Starting phenix.real_space_refine on Thu Feb 22 03:40:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7x_20272/02_2024/6p7x_20272.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7x_20272/02_2024/6p7x_20272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7x_20272/02_2024/6p7x_20272.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7x_20272/02_2024/6p7x_20272.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7x_20272/02_2024/6p7x_20272.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7x_20272/02_2024/6p7x_20272.pdb" } resolution = 4.3 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 Anisotropic ADP refinement not supported. Converting 2377 atoms to isotropic. 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 68 5.16 5 C 9925 2.51 5 N 2511 2.21 5 O 2745 1.98 5 H 15288 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 "E PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 142": "OD1" <-> "OD2" Residue "E PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 156": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 274": "OE1" <-> "OE2" Residue "E ASP 280": "OD1" <-> "OD2" Residue "E PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 295": "OD1" <-> "OD2" Residue "E PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 308": "OE1" <-> "OE2" Residue "E ASP 333": "OD1" <-> "OD2" Residue "E ASP 339": "OD1" <-> "OD2" Residue "E PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 383": "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: 30537 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 6326 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 26, 'TRANS': 358} Chain breaks: 2 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: 13.61, per 1000 atoms: 0.45 Number of scatterers: 30537 At special positions: 0 Unit cell: (123.018, 164.378, 126.2, 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 68 16.00 O 2745 8.00 N 2511 7.00 C 9925 6.00 H 15288 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: 24.95 Conformation dependent library (CDL) restraints added in 3.2 seconds 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3570 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 7 sheets defined 65.4% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 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: 4.198A pdb=" N PHE E 101 " --> pdb=" O LYS E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 119 removed outlier: 3.989A pdb=" N ASN E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 150 removed outlier: 4.049A pdb=" N LYS E 136 " --> pdb=" O THR E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 159 Processing helix chain 'E' and resid 193 through 196 Processing helix chain 'E' and resid 197 through 211 Processing helix chain 'E' and resid 223 through 228 removed outlier: 4.126A pdb=" N GLN E 227 " --> pdb=" O GLN E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 260 Proline residue: E 253 - end of helix Processing helix chain 'E' and resid 264 through 270 removed outlier: 3.945A pdb=" N TRP E 268 " --> pdb=" O THR E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 311 removed outlier: 3.918A pdb=" N ILE E 307 " --> pdb=" O PRO E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 356 removed outlier: 4.049A pdb=" N ALA E 336 " --> pdb=" O PRO E 332 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL E 337 " --> pdb=" O ASP E 333 " (cutoff:3.500A) Proline residue: E 350 - end of helix Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 365 through 368 Processing helix chain 'E' and resid 369 through 377 Processing helix chain 'E' and resid 383 through 386 Processing helix chain 'E' and resid 387 through 392 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: 3.764A 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: 3.659A 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: 3.674A 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: 3.672A 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: 3.585A 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: 3.629A 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: 4.306A 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: 4.016A 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 'E' and resid 165 through 169 Processing sheet with id=AA2, first strand: chain 'E' and resid 212 through 213 Processing sheet with id=AA3, 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=AA4, 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=AA5, first strand: chain 'C' and resid 276 through 277 removed outlier: 7.108A pdb=" N ILE C 276 " --> pdb=" O ILE C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 363 through 366 Processing sheet with id=AA7, first strand: chain 'D' and resid 16 through 21 863 hydrogen bonds defined for protein. 2523 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: 10.84 Time building geometry restraints manager: 25.94 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: 15251 1.03 - 1.23: 151 1.23 - 1.43: 6506 1.43 - 1.62: 8897 1.62 - 1.82: 99 Bond restraints: 30904 Sorted by residual: bond pdb=" CA ILE E 300 " pdb=" CB ILE E 300 " ideal model delta sigma weight residual 1.540 1.586 -0.046 1.36e-02 5.41e+03 1.16e+01 bond pdb=" N ILE E 107 " pdb=" CA ILE E 107 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.12e+01 bond pdb=" N TYR E 103 " pdb=" CA TYR E 103 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.18e-02 7.18e+03 1.06e+01 bond pdb=" N VAL E 106 " pdb=" CA VAL E 106 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.67e+00 bond pdb=" N ASP E 102 " pdb=" CA ASP E 102 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.22e-02 6.72e+03 9.29e+00 ... (remaining 30899 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.97: 514 105.97 - 113.13: 35973 113.13 - 120.30: 10500 120.30 - 127.46: 8745 127.46 - 134.63: 185 Bond angle restraints: 55917 Sorted by residual: angle pdb=" C TRP E 275 " pdb=" N PRO E 276 " pdb=" CA PRO E 276 " ideal model delta sigma weight residual 119.89 128.27 -8.38 1.02e+00 9.61e-01 6.75e+01 angle pdb=" N ILE E 302 " pdb=" CA ILE E 302 " pdb=" C ILE E 302 " ideal model delta sigma weight residual 107.89 116.60 -8.71 1.09e+00 8.42e-01 6.38e+01 angle pdb=" C CYS E 197 " pdb=" N PRO E 198 " pdb=" CA PRO E 198 " ideal model delta sigma weight residual 119.19 125.11 -5.92 1.06e+00 8.90e-01 3.12e+01 angle pdb=" N GLY E 219 " pdb=" CA GLY E 219 " pdb=" C GLY E 219 " ideal model delta sigma weight residual 112.54 105.72 6.82 1.28e+00 6.10e-01 2.84e+01 angle pdb=" N PHE E 185 " pdb=" CA PHE E 185 " pdb=" C PHE E 185 " ideal model delta sigma weight residual 108.60 116.12 -7.52 1.46e+00 4.69e-01 2.65e+01 ... (remaining 55912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 12568 17.85 - 35.70: 1513 35.70 - 53.55: 310 53.55 - 71.40: 80 71.40 - 89.25: 8 Dihedral angle restraints: 14479 sinusoidal: 7776 harmonic: 6703 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 180.00 144.33 35.67 0 5.00e+00 4.00e-02 5.09e+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 -148.60 -31.40 0 5.00e+00 4.00e-02 3.94e+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 180.00 148.78 31.22 0 5.00e+00 4.00e-02 3.90e+01 ... (remaining 14476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1779 0.056 - 0.111: 456 0.111 - 0.167: 114 0.167 - 0.223: 19 0.223 - 0.278: 5 Chirality restraints: 2373 Sorted by residual: chirality pdb=" CA ILE E 107 " pdb=" N ILE E 107 " pdb=" C ILE E 107 " pdb=" CB ILE E 107 " both_signs ideal model delta sigma weight residual False 2.43 2.15 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA THR E 299 " pdb=" N THR E 299 " pdb=" C THR E 299 " pdb=" CB THR E 299 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA LEU E 161 " pdb=" N LEU E 161 " pdb=" C LEU E 161 " pdb=" CB LEU E 161 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 2370 not shown) Planarity restraints: 4381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 211 " 0.039 2.00e-02 2.50e+03 7.75e-02 6.00e+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 ASN E 105 " 0.024 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C ASN E 105 " -0.082 2.00e-02 2.50e+03 pdb=" O ASN E 105 " 0.030 2.00e-02 2.50e+03 pdb=" N VAL E 106 " 0.028 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 3.82e-02 1.46e+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 ... (remaining 4378 not shown) Histogram of nonbonded interaction distances: 0.97 - 1.70: 49 1.70 - 2.42: 15585 2.42 - 3.15: 96629 3.15 - 3.87: 119922 3.87 - 4.60: 191021 Warning: very small nonbonded interaction distances. Nonbonded interactions: 423206 Sorted by model distance: nonbonded pdb=" CZ ARG E 91 " pdb=" HB3 PRO E 279 " model vdw 0.970 2.920 nonbonded pdb=" NH1 ARG E 91 " pdb=" HB3 PRO E 279 " model vdw 0.984 2.770 nonbonded pdb="HD23 LEU E 98 " pdb=" HB3 PRO E 276 " model vdw 1.020 2.440 nonbonded pdb="HH22 ARG E 91 " pdb=" N ASP E 280 " model vdw 1.144 2.600 nonbonded pdb="HD21 LEU E 95 " pdb=" OH TYR E 306 " model vdw 1.304 2.620 ... (remaining 423201 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.450 Extract box with map and model: 6.580 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 97.010 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.100 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 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 15616 Z= 0.450 Angle : 1.007 10.439 21159 Z= 0.601 Chirality : 0.055 0.278 2373 Planarity : 0.006 0.077 2644 Dihedral : 15.452 89.251 5783 Min Nonbonded Distance : 1.495 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.32 % Favored : 89.40 % Rotamer: Outliers : 1.27 % Allowed : 5.54 % Favored : 93.19 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.84 (0.16), residues: 1793 helix: -1.96 (0.13), residues: 1093 sheet: -3.56 (0.50), residues: 80 loop : -3.28 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 268 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) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 306 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 178 time to evaluate : 2.492 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 246 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8214 (mm) REVERT: E 359 HIS cc_start: 0.6406 (t-90) cc_final: 0.5720 (t70) REVERT: E 388 GLU cc_start: 0.5031 (OUTLIER) cc_final: 0.4762 (mp0) REVERT: C 13 ASP cc_start: 0.8454 (p0) cc_final: 0.8028 (p0) REVERT: B 400 MET cc_start: 0.8976 (mtp) cc_final: 0.8656 (mtp) REVERT: B 485 VAL cc_start: 0.9008 (t) cc_final: 0.8769 (p) REVERT: A 330 ASP cc_start: 0.8539 (t70) cc_final: 0.8024 (t0) outliers start: 22 outliers final: 4 residues processed: 199 average time/residue: 0.6537 time to fit residues: 189.6823 Evaluate side-chains 121 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.7980 chunk 136 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 47 GLN E 150 ASN E 230 HIS ** E 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN C 107 GLN C 160 ASN ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 GLN C 336 ASN C 362 ASN ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15616 Z= 0.210 Angle : 0.641 7.233 21159 Z= 0.349 Chirality : 0.040 0.170 2373 Planarity : 0.005 0.059 2644 Dihedral : 6.420 35.881 1982 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.37 % Favored : 91.52 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.10 (0.18), residues: 1793 helix: -0.43 (0.14), residues: 1098 sheet: -3.23 (0.51), residues: 83 loop : -2.84 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 251 HIS 0.009 0.001 HIS A 292 PHE 0.018 0.001 PHE C 201 TYR 0.015 0.002 TYR E 206 ARG 0.022 0.001 ARG E 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 306 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.645 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 ASP cc_start: 0.8518 (p0) cc_final: 0.8067 (p0) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.7059 time to fit residues: 149.5695 Evaluate side-chains 116 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 176 optimal weight: 9.9990 chunk 145 optimal weight: 8.9990 chunk 162 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN D 69 ASN ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 HIS B 245 HIS ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 15616 Z= 0.454 Angle : 0.809 8.835 21159 Z= 0.453 Chirality : 0.042 0.194 2373 Planarity : 0.006 0.070 2644 Dihedral : 6.430 40.358 1982 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 23.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.93 % Favored : 88.90 % Rotamer: Outliers : 0.12 % Allowed : 4.45 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.22 (0.18), residues: 1793 helix: -0.63 (0.14), residues: 1103 sheet: -2.60 (0.61), residues: 64 loop : -2.79 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 314 HIS 0.016 0.002 HIS B 320 PHE 0.037 0.002 PHE B 522 TYR 0.022 0.002 TYR C 131 ARG 0.005 0.001 ARG E 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 306 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 2.573 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: A 319 MET cc_start: 0.8088 (ttm) cc_final: 0.7849 (ttm) outliers start: 2 outliers final: 1 residues processed: 117 average time/residue: 0.6375 time to fit residues: 109.9502 Evaluate side-chains 94 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 30.0000 chunk 78 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 272 ASN A 284 ASN ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15616 Z= 0.184 Angle : 0.581 6.339 21159 Z= 0.314 Chirality : 0.038 0.157 2373 Planarity : 0.005 0.064 2644 Dihedral : 5.927 43.447 1982 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.38 (0.19), residues: 1793 helix: 0.18 (0.15), residues: 1106 sheet: -2.98 (0.59), residues: 72 loop : -2.67 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 378 HIS 0.008 0.001 HIS A 320 PHE 0.028 0.002 PHE C 201 TYR 0.013 0.001 TYR B 447 ARG 0.003 0.000 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 306 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 2.952 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: C 13 ASP cc_start: 0.8713 (p0) cc_final: 0.8178 (p0) REVERT: B 485 VAL cc_start: 0.8942 (t) cc_final: 0.8689 (p) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.6532 time to fit residues: 122.3167 Evaluate side-chains 101 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN A 156 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15616 Z= 0.325 Angle : 0.659 6.825 21159 Z= 0.366 Chirality : 0.039 0.177 2373 Planarity : 0.005 0.063 2644 Dihedral : 5.896 46.161 1982 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.66 (0.19), residues: 1793 helix: -0.10 (0.15), residues: 1117 sheet: -2.42 (0.66), residues: 62 loop : -2.82 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 251 HIS 0.008 0.001 HIS A 320 PHE 0.022 0.002 PHE B 324 TYR 0.029 0.002 TYR E 206 ARG 0.003 0.000 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 306 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 2.582 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: C 13 ASP cc_start: 0.8979 (p0) cc_final: 0.8555 (p0) REVERT: A 319 MET cc_start: 0.8066 (ttm) cc_final: 0.7864 (ttm) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.7075 time to fit residues: 116.9697 Evaluate side-chains 94 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 5.9990 chunk 156 optimal weight: 8.9990 chunk 34 optimal weight: 30.0000 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 14 optimal weight: 30.0000 chunk 57 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN D 7 ASN ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15616 Z= 0.226 Angle : 0.586 6.014 21159 Z= 0.321 Chirality : 0.038 0.191 2373 Planarity : 0.004 0.058 2644 Dihedral : 5.682 46.448 1982 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: -1.35 (0.19), residues: 1793 helix: 0.19 (0.15), residues: 1119 sheet: -3.03 (0.60), residues: 72 loop : -2.69 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 378 HIS 0.008 0.001 HIS E 17 PHE 0.028 0.002 PHE A 255 TYR 0.018 0.001 TYR E 206 ARG 0.003 0.000 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 306 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.545 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: C 13 ASP cc_start: 0.8944 (p0) cc_final: 0.8510 (p0) REVERT: A 196 MET cc_start: 0.8876 (mmm) cc_final: 0.8580 (mmm) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.6345 time to fit residues: 110.2926 Evaluate side-chains 99 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 4.9990 chunk 19 optimal weight: 50.0000 chunk 99 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15616 Z= 0.185 Angle : 0.548 5.711 21159 Z= 0.296 Chirality : 0.038 0.191 2373 Planarity : 0.004 0.054 2644 Dihedral : 5.410 45.795 1982 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: -0.95 (0.20), residues: 1793 helix: 0.53 (0.15), residues: 1126 sheet: -3.00 (0.58), residues: 74 loop : -2.58 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 378 HIS 0.007 0.001 HIS A 320 PHE 0.026 0.001 PHE C 51 TYR 0.014 0.001 TYR A 113 ARG 0.003 0.000 ARG B 352 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 306 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 2.538 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: C 13 ASP cc_start: 0.8878 (p0) cc_final: 0.8434 (p0) REVERT: A 196 MET cc_start: 0.8850 (mmm) cc_final: 0.8519 (mmm) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.7057 time to fit residues: 122.0399 Evaluate side-chains 99 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 34 optimal weight: 40.0000 chunk 33 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 HIS ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 272 ASN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15616 Z= 0.241 Angle : 0.581 5.736 21159 Z= 0.318 Chirality : 0.038 0.180 2373 Planarity : 0.005 0.057 2644 Dihedral : 5.409 45.804 1982 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: -0.98 (0.20), residues: 1793 helix: 0.49 (0.15), residues: 1125 sheet: -3.11 (0.57), residues: 74 loop : -2.54 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 378 HIS 0.008 0.001 HIS A 320 PHE 0.020 0.002 PHE A 255 TYR 0.019 0.001 TYR E 206 ARG 0.003 0.000 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 306 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.675 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: C 13 ASP cc_start: 0.8936 (p0) cc_final: 0.8561 (p0) REVERT: C 259 LEU cc_start: 0.8962 (mt) cc_final: 0.8622 (mp) REVERT: A 196 MET cc_start: 0.8855 (mmm) cc_final: 0.8512 (mmm) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.7013 time to fit residues: 112.4832 Evaluate side-chains 89 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 8.9990 chunk 166 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 97 optimal weight: 0.3980 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 106 optimal weight: 0.0670 overall best weight: 1.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 ASN ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15616 Z= 0.163 Angle : 0.532 5.863 21159 Z= 0.285 Chirality : 0.038 0.166 2373 Planarity : 0.004 0.057 2644 Dihedral : 5.248 45.096 1982 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.53 (0.20), residues: 1793 helix: 0.88 (0.15), residues: 1126 sheet: -3.15 (0.55), residues: 76 loop : -2.40 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 378 HIS 0.007 0.001 HIS C 168 PHE 0.022 0.001 PHE A 255 TYR 0.013 0.001 TYR B 447 ARG 0.006 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 306 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.724 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: C 13 ASP cc_start: 0.8882 (p0) cc_final: 0.8475 (p0) REVERT: B 201 MET cc_start: 0.8944 (mmm) cc_final: 0.8494 (tpp) REVERT: A 196 MET cc_start: 0.8798 (mmm) cc_final: 0.8483 (mmm) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.7101 time to fit residues: 115.5047 Evaluate side-chains 93 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 chunk 165 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 113 optimal weight: 7.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 359 HIS ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15616 Z= 0.184 Angle : 0.533 5.874 21159 Z= 0.289 Chirality : 0.037 0.168 2373 Planarity : 0.004 0.058 2644 Dihedral : 5.176 44.667 1982 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: -0.46 (0.20), residues: 1793 helix: 0.92 (0.15), residues: 1128 sheet: -2.94 (0.53), residues: 83 loop : -2.37 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 378 HIS 0.007 0.001 HIS A 320 PHE 0.019 0.001 PHE A 255 TYR 0.012 0.001 TYR B 447 ARG 0.003 0.000 ARG C 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 306 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.816 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: C 13 ASP cc_start: 0.8883 (p0) cc_final: 0.8470 (p0) REVERT: C 259 LEU cc_start: 0.8905 (mt) cc_final: 0.8552 (mp) REVERT: A 196 MET cc_start: 0.8812 (mmm) cc_final: 0.8479 (mmm) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.7486 time to fit residues: 118.3328 Evaluate side-chains 89 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 4.9990 chunk 43 optimal weight: 0.0770 chunk 131 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 overall best weight: 1.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.075459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.047521 restraints weight = 310846.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.045441 restraints weight = 232294.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.045832 restraints weight = 157981.338| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15616 Z= 0.167 Angle : 0.520 5.863 21159 Z= 0.280 Chirality : 0.037 0.166 2373 Planarity : 0.004 0.057 2644 Dihedral : 5.065 43.811 1982 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: -0.32 (0.20), residues: 1793 helix: 1.04 (0.15), residues: 1134 sheet: -2.98 (0.53), residues: 85 loop : -2.35 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 378 HIS 0.007 0.001 HIS A 320 PHE 0.020 0.001 PHE B 324 TYR 0.011 0.001 TYR B 447 ARG 0.002 0.000 ARG C 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5195.65 seconds wall clock time: 93 minutes 59.77 seconds (5639.77 seconds total)