta sigma weight residual 121.19 129.89 -8.70 1.59e+00 3.96e-01 2.99e+01 angle pdb=" N LEU B 257 " pdb=" CA LEU B 257 " pdb=" C LEU B 257 " ideal model delta sigma weight residual 108.22 112.98 -4.76 9.00e-01 1.23e+00 2.80e+01 angle pdb=" C PHE B 522 " pdb=" N ASP B 523 " pdb=" CA ASP B 523 " ideal model delta sigma weight residual 119.78 126.22 -6.44 1.24e+00 6.50e-01 2.70e+01 angle pdb=" C PHE A 117 " pdb=" CA PHE A 117 " pdb=" HA PHE A 117 " ideal model delta sigma weight residual 109.00 94.20 14.80 3.00e+00 1.11e-01 2.43e+01 angle pdb=" CA ARG A 575 " pdb=" CB ARG A 575 " pdb=" CG ARG A 575 " ideal model delta sigma weight residual 114.10 123.67 -9.57 2.00e+00 2.50e-01 2.29e+01 ... (remaining 42330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 9299 17.66 - 35.32: 1279 35.32 - 52.97: 249 52.97 - 70.63: 73 70.63 - 88.29: 17 Dihedral angle restraints: 10917 sinusoidal: 5877 harmonic: 5040 Sorted by residual: dihedral pdb=" CA TYR C 246 " pdb=" C TYR C 246 " pdb=" N THR C 247 " pdb=" CA THR C 247 " ideal model delta harmonic sigma weight residual 180.00 140.21 39.79 0 5.00e+00 4.00e-02 6.33e+01 dihedral pdb=" CA PHE C 201 " pdb=" C PHE C 201 " pdb=" N ASN C 202 " pdb=" CA ASN C 202 " ideal model delta harmonic sigma weight residual 180.00 -149.83 -30.17 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA PHE B 117 " pdb=" C PHE B 117 " pdb=" N SER B 118 " pdb=" CA SER B 118 " ideal model delta harmonic sigma weight residual 180.00 150.64 29.36 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 10914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1307 0.060 - 0.121: 388 0.121 - 0.181: 88 0.181 - 0.242: 13 0.242 - 0.302: 3 Chirality restraints: 1799 Sorted by residual: chirality pdb=" CG LEU A 185 " pdb=" CB LEU A 185 " pdb=" CD1 LEU A 185 " pdb=" CD2 LEU A 185 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CG LEU A 268 " pdb=" CB LEU A 268 " pdb=" CD1 LEU A 268 " pdb=" CD2 LEU A 268 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA LEU A 268 " pdb=" N LEU A 268 " pdb=" C LEU A 268 " pdb=" CB LEU A 268 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 1796 not shown) Planarity restraints: 3304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 211 " 0.028 2.00e-02 2.50e+03 5.69e-02 3.24e+01 pdb=" C ASP A 211 " -0.098 2.00e-02 2.50e+03 pdb=" O ASP A 211 " 0.037 2.00e-02 2.50e+03 pdb=" N ILE A 212 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 110 " -0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C PHE A 110 " 0.073 2.00e-02 2.50e+03 pdb=" O PHE A 110 " -0.027 2.00e-02 2.50e+03 pdb=" N TYR A 111 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 532 " -0.020 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C PHE A 532 " 0.071 2.00e-02 2.50e+03 pdb=" O PHE A 532 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE A 533 " -0.024 2.00e-02 2.50e+03 ... (remaining 3301 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 4643 2.29 - 2.87: 54009 2.87 - 3.44: 60588 3.44 - 4.02: 77798 4.02 - 4.60: 121085 Nonbonded interactions: 318123 Sorted by model distance: nonbonded pdb=" O LEU A 270 " pdb=" HG1 THR A 273 " model vdw 1.712 1.850 nonbonded pdb=" O VAL C 341 " pdb=" HG1 THR C 344 " model vdw 1.716 1.850 nonbonded pdb=" O SER D 12 " pdb=" H GLY D 15 " model vdw 1.738 1.850 nonbonded pdb=" OE1 GLU A 477 " pdb=" H GLU A 477 " model vdw 1.740 1.850 nonbonded pdb=" OD2 ASP B 330 " pdb=" H LEU B 342 " model vdw 1.743 1.850 ... (remaining 318118 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 62 through 347 or (resid 372 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name HA or name H \ B2 or name HB3 or name HD21 or name HD22)) or resid 373 through 618)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.330 Extract box with map and model: 6.420 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 71.320 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.011 0.108 11789 Z= 0.693 Angle : 1.207 12.578 15945 Z= 0.683 Chirality : 0.060 0.302 1799 Planarity : 0.008 0.075 1981 Dihedral : 15.861 85.657 4372 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.79 % Favored : 89.99 % Rotamer: Outliers : 0.08 % Allowed : 4.59 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.19 (0.19), residues: 1348 helix: -1.27 (0.14), residues: 874 sheet: -2.61 (0.88), residues: 36 loop : -3.71 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP A 378 HIS 0.019 0.004 HIS A 320 PHE 0.039 0.004 PHE A 444 TYR 0.054 0.004 TYR A 111 ARG 0.012 0.001 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 ASP cc_start: 0.9264 (t0) cc_final: 0.8894 (p0) REVERT: C 116 GLU cc_start: 0.6877 (tt0) cc_final: 0.6319 (mp0) REVERT: C 244 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7606 (mt-10) REVERT: D 76 GLN cc_start: 0.9395 (tt0) cc_final: 0.8997 (tp-100) REVERT: D 132 LYS cc_start: 0.9495 (mmtt) cc_final: 0.9227 (mmmt) REVERT: B 277 GLN cc_start: 0.9312 (mp10) cc_final: 0.9091 (mp10) REVERT: B 330 ASP cc_start: 0.8087 (t0) cc_final: 0.7824 (t70) REVERT: A 76 GLU cc_start: 0.8957 (pt0) cc_final: 0.8691 (pt0) REVERT: A 295 LYS cc_start: 0.9452 (mttt) cc_final: 0.9174 (mttp) REVERT: A 330 ASP cc_start: 0.8841 (t70) cc_final: 0.8460 (t70) REVERT: A 436 MET cc_start: 0.9074 (mmm) cc_final: 0.8655 (mtm) outliers start: 1 outliers final: 1 residues processed: 182 average time/residue: 0.5836 time to fit residues: 147.3838 Evaluate side-chains 114 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 175 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 123 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 160 ASN ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN C 336 ASN B 346 ASN B 431 GLN ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN ** A 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11789 Z= 0.187 Angle : 0.653 6.382 15945 Z= 0.349 Chirality : 0.039 0.153 1799 Planarity : 0.005 0.052 1981 Dihedral : 6.559 30.529 1500 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.86 % Favored : 91.99 % Rotamer: Outliers : 0.76 % Allowed : 9.48 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.22), residues: 1348 helix: 0.28 (0.17), residues: 870 sheet: -2.65 (0.71), residues: 51 loop : -3.28 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 79 HIS 0.007 0.001 HIS A 320 PHE 0.016 0.001 PHE A 110 TYR 0.023 0.002 TYR C 177 ARG 0.004 0.001 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 ASP cc_start: 0.9256 (t0) cc_final: 0.8860 (p0) REVERT: C 116 GLU cc_start: 0.6668 (tt0) cc_final: 0.6416 (mp0) REVERT: C 352 GLU cc_start: 0.7888 (tt0) cc_final: 0.7307 (tm-30) REVERT: D 76 GLN cc_start: 0.9412 (tt0) cc_final: 0.9065 (tp-100) REVERT: B 76 GLU cc_start: 0.9130 (pt0) cc_final: 0.8762 (pt0) REVERT: B 400 MET cc_start: 0.9291 (mtm) cc_final: 0.8874 (mtp) REVERT: A 76 GLU cc_start: 0.8903 (pt0) cc_final: 0.8610 (pt0) REVERT: A 330 ASP cc_start: 0.8843 (t70) cc_final: 0.8388 (t70) REVERT: A 436 MET cc_start: 0.8948 (mmm) cc_final: 0.8566 (mtm) outliers start: 10 outliers final: 6 residues processed: 158 average time/residue: 0.5645 time to fit residues: 132.0860 Evaluate side-chains 118 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 126 PHE Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain A residue 187 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN D 7 ASN ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11789 Z= 0.298 Angle : 0.657 6.686 15945 Z= 0.360 Chirality : 0.039 0.151 1799 Planarity : 0.004 0.045 1981 Dihedral : 6.034 27.941 1499 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.16 % Favored : 89.76 % Rotamer: Outliers : 1.61 % Allowed : 12.39 % Favored : 86.01 % 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 (0.23), residues: 1348 helix: 0.79 (0.17), residues: 881 sheet: -2.51 (0.63), residues: 65 loop : -3.31 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 155 HIS 0.009 0.001 HIS A 320 PHE 0.016 0.002 PHE A 110 TYR 0.016 0.002 TYR A 331 ARG 0.004 0.001 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 ASP cc_start: 0.9369 (t0) cc_final: 0.8740 (t70) REVERT: C 116 GLU cc_start: 0.6586 (tt0) cc_final: 0.6134 (mp0) REVERT: C 352 GLU cc_start: 0.8191 (tt0) cc_final: 0.7581 (tm-30) REVERT: D 76 GLN cc_start: 0.9559 (tt0) cc_final: 0.9101 (tp-100) REVERT: B 76 GLU cc_start: 0.9243 (pt0) cc_final: 0.8779 (pt0) REVERT: A 76 GLU cc_start: 0.8921 (pt0) cc_final: 0.8660 (pt0) REVERT: A 330 ASP cc_start: 0.9097 (t70) cc_final: 0.8727 (t70) REVERT: A 436 MET cc_start: 0.9007 (mmm) cc_final: 0.8578 (mtm) outliers start: 21 outliers final: 17 residues processed: 131 average time/residue: 0.4711 time to fit residues: 93.3516 Evaluate side-chains 123 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 126 PHE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 564 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11789 Z= 0.209 Angle : 0.575 5.902 15945 Z= 0.311 Chirality : 0.038 0.141 1799 Planarity : 0.004 0.047 1981 Dihedral : 5.585 28.315 1499 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.16 % Favored : 91.77 % Rotamer: Outliers : 1.45 % Allowed : 14.68 % Favored : 83.87 % 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: -0.27 (0.24), residues: 1348 helix: 1.24 (0.17), residues: 883 sheet: -2.44 (0.64), residues: 65 loop : -3.13 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 79 HIS 0.009 0.001 HIS A 320 PHE 0.010 0.001 PHE B 483 TYR 0.016 0.001 TYR C 177 ARG 0.004 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 ASP cc_start: 0.9360 (t0) cc_final: 0.8969 (p0) REVERT: C 116 GLU cc_start: 0.6657 (tt0) cc_final: 0.6456 (mp0) REVERT: C 352 GLU cc_start: 0.8201 (tt0) cc_final: 0.7691 (tm-30) REVERT: D 76 GLN cc_start: 0.9451 (tt0) cc_final: 0.9114 (tp-100) REVERT: B 76 GLU cc_start: 0.9239 (pt0) cc_final: 0.8768 (pt0) REVERT: A 76 GLU cc_start: 0.8879 (pt0) cc_final: 0.8622 (pt0) REVERT: A 111 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7900 (m-80) REVERT: A 436 MET cc_start: 0.8998 (mmm) cc_final: 0.8561 (mtm) REVERT: A 458 CYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8611 (m) outliers start: 19 outliers final: 13 residues processed: 131 average time/residue: 0.4860 time to fit residues: 94.2341 Evaluate side-chains 124 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 458 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 GLN C 168 HIS ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11789 Z= 0.305 Angle : 0.624 6.836 15945 Z= 0.342 Chirality : 0.038 0.144 1799 Planarity : 0.004 0.045 1981 Dihedral : 5.542 27.498 1499 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.39 % Favored : 89.54 % Rotamer: Outliers : 1.99 % Allowed : 15.60 % Favored : 82.42 % 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: -0.21 (0.24), residues: 1348 helix: 1.17 (0.17), residues: 897 sheet: -2.54 (0.74), residues: 51 loop : -2.93 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 79 HIS 0.006 0.001 HIS A 320 PHE 0.013 0.001 PHE A 494 TYR 0.014 0.002 TYR B 236 ARG 0.004 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 2.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 ASP cc_start: 0.9386 (t0) cc_final: 0.8973 (p0) REVERT: C 352 GLU cc_start: 0.8463 (tt0) cc_final: 0.7769 (tm-30) REVERT: D 76 GLN cc_start: 0.9474 (tt0) cc_final: 0.9148 (tp-100) REVERT: B 76 GLU cc_start: 0.9238 (pt0) cc_final: 0.8679 (pt0) REVERT: B 111 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7015 (t80) REVERT: B 373 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8578 (pp) REVERT: B 390 SER cc_start: 0.8358 (m) cc_final: 0.8020 (p) REVERT: A 76 GLU cc_start: 0.8887 (pt0) cc_final: 0.8649 (pt0) REVERT: A 111 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: A 436 MET cc_start: 0.9028 (mmm) cc_final: 0.8668 (mtm) REVERT: A 458 CYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8616 (m) outliers start: 26 outliers final: 19 residues processed: 132 average time/residue: 0.4539 time to fit residues: 91.6451 Evaluate side-chains 128 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 104 PHE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 458 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 131 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 0.0970 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 107 GLN ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11789 Z= 0.176 Angle : 0.558 5.799 15945 Z= 0.300 Chirality : 0.037 0.138 1799 Planarity : 0.004 0.048 1981 Dihedral : 5.310 27.846 1499 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.68 % Favored : 91.25 % Rotamer: Outliers : 1.61 % Allowed : 16.28 % Favored : 82.11 % 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 (0.24), residues: 1348 helix: 1.51 (0.17), residues: 884 sheet: -2.19 (0.69), residues: 60 loop : -2.94 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 79 HIS 0.007 0.001 HIS A 320 PHE 0.009 0.001 PHE A 324 TYR 0.017 0.001 TYR B 236 ARG 0.004 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 ASP cc_start: 0.9364 (t0) cc_final: 0.8960 (p0) REVERT: C 352 GLU cc_start: 0.8435 (tt0) cc_final: 0.7799 (tm-30) REVERT: C 376 LYS cc_start: 0.8896 (mttt) cc_final: 0.8653 (ttmt) REVERT: D 76 GLN cc_start: 0.9469 (tt0) cc_final: 0.9139 (tp-100) REVERT: B 76 GLU cc_start: 0.9265 (pt0) cc_final: 0.8730 (pt0) REVERT: B 373 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8484 (pp) REVERT: B 390 SER cc_start: 0.8264 (m) cc_final: 0.7910 (p) REVERT: A 76 GLU cc_start: 0.8874 (pt0) cc_final: 0.8637 (pt0) REVERT: A 111 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.8182 (m-80) REVERT: A 436 MET cc_start: 0.8986 (mmm) cc_final: 0.8546 (mtm) outliers start: 21 outliers final: 15 residues processed: 136 average time/residue: 0.4620 time to fit residues: 95.3221 Evaluate side-chains 131 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 104 PHE Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 330 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11789 Z= 0.185 Angle : 0.557 5.875 15945 Z= 0.300 Chirality : 0.037 0.136 1799 Planarity : 0.004 0.047 1981 Dihedral : 5.200 27.691 1499 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.35 % Favored : 90.58 % Rotamer: Outliers : 1.68 % Allowed : 16.82 % Favored : 81.50 % 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: 0.21 (0.24), residues: 1348 helix: 1.58 (0.18), residues: 886 sheet: -2.21 (0.68), residues: 60 loop : -2.91 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 79 HIS 0.007 0.001 HIS A 320 PHE 0.017 0.001 PHE C 120 TYR 0.016 0.001 TYR B 236 ARG 0.004 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 ASP cc_start: 0.9381 (t0) cc_final: 0.8982 (p0) REVERT: C 352 GLU cc_start: 0.8456 (tt0) cc_final: 0.7828 (tm-30) REVERT: C 376 LYS cc_start: 0.8934 (mttt) cc_final: 0.8685 (ttmt) REVERT: D 76 GLN cc_start: 0.9464 (tt0) cc_final: 0.9131 (tp-100) REVERT: B 76 GLU cc_start: 0.9269 (pt0) cc_final: 0.8734 (pt0) REVERT: B 319 MET cc_start: 0.9302 (OUTLIER) cc_final: 0.9089 (mtm) REVERT: B 373 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8426 (pp) REVERT: B 390 SER cc_start: 0.8259 (m) cc_final: 0.7859 (p) REVERT: A 76 GLU cc_start: 0.8947 (pt0) cc_final: 0.8691 (pt0) REVERT: A 436 MET cc_start: 0.8989 (mmm) cc_final: 0.8591 (mtm) REVERT: A 458 CYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8672 (m) outliers start: 22 outliers final: 18 residues processed: 131 average time/residue: 0.4537 time to fit residues: 89.8829 Evaluate side-chains 136 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 104 PHE Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 458 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 64 optimal weight: 0.3980 chunk 12 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11789 Z= 0.177 Angle : 0.551 5.596 15945 Z= 0.295 Chirality : 0.037 0.139 1799 Planarity : 0.004 0.047 1981 Dihedral : 5.047 27.395 1499 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.83 % Favored : 91.10 % Rotamer: Outliers : 1.45 % Allowed : 17.28 % Favored : 81.27 % 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: 0.37 (0.24), residues: 1348 helix: 1.72 (0.18), residues: 887 sheet: -2.19 (0.64), residues: 69 loop : -2.88 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 79 HIS 0.007 0.001 HIS A 320 PHE 0.013 0.001 PHE C 120 TYR 0.017 0.001 TYR B 236 ARG 0.004 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 2.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 ASP cc_start: 0.9378 (t0) cc_final: 0.8982 (p0) REVERT: C 352 GLU cc_start: 0.8560 (tt0) cc_final: 0.7900 (tm-30) REVERT: C 376 LYS cc_start: 0.8985 (mttt) cc_final: 0.8744 (ttmt) REVERT: D 76 GLN cc_start: 0.9477 (tt0) cc_final: 0.9141 (tp-100) REVERT: B 76 GLU cc_start: 0.9260 (pt0) cc_final: 0.8724 (pt0) REVERT: B 319 MET cc_start: 0.9310 (mtt) cc_final: 0.9091 (mtm) REVERT: B 373 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8347 (pp) REVERT: B 390 SER cc_start: 0.8175 (m) cc_final: 0.7816 (p) REVERT: A 76 GLU cc_start: 0.8872 (pt0) cc_final: 0.8656 (pt0) REVERT: A 436 MET cc_start: 0.8994 (mmm) cc_final: 0.8602 (mtm) REVERT: A 458 CYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8654 (m) outliers start: 19 outliers final: 16 residues processed: 134 average time/residue: 0.4908 time to fit residues: 98.3359 Evaluate side-chains 134 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 104 PHE Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 458 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11789 Z= 0.172 Angle : 0.543 6.247 15945 Z= 0.290 Chirality : 0.037 0.140 1799 Planarity : 0.004 0.047 1981 Dihedral : 4.972 27.322 1499 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.75 % Favored : 91.17 % Rotamer: Outliers : 1.61 % Allowed : 17.51 % Favored : 80.89 % 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: 0.45 (0.24), residues: 1348 helix: 1.78 (0.18), residues: 888 sheet: -2.73 (0.59), residues: 79 loop : -2.72 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 79 HIS 0.007 0.001 HIS A 320 PHE 0.014 0.001 PHE C 120 TYR 0.017 0.001 TYR B 236 ARG 0.004 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 ASP cc_start: 0.9364 (t0) cc_final: 0.8937 (p0) REVERT: C 289 MET cc_start: 0.8131 (ttp) cc_final: 0.7878 (ttm) REVERT: C 352 GLU cc_start: 0.8559 (tt0) cc_final: 0.7946 (tm-30) REVERT: C 376 LYS cc_start: 0.8965 (mttt) cc_final: 0.8738 (ttmt) REVERT: D 76 GLN cc_start: 0.9486 (tt0) cc_final: 0.9150 (tp-100) REVERT: B 76 GLU cc_start: 0.9251 (pt0) cc_final: 0.8682 (pt0) REVERT: B 254 ILE cc_start: 0.8069 (mt) cc_final: 0.7819 (mt) REVERT: B 319 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.9103 (mtm) REVERT: B 373 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8350 (pp) REVERT: B 390 SER cc_start: 0.8122 (m) cc_final: 0.7740 (p) REVERT: A 76 GLU cc_start: 0.8825 (pt0) cc_final: 0.8604 (pt0) REVERT: A 111 TYR cc_start: 0.8040 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: A 436 MET cc_start: 0.8996 (mmm) cc_final: 0.8598 (mtm) REVERT: A 458 CYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8638 (m) outliers start: 21 outliers final: 15 residues processed: 135 average time/residue: 0.4527 time to fit residues: 91.7074 Evaluate side-chains 137 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 104 PHE Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 458 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN A 446 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11789 Z= 0.300 Angle : 0.610 6.040 15945 Z= 0.334 Chirality : 0.038 0.140 1799 Planarity : 0.004 0.043 1981 Dihedral : 5.099 26.929 1499 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.16 % Favored : 89.76 % Rotamer: Outliers : 1.45 % Allowed : 17.58 % Favored : 80.96 % 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: 0.15 (0.24), residues: 1348 helix: 1.50 (0.17), residues: 899 sheet: -3.09 (0.59), residues: 75 loop : -2.78 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 79 HIS 0.007 0.001 HIS A 320 PHE 0.028 0.002 PHE A 138 TYR 0.016 0.002 TYR B 236 ARG 0.004 0.000 ARG D 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 ASP cc_start: 0.9387 (t0) cc_final: 0.8990 (p0) REVERT: C 352 GLU cc_start: 0.8680 (tt0) cc_final: 0.7766 (tm-30) REVERT: D 76 GLN cc_start: 0.9511 (tt0) cc_final: 0.9180 (tp-100) REVERT: B 76 GLU cc_start: 0.9260 (pt0) cc_final: 0.8683 (pt0) REVERT: B 345 ASP cc_start: 0.8683 (t0) cc_final: 0.8069 (t0) REVERT: B 373 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8269 (pp) REVERT: B 390 SER cc_start: 0.8265 (m) cc_final: 0.7859 (p) REVERT: A 76 GLU cc_start: 0.8816 (pt0) cc_final: 0.8600 (pt0) REVERT: A 111 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7756 (m-10) REVERT: A 436 MET cc_start: 0.9054 (mmm) cc_final: 0.8655 (mtm) REVERT: A 458 CYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8661 (m) outliers start: 19 outliers final: 16 residues processed: 127 average time/residue: 0.4996 time to fit residues: 94.8703 Evaluate side-chains 130 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 104 PHE Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 458 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 13 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.069761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.053642 restraints weight = 169160.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.056234 restraints weight = 75646.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.057863 restraints weight = 45122.157| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11789 Z= 0.261 Angle : 0.589 5.927 15945 Z= 0.319 Chirality : 0.038 0.147 1799 Planarity : 0.004 0.044 1981 Dihedral : 5.082 27.099 1499 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.87 % Favored : 90.06 % Rotamer: Outliers : 1.53 % Allowed : 17.89 % Favored : 80.58 % 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: 0.16 (0.24), residues: 1348 helix: 1.48 (0.17), residues: 899 sheet: -2.81 (0.59), residues: 79 loop : -2.77 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 79 HIS 0.006 0.001 HIS A 320 PHE 0.012 0.001 PHE B 483 TYR 0.018 0.001 TYR B 236 ARG 0.004 0.000 ARG D 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4209.41 seconds wall clock time: 75 minutes 52.95 seconds (4552.95 seconds total)