Starting phenix.real_space_refine on Mon Feb 19 20:24:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7w_20271/02_2024/6p7w_20271.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7w_20271/02_2024/6p7w_20271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7w_20271/02_2024/6p7w_20271.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7w_20271/02_2024/6p7w_20271.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7w_20271/02_2024/6p7w_20271.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7w_20271/02_2024/6p7w_20271.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 60 5.16 5 C 8370 2.51 5 N 2126 2.21 5 O 2308 1.98 5 H 12936 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ASP 40": "OD1" <-> "OD2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 63": "OD1" <-> "OD2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 67": "OD1" <-> "OD2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "C ARG 92": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 237": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 338": "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 "D ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 95": "OD1" <-> "OD2" Residue "D ASP 105": "OD1" <-> "OD2" Residue "D ASP 136": "OD1" <-> "OD2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 384": "OD1" <-> "OD2" Residue "B ARG 409": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 424": "OE1" <-> "OE2" Residue "B TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 462": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 ARG 615": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 76": "OE1" <-> "OE2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A ASP 187": "OD1" <-> "OD2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A ASP 260": "OD1" <-> "OD2" Residue "A ASP 308": "OD1" <-> "OD2" Residue "A ARG 333": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 377": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 384": "OD1" <-> "OD2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A ARG 409": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 416": "OD1" <-> "OD2" 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 ARG 508": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 511": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 523": "OD1" <-> "OD2" 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 ARG 615": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 616": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25800 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1589 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain breaks: 1 Chain: "C" Number of atoms: 6464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 6464 Classifications: {'peptide': 387} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 373} 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: 7711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 7711 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 14, 'TRANS': 444} Chain breaks: 6 Time building chain proxies: 11.11, per 1000 atoms: 0.43 Number of scatterers: 25800 At special positions: 0 Unit cell: (93.324, 135.744, 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 60 16.00 O 2308 8.00 N 2126 7.00 C 8370 6.00 H 12936 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: 20.26 Conformation dependent library (CDL) restraints added in 2.7 seconds 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3008 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 5 sheets defined 67.8% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'E' and resid 4 through 10 Processing helix chain 'E' and resid 12 through 32 removed outlier: 3.573A pdb=" N ALA E 16 " --> pdb=" O PRO E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 59 through 63 Processing helix chain 'E' and resid 64 through 76 Processing helix chain 'E' and resid 81 through 101 removed outlier: 4.138A pdb=" N PHE E 101 " --> pdb=" O LYS E 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 11 through 22 removed outlier: 3.882A pdb=" N ARG C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 Processing helix chain 'C' and resid 72 through 83 Processing helix chain 'C' and resid 86 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 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'C' and resid 211 through 217 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 371 Processing helix chain 'D' and resid 22 through 27 Processing helix chain 'D' and resid 29 through 35 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 removed outlier: 3.716A pdb=" N LEU D 119 " --> pdb=" O ASP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 148 removed outlier: 3.825A pdb=" N LEU D 135 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 156 removed outlier: 4.019A 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 Processing helix chain 'B' and resid 118 through 133 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: 3.594A pdb=" N ILE B 206 " --> pdb=" O PRO B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 218 removed outlier: 3.763A 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 272 removed outlier: 3.660A pdb=" N GLN B 265 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 279 through 298 removed outlier: 3.673A 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 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: 3.597A pdb=" N THR B 479 " --> pdb=" O TYR B 475 " (cutoff:3.500A) removed outlier: 3.671A 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: 3.639A pdb=" N VAL B 485 " --> pdb=" O HIS B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 522 Processing helix chain 'B' and resid 525 through 548 Processing helix chain 'B' and resid 560 through 578 removed outlier: 4.545A 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 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: 3.584A pdb=" N ILE A 206 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 218 Processing helix chain 'A' and resid 232 through 256 removed outlier: 3.655A pdb=" N ARG A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 272 removed outlier: 3.599A pdb=" N GLN A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 4.017A 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 297 Processing helix chain 'A' and resid 309 through 333 Processing helix chain 'A' and resid 373 through 389 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: 3.533A pdb=" N THR A 479 " --> pdb=" O TYR A 475 " (cutoff:3.500A) removed outlier: 3.694A 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: 3.640A pdb=" N VAL A 485 " --> pdb=" O HIS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 522 removed outlier: 3.601A pdb=" N PHE A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 548 Processing helix chain 'A' and resid 560 through 578 removed outlier: 4.307A 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: 3.601A pdb=" N VAL C 129 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 148 through 151 removed outlier: 4.242A 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: 7.107A 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 363 through 366 Processing sheet with id=AA5, first strand: chain 'D' and resid 16 through 21 767 hydrogen bonds defined for protein. 2265 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: 8.86 Time building geometry restraints manager: 20.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12905 1.03 - 1.23: 80 1.23 - 1.43: 5533 1.43 - 1.62: 7488 1.62 - 1.82: 89 Bond restraints: 26095 Sorted by residual: bond pdb=" C ASP B 523 " pdb=" N PRO B 524 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.37e+00 bond pdb=" CG1 ILE A 254 " pdb=" CD1 ILE A 254 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.26e+00 bond pdb=" C LYS B 305 " pdb=" N ILE B 306 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.73e-02 3.34e+03 3.20e+00 bond pdb=" CA ILE A 212 " pdb=" C ILE A 212 " ideal model delta sigma weight residual 1.523 1.501 0.022 1.27e-02 6.20e+03 3.07e+00 bond pdb=" C ASP A 211 " pdb=" N ILE A 212 " ideal model delta sigma weight residual 1.332 1.310 0.022 1.36e-02 5.41e+03 2.71e+00 ... (remaining 26090 not shown) Histogram of bond angle deviations from ideal: 98.81 - 105.98: 317 105.98 - 113.15: 30543 113.15 - 120.32: 8902 120.32 - 127.49: 7279 127.49 - 134.66: 158 Bond angle restraints: 47199 Sorted by residual: angle pdb=" N VAL A 389 " pdb=" CA VAL A 389 " pdb=" C VAL A 389 " ideal model delta sigma weight residual 111.58 116.32 -4.74 1.06e+00 8.90e-01 2.00e+01 angle pdb=" N LEU A 116 " pdb=" CA LEU A 116 " pdb=" C LEU A 116 " ideal model delta sigma weight residual 110.80 119.93 -9.13 2.13e+00 2.20e-01 1.84e+01 angle pdb=" N ILE A 212 " pdb=" CA ILE A 212 " pdb=" C ILE A 212 " ideal model delta sigma weight residual 109.34 101.63 7.71 2.08e+00 2.31e-01 1.37e+01 angle pdb=" C SER A 390 " pdb=" N GLU A 391 " pdb=" CA GLU A 391 " ideal model delta sigma weight residual 121.80 130.64 -8.84 2.44e+00 1.68e-01 1.31e+01 angle pdb=" C ILE A 212 " pdb=" N ASP A 213 " pdb=" CA ASP A 213 " ideal model delta sigma weight residual 120.28 115.08 5.20 1.44e+00 4.82e-01 1.30e+01 ... (remaining 47194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 10515 17.78 - 35.55: 1338 35.55 - 53.33: 254 53.33 - 71.11: 69 71.11 - 88.88: 6 Dihedral angle restraints: 12182 sinusoidal: 6548 harmonic: 5634 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 180.00 144.35 35.65 0 5.00e+00 4.00e-02 5.08e+01 dihedral pdb=" CA PHE B 110 " pdb=" C PHE B 110 " pdb=" N TYR B 111 " pdb=" CA TYR B 111 " ideal model delta harmonic sigma weight residual -180.00 -148.57 -31.43 0 5.00e+00 4.00e-02 3.95e+01 dihedral pdb=" CA LEU A 220 " pdb=" C LEU A 220 " pdb=" N ASP A 221 " pdb=" CA ASP A 221 " ideal model delta harmonic sigma weight residual 180.00 148.81 31.19 0 5.00e+00 4.00e-02 3.89e+01 ... (remaining 12179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1332 0.041 - 0.082: 465 0.082 - 0.124: 169 0.124 - 0.165: 33 0.165 - 0.206: 3 Chirality restraints: 2002 Sorted by residual: chirality pdb=" CA LEU A 116 " pdb=" N LEU A 116 " pdb=" C LEU A 116 " pdb=" CB LEU A 116 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE C 69 " pdb=" CA ILE C 69 " pdb=" CG1 ILE C 69 " pdb=" CG2 ILE C 69 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.29e-01 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 -2.42 -0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 1999 not shown) Planarity restraints: 3687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 211 " 0.039 2.00e-02 2.50e+03 7.74e-02 5.99e+01 pdb=" C ASP A 211 " -0.134 2.00e-02 2.50e+03 pdb=" O ASP A 211 " 0.051 2.00e-02 2.50e+03 pdb=" N ILE A 212 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 532 " -0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C PHE A 532 " 0.066 2.00e-02 2.50e+03 pdb=" O PHE A 532 " -0.025 2.00e-02 2.50e+03 pdb=" N PHE A 533 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 535 " -0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C ASN A 535 " 0.065 2.00e-02 2.50e+03 pdb=" O ASN A 535 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU A 536 " -0.022 2.00e-02 2.50e+03 ... (remaining 3684 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 3186 2.24 - 2.83: 59708 2.83 - 3.42: 67968 3.42 - 4.01: 87619 4.01 - 4.60: 136717 Nonbonded interactions: 355198 Sorted by model distance: nonbonded pdb=" O SER D 12 " pdb=" H GLY D 15 " model vdw 1.655 1.850 nonbonded pdb=" O VAL C 341 " pdb=" HG1 THR C 344 " model vdw 1.675 1.850 nonbonded pdb=" OH TYR C 338 " pdb=" HE ARG C 368 " model vdw 1.677 1.850 nonbonded pdb=" OD2 ASP D 105 " pdb=" H ASP D 108 " model vdw 1.678 1.850 nonbonded pdb=" OD1 ASN B 248 " pdb=" HE ARG B 252 " model vdw 1.684 1.850 ... (remaining 355193 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' and (resid 62 through 220 or resid 231 through 618)) 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: 1.010 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: 0.360 Extract box with map and model: 6.130 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 79.210 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 : 0.007 0.070 13159 Z= 0.445 Angle : 0.942 9.125 17809 Z= 0.526 Chirality : 0.049 0.206 2002 Planarity : 0.006 0.077 2217 Dihedral : 15.401 88.882 4880 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.10 % Favored : 88.63 % Rotamer: Outliers : 0.07 % Allowed : 4.12 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.77 (0.18), residues: 1504 helix: -1.70 (0.14), residues: 969 sheet: -3.94 (0.55), residues: 66 loop : -3.77 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 378 HIS 0.011 0.002 HIS A 320 PHE 0.040 0.003 PHE C 201 TYR 0.018 0.002 TYR C 338 ARG 0.012 0.001 ARG C 368 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 2.284 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: symmetry clash revert: symmetry clash REVERT: E 48 LYS cc_start: 0.9146 (mtpt) cc_final: 0.8944 (ptpp) REVERT: E 89 GLN cc_start: 0.9263 (tt0) cc_final: 0.9050 (tp-100) REVERT: D 132 LYS cc_start: 0.9231 (mmtt) cc_final: 0.8997 (mmmm) REVERT: B 378 TRP cc_start: 0.8580 (t-100) cc_final: 0.7937 (t-100) REVERT: A 75 TYR cc_start: 0.8749 (t80) cc_final: 0.8522 (t80) REVERT: A 319 MET cc_start: 0.8564 (ttm) cc_final: 0.8146 (ttm) REVERT: A 330 ASP cc_start: 0.8722 (t70) cc_final: 0.8287 (t70) REVERT: A 436 MET cc_start: 0.8895 (mmm) cc_final: 0.8552 (tpp) outliers start: 1 outliers final: 1 residues processed: 211 average time/residue: 0.6178 time to fit residues: 184.4434 Evaluate side-chains 141 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 HIS C 107 GLN C 160 ASN C 336 ASN ** C 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN ** B 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 HIS ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN A 454 GLN A 576 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13159 Z= 0.199 Angle : 0.636 6.239 17809 Z= 0.346 Chirality : 0.039 0.171 2002 Planarity : 0.005 0.060 2217 Dihedral : 6.546 35.913 1673 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.84 % Favored : 90.09 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.20), residues: 1504 helix: -0.21 (0.15), residues: 982 sheet: -3.51 (0.52), residues: 80 loop : -3.58 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 323 HIS 0.009 0.001 HIS A 292 PHE 0.022 0.001 PHE C 201 TYR 0.018 0.001 TYR A 111 ARG 0.004 0.000 ARG B 352 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.152 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 89 GLN cc_start: 0.9323 (tt0) cc_final: 0.9036 (tp-100) REVERT: D 132 LYS cc_start: 0.9298 (mmtt) cc_final: 0.9065 (mmmm) REVERT: A 75 TYR cc_start: 0.8689 (t80) cc_final: 0.8488 (t80) REVERT: A 76 GLU cc_start: 0.8933 (tp30) cc_final: 0.8669 (mt-10) REVERT: A 275 PHE cc_start: 0.9048 (t80) cc_final: 0.8780 (t80) REVERT: A 330 ASP cc_start: 0.8821 (t70) cc_final: 0.8287 (t0) REVERT: A 436 MET cc_start: 0.8835 (mmm) cc_final: 0.8564 (tpp) REVERT: A 563 MET cc_start: 0.6494 (ppp) cc_final: 0.6259 (tmm) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.5494 time to fit residues: 146.7682 Evaluate side-chains 141 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 0.0770 chunk 93 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 137 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 46 optimal weight: 0.3980 chunk 110 optimal weight: 1.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 ASN ** C 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13159 Z= 0.207 Angle : 0.595 5.940 17809 Z= 0.325 Chirality : 0.038 0.187 2002 Planarity : 0.004 0.057 2217 Dihedral : 6.063 37.340 1673 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 0.07 % Allowed : 3.02 % Favored : 96.91 % 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: -1.25 (0.22), residues: 1504 helix: 0.50 (0.16), residues: 986 sheet: -3.18 (0.55), residues: 80 loop : -3.48 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 79 HIS 0.008 0.001 HIS C 168 PHE 0.020 0.001 PHE B 522 TYR 0.013 0.001 TYR B 447 ARG 0.004 0.000 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 1.917 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: 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: D 132 LYS cc_start: 0.9331 (mmtt) cc_final: 0.9038 (mmmm) REVERT: B 400 MET cc_start: 0.9130 (mtp) cc_final: 0.8910 (mtp) REVERT: A 76 GLU cc_start: 0.8838 (tp30) cc_final: 0.8624 (mt-10) REVERT: A 319 MET cc_start: 0.8339 (ttm) cc_final: 0.7940 (ttm) REVERT: A 330 ASP cc_start: 0.8937 (t70) cc_final: 0.8565 (t0) REVERT: A 436 MET cc_start: 0.8819 (mmm) cc_final: 0.8372 (tpp) REVERT: A 563 MET cc_start: 0.6421 (ppp) cc_final: 0.6137 (tmm) outliers start: 1 outliers final: 1 residues processed: 181 average time/residue: 0.5816 time to fit residues: 152.1617 Evaluate side-chains 142 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 71 optimal weight: 0.0870 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13159 Z= 0.172 Angle : 0.560 6.425 17809 Z= 0.303 Chirality : 0.038 0.176 2002 Planarity : 0.004 0.057 2217 Dihedral : 5.710 41.405 1673 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 0.07 % Allowed : 1.17 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.22), residues: 1504 helix: 0.91 (0.16), residues: 991 sheet: -3.10 (0.56), residues: 80 loop : -3.31 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 79 HIS 0.008 0.001 HIS A 292 PHE 0.016 0.001 PHE A 117 TYR 0.024 0.001 TYR B 154 ARG 0.005 0.000 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 2.185 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: 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: D 132 LYS cc_start: 0.9293 (mmtt) cc_final: 0.9028 (mmmm) REVERT: B 270 LEU cc_start: 0.9507 (mt) cc_final: 0.9260 (mt) REVERT: B 276 LEU cc_start: 0.9189 (mt) cc_final: 0.8863 (mt) REVERT: B 400 MET cc_start: 0.9150 (mtp) cc_final: 0.8919 (mtp) REVERT: A 295 LYS cc_start: 0.9535 (mttt) cc_final: 0.9307 (mtmm) REVERT: A 319 MET cc_start: 0.8348 (ttm) cc_final: 0.7973 (ttm) REVERT: A 330 ASP cc_start: 0.9083 (t70) cc_final: 0.8729 (t0) REVERT: A 436 MET cc_start: 0.8791 (mmm) cc_final: 0.8337 (tpp) REVERT: A 544 HIS cc_start: 0.8424 (m-70) cc_final: 0.8075 (m-70) REVERT: A 563 MET cc_start: 0.6472 (ppp) cc_final: 0.6262 (tmm) outliers start: 1 outliers final: 1 residues processed: 180 average time/residue: 0.5112 time to fit residues: 136.8430 Evaluate side-chains 145 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 GLN ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 13159 Z= 0.225 Angle : 0.568 6.109 17809 Z= 0.311 Chirality : 0.037 0.167 2002 Planarity : 0.004 0.055 2217 Dihedral : 5.565 41.970 1673 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: -0.52 (0.22), residues: 1504 helix: 1.03 (0.16), residues: 991 sheet: -3.00 (0.57), residues: 80 loop : -3.15 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 72 HIS 0.009 0.001 HIS C 168 PHE 0.023 0.001 PHE A 255 TYR 0.043 0.001 TYR A 75 ARG 0.006 0.000 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 2.045 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 132 LYS cc_start: 0.9330 (mmtt) cc_final: 0.9083 (mmmm) REVERT: B 270 LEU cc_start: 0.9531 (mt) cc_final: 0.9272 (mt) REVERT: B 400 MET cc_start: 0.9207 (mtp) cc_final: 0.8887 (mtp) REVERT: A 275 PHE cc_start: 0.8798 (t80) cc_final: 0.8568 (t80) REVERT: A 295 LYS cc_start: 0.9537 (mttt) cc_final: 0.9322 (mtmm) REVERT: A 319 MET cc_start: 0.8343 (ttm) cc_final: 0.8001 (ttm) REVERT: A 330 ASP cc_start: 0.9147 (t70) cc_final: 0.8819 (t0) REVERT: A 436 MET cc_start: 0.8793 (mmm) cc_final: 0.8354 (tpp) REVERT: A 544 HIS cc_start: 0.8448 (m-70) cc_final: 0.8081 (m-70) REVERT: A 563 MET cc_start: 0.6313 (ppp) cc_final: 0.6067 (tmm) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.5477 time to fit residues: 137.2063 Evaluate side-chains 134 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 0.4980 chunk 131 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 121 optimal weight: 0.0970 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 415 ASN ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13159 Z= 0.217 Angle : 0.569 6.222 17809 Z= 0.313 Chirality : 0.038 0.217 2002 Planarity : 0.004 0.055 2217 Dihedral : 5.497 43.772 1673 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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 (0.23), residues: 1504 helix: 1.16 (0.16), residues: 991 sheet: -2.98 (0.59), residues: 78 loop : -3.10 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 79 HIS 0.009 0.001 HIS C 168 PHE 0.052 0.002 PHE A 255 TYR 0.017 0.001 TYR A 75 ARG 0.003 0.000 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 2.264 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 132 LYS cc_start: 0.9334 (mmtt) cc_final: 0.9092 (mmmm) REVERT: B 270 LEU cc_start: 0.9528 (mt) cc_final: 0.9290 (mt) REVERT: A 295 LYS cc_start: 0.9536 (mttt) cc_final: 0.9320 (mtmm) REVERT: A 319 MET cc_start: 0.8259 (ttm) cc_final: 0.7918 (ttm) REVERT: A 320 HIS cc_start: 0.8752 (t-90) cc_final: 0.8520 (t70) REVERT: A 330 ASP cc_start: 0.9177 (t70) cc_final: 0.8889 (t0) REVERT: A 339 ILE cc_start: 0.8734 (tp) cc_final: 0.8366 (mt) REVERT: A 436 MET cc_start: 0.8791 (mmm) cc_final: 0.8349 (tpp) REVERT: A 544 HIS cc_start: 0.8390 (m-70) cc_final: 0.8017 (m-70) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.5175 time to fit residues: 128.8453 Evaluate side-chains 134 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 69 ASN ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 HIS A 74 GLN A 156 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13159 Z= 0.233 Angle : 0.568 6.130 17809 Z= 0.312 Chirality : 0.038 0.213 2002 Planarity : 0.004 0.054 2217 Dihedral : 5.452 43.654 1673 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: -0.29 (0.23), residues: 1504 helix: 1.18 (0.16), residues: 1001 sheet: -3.05 (0.57), residues: 78 loop : -3.04 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 79 HIS 0.008 0.001 HIS C 168 PHE 0.040 0.002 PHE A 255 TYR 0.012 0.001 TYR B 331 ARG 0.006 0.000 ARG B 441 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 2.077 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 96 VAL cc_start: 0.8879 (p) cc_final: 0.8398 (p) REVERT: C 13 ASP cc_start: 0.8240 (p0) cc_final: 0.7784 (p0) REVERT: D 132 LYS cc_start: 0.9359 (mmtt) cc_final: 0.9117 (mmmm) REVERT: B 270 LEU cc_start: 0.9546 (mt) cc_final: 0.9341 (mt) REVERT: B 362 ASP cc_start: 0.8327 (p0) cc_final: 0.7983 (p0) REVERT: A 275 PHE cc_start: 0.8809 (t80) cc_final: 0.8546 (t80) REVERT: A 319 MET cc_start: 0.8197 (ttm) cc_final: 0.7829 (ttm) REVERT: A 320 HIS cc_start: 0.8749 (t-90) cc_final: 0.8538 (t70) REVERT: A 330 ASP cc_start: 0.9247 (t70) cc_final: 0.8947 (t0) REVERT: A 436 MET cc_start: 0.8782 (mmm) cc_final: 0.8342 (tpp) REVERT: A 544 HIS cc_start: 0.8377 (m-70) cc_final: 0.7975 (m-70) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.5282 time to fit residues: 127.4761 Evaluate side-chains 138 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 71 optimal weight: 0.0970 chunk 13 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 13159 Z= 0.152 Angle : 0.524 5.858 17809 Z= 0.284 Chirality : 0.037 0.198 2002 Planarity : 0.004 0.069 2217 Dihedral : 5.253 43.564 1673 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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: 0.02 (0.23), residues: 1504 helix: 1.46 (0.17), residues: 996 sheet: -3.06 (0.55), residues: 83 loop : -2.96 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 79 HIS 0.008 0.001 HIS C 168 PHE 0.028 0.001 PHE A 255 TYR 0.012 0.001 TYR C 177 ARG 0.002 0.000 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 2.238 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 96 VAL cc_start: 0.8961 (p) cc_final: 0.8553 (p) REVERT: C 291 ILE cc_start: 0.9361 (mt) cc_final: 0.9100 (mm) REVERT: D 132 LYS cc_start: 0.9273 (mmtt) cc_final: 0.8993 (mmmm) REVERT: B 268 LEU cc_start: 0.9390 (mt) cc_final: 0.9187 (mt) REVERT: A 275 PHE cc_start: 0.8712 (t80) cc_final: 0.8492 (t80) REVERT: A 295 LYS cc_start: 0.9532 (mttt) cc_final: 0.9296 (mtmm) REVERT: A 319 MET cc_start: 0.8182 (ttm) cc_final: 0.7826 (ttm) REVERT: A 320 HIS cc_start: 0.8694 (t-90) cc_final: 0.8479 (t70) REVERT: A 330 ASP cc_start: 0.9211 (t70) cc_final: 0.8943 (t0) REVERT: A 339 ILE cc_start: 0.8707 (tp) cc_final: 0.8329 (mt) REVERT: A 436 MET cc_start: 0.8761 (mmm) cc_final: 0.8282 (tpp) REVERT: A 544 HIS cc_start: 0.8380 (m-70) cc_final: 0.7981 (m-70) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.5269 time to fit residues: 132.7959 Evaluate side-chains 141 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 10.0000 chunk 127 optimal weight: 0.6980 chunk 135 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 ASN A 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13159 Z= 0.290 Angle : 0.603 7.574 17809 Z= 0.333 Chirality : 0.039 0.216 2002 Planarity : 0.004 0.054 2217 Dihedral : 5.346 40.117 1673 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: -0.26 (0.22), residues: 1504 helix: 1.22 (0.16), residues: 998 sheet: -3.15 (0.56), residues: 78 loop : -3.03 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP B 378 HIS 0.008 0.002 HIS C 168 PHE 0.042 0.002 PHE C 201 TYR 0.015 0.002 TYR B 331 ARG 0.006 0.000 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.163 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: symmetry clash revert: symmetry clash REVERT: E 96 VAL cc_start: 0.8917 (p) cc_final: 0.8504 (p) REVERT: C 13 ASP cc_start: 0.8313 (p0) cc_final: 0.7943 (p0) REVERT: D 132 LYS cc_start: 0.9384 (mmtt) cc_final: 0.9088 (mmmm) REVERT: A 275 PHE cc_start: 0.8864 (t80) cc_final: 0.8603 (t80) REVERT: A 319 MET cc_start: 0.8218 (ttm) cc_final: 0.7897 (ttm) REVERT: A 330 ASP cc_start: 0.9277 (t70) cc_final: 0.9021 (t0) REVERT: A 378 TRP cc_start: 0.7897 (t-100) cc_final: 0.7693 (t-100) REVERT: A 436 MET cc_start: 0.8842 (mmm) cc_final: 0.8420 (tpp) REVERT: A 544 HIS cc_start: 0.8434 (m-70) cc_final: 0.8025 (m-70) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.5445 time to fit residues: 128.4245 Evaluate side-chains 131 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13159 Z= 0.173 Angle : 0.539 6.228 17809 Z= 0.293 Chirality : 0.037 0.188 2002 Planarity : 0.004 0.055 2217 Dihedral : 5.248 41.625 1673 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: 0.03 (0.23), residues: 1504 helix: 1.46 (0.17), residues: 999 sheet: -3.17 (0.53), residues: 83 loop : -2.92 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 378 HIS 0.008 0.001 HIS C 168 PHE 0.032 0.001 PHE C 201 TYR 0.011 0.001 TYR B 236 ARG 0.003 0.000 ARG B 377 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 2.180 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: E 96 VAL cc_start: 0.8940 (p) cc_final: 0.8604 (p) REVERT: C 13 ASP cc_start: 0.8268 (p0) cc_final: 0.7892 (p0) REVERT: D 132 LYS cc_start: 0.9343 (mmtt) cc_final: 0.9013 (mmmm) REVERT: D 145 MET cc_start: 0.8558 (tmm) cc_final: 0.8295 (tmm) REVERT: B 268 LEU cc_start: 0.9388 (mt) cc_final: 0.9177 (mt) REVERT: A 295 LYS cc_start: 0.9505 (mttt) cc_final: 0.9283 (mtmm) REVERT: A 319 MET cc_start: 0.8168 (ttm) cc_final: 0.7828 (ttm) REVERT: A 330 ASP cc_start: 0.9263 (t70) cc_final: 0.9025 (t0) REVERT: A 378 TRP cc_start: 0.7870 (t-100) cc_final: 0.7662 (t-100) REVERT: A 436 MET cc_start: 0.8809 (mmm) cc_final: 0.8375 (tpp) REVERT: A 544 HIS cc_start: 0.8394 (m-70) cc_final: 0.7968 (m-70) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.5625 time to fit residues: 132.7381 Evaluate side-chains 133 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.084724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.064132 restraints weight = 168273.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.066722 restraints weight = 82692.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.068322 restraints weight = 53549.314| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 13159 Z= 0.179 Angle : 0.526 5.929 17809 Z= 0.287 Chirality : 0.037 0.193 2002 Planarity : 0.004 0.054 2217 Dihedral : 5.123 41.161 1673 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 0.18 (0.23), residues: 1504 helix: 1.57 (0.17), residues: 999 sheet: -3.14 (0.53), residues: 83 loop : -2.86 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 378 HIS 0.008 0.001 HIS C 168 PHE 0.031 0.001 PHE C 201 TYR 0.011 0.001 TYR B 236 ARG 0.003 0.000 ARG A 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4883.09 seconds wall clock time: 87 minutes 58.53 seconds (5278.53 seconds total)