Starting phenix.real_space_refine on Fri Aug 9 10:23:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7w_20271/08_2024/6p7w_20271.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7w_20271/08_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_20271/08_2024/6p7w_20271.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7w_20271/08_2024/6p7w_20271.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7w_20271/08_2024/6p7w_20271.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7w_20271/08_2024/6p7w_20271.cif" } 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-5409/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: 12.00, per 1000 atoms: 0.47 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: 22.75 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: 1.74 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: 10.94 Time building geometry restraints manager: 23.80 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 2.450 nonbonded pdb=" O VAL C 341 " pdb=" HG1 THR C 344 " model vdw 1.675 2.450 nonbonded pdb=" OH TYR C 338 " pdb=" HE ARG C 368 " model vdw 1.677 2.450 nonbonded pdb=" OD2 ASP D 105 " pdb=" H ASP D 108 " model vdw 1.678 2.450 nonbonded pdb=" OD1 ASN B 248 " pdb=" HE ARG B 252 " model vdw 1.684 2.450 ... (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 Time spend for trying shortcut: 0.00 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: 1.640 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: 0.410 Extract box with map and model: 1.090 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 89.030 Find NCS groups from input model: 0.550 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.970 ------------------------------------------------------------------------------- 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 : 2.325 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: 0.5235 time to fit residues: 156.2675 Evaluate side-chains 141 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.619 ------------------------------------------------------------------------------- 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: 6.9990 chunk 63 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: