Starting phenix.real_space_refine on Sun Dec 10 06:07:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja7_36125/12_2023/8ja7_36125.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja7_36125/12_2023/8ja7_36125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja7_36125/12_2023/8ja7_36125.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja7_36125/12_2023/8ja7_36125.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja7_36125/12_2023/8ja7_36125.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja7_36125/12_2023/8ja7_36125.pdb" } resolution = 3.02 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= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 8728 2.51 5 N 2326 2.21 5 O 2504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 19": "NH1" <-> "NH2" Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 112": "NH1" <-> "NH2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4": "NH1" <-> "NH2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ASP 132": "OD1" <-> "OD2" Residue "B TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "E TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 77": "NH1" <-> "NH2" Residue "E ARG 82": "NH1" <-> "NH2" Residue "E TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 380": "NH1" <-> "NH2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 412": "NH1" <-> "NH2" Residue "E TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 264": "OE1" <-> "OE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 317": "OD1" <-> "OD2" Residue "C PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 372": "OD1" <-> "OD2" Residue "D PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 194": "OD1" <-> "OD2" Residue "D TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "D GLU 264": "OE1" <-> "OE2" Residue "D TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 325": "OE1" <-> "OE2" Residue "D GLU 336": "OE1" <-> "OE2" Residue "D GLU 341": "OE1" <-> "OE2" Residue "D PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 380": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13601 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2164 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain: "B" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2043 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 16, 'TRANS': 254} Chain: "E" Number of atoms: 3335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3335 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 410} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3018 Classifications: {'peptide': 393} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 372} Chain: "D" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3018 Classifications: {'peptide': 393} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 372} Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.26, per 1000 atoms: 0.53 Number of scatterers: 13601 At special positions: 0 Unit cell: (84.864, 92.352, 163.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 2504 8.00 N 2326 7.00 C 8728 6.00 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 Links applied ALPHA1-1 " GLC F 1 " - " GLC F 2 " Time building additional restraints: 5.23 Conformation dependent library (CDL) restraints added in 2.6 seconds 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3312 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 14 sheets defined 51.6% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 19 through 52 removed outlier: 3.652A pdb=" N MET A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA A 31 " --> pdb=" O PHE A 27 " (cutoff:3.500A) Proline residue: A 32 - end of helix removed outlier: 4.354A pdb=" N TYR A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Proline residue: A 44 - end of helix Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 79 through 113 removed outlier: 3.682A pdb=" N VAL A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 130 removed outlier: 3.895A pdb=" N VAL A 120 " --> pdb=" O GLY A 116 " (cutoff:3.500A) Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 163 through 192 Proline residue: A 181 - end of helix removed outlier: 3.646A pdb=" N GLY A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.817A pdb=" N LEU A 199 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 removed outlier: 5.497A pdb=" N LEU A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 221 through 237 Processing helix chain 'A' and resid 240 through 247 Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.702A pdb=" N GLY A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 265 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 294 removed outlier: 4.137A pdb=" N ALA A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 31 removed outlier: 3.901A pdb=" N THR B 7 " --> pdb=" O ALA B 3 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU B 15 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) Proline residue: B 23 - end of helix removed outlier: 4.044A pdb=" N ILE B 27 " --> pdb=" O PRO B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 4.122A pdb=" N LYS B 39 " --> pdb=" O SER B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 58 Processing helix chain 'B' and resid 62 through 94 removed outlier: 4.245A pdb=" N ASN B 68 " --> pdb=" O SER B 64 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 79 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET B 86 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA B 90 " --> pdb=" O MET B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 110 through 113 Proline residue: B 113 - end of helix No H-bonds generated for 'chain 'B' and resid 110 through 113' Processing helix chain 'B' and resid 114 through 129 removed outlier: 3.697A pdb=" N VAL B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR B 119 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Proline residue: B 120 - end of helix removed outlier: 4.192A pdb=" N ALA B 127 " --> pdb=" O ASN B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 158 Proline residue: B 140 - end of helix removed outlier: 4.436A pdb=" N THR B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE B 144 " --> pdb=" O PRO B 140 " (cutoff:3.500A) Proline residue: B 147 - end of helix removed outlier: 3.576A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 162 through 172 removed outlier: 4.222A pdb=" N LYS B 166 " --> pdb=" O TRP B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 182 Processing helix chain 'B' and resid 187 through 204 removed outlier: 3.502A pdb=" N LEU B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASN B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 236 through 268 removed outlier: 4.754A pdb=" N SER B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) Proline residue: B 251 - end of helix removed outlier: 5.656A pdb=" N ARG B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 55 removed outlier: 3.599A pdb=" N ALA E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 86 removed outlier: 3.646A pdb=" N ARG E 77 " --> pdb=" O PRO E 73 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU E 78 " --> pdb=" O ASN E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 112 through 116 Processing helix chain 'E' and resid 120 through 125 Processing helix chain 'E' and resid 130 through 135 removed outlier: 3.528A pdb=" N LEU E 134 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA E 135 " --> pdb=" O PRO E 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 130 through 135' Processing helix chain 'E' and resid 168 through 182 Processing helix chain 'E' and resid 195 through 209 removed outlier: 4.152A pdb=" N VAL E 199 " --> pdb=" O GLY E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 243 Processing helix chain 'E' and resid 252 through 256 removed outlier: 3.622A pdb=" N THR E 256 " --> pdb=" O ILE E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 267 Processing helix chain 'E' and resid 278 through 289 removed outlier: 3.691A pdb=" N SER E 282 " --> pdb=" O PHE E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 304 Processing helix chain 'E' and resid 318 through 328 removed outlier: 3.592A pdb=" N SER E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 374 removed outlier: 3.553A pdb=" N ARG E 371 " --> pdb=" O PHE E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 386 Processing helix chain 'E' and resid 394 through 397 Processing helix chain 'E' and resid 398 through 404 Processing helix chain 'E' and resid 407 through 417 removed outlier: 4.176A pdb=" N ASP E 417 " --> pdb=" O GLN E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 438 removed outlier: 3.713A pdb=" N ILE E 432 " --> pdb=" O GLN E 428 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG E 433 " --> pdb=" O ALA E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 463 removed outlier: 3.561A pdb=" N ASP E 451 " --> pdb=" O GLU E 447 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA E 454 " --> pdb=" O ALA E 450 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA E 455 " --> pdb=" O ASP E 451 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN E 456 " --> pdb=" O GLU E 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 92 through 104 Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 107 through 123 Processing helix chain 'C' and resid 131 through 135 Processing helix chain 'C' and resid 136 through 150 Processing helix chain 'C' and resid 166 through 185 Processing helix chain 'C' and resid 194 through 202 removed outlier: 4.277A pdb=" N ALA C 198 " --> pdb=" O ASP C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 228 through 235 Processing helix chain 'C' and resid 262 through 272 Processing helix chain 'C' and resid 294 through 299 removed outlier: 3.871A pdb=" N ARG C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 51 Processing helix chain 'D' and resid 92 through 104 Proline residue: D 100 - end of helix Processing helix chain 'D' and resid 107 through 122 Processing helix chain 'D' and resid 123 through 128 removed outlier: 3.866A pdb=" N ASN D 126 " --> pdb=" O ASP D 123 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU D 128 " --> pdb=" O THR D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 135 removed outlier: 3.760A pdb=" N LEU D 135 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 151 removed outlier: 4.563A pdb=" N ARG D 151 " --> pdb=" O ARG D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 185 Processing helix chain 'D' and resid 194 through 202 Processing helix chain 'D' and resid 218 through 225 removed outlier: 3.512A pdb=" N LEU D 222 " --> pdb=" O THR D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 235 Processing helix chain 'D' and resid 262 through 271 removed outlier: 4.144A pdb=" N GLN D 266 " --> pdb=" O ALA D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 285 No H-bonds generated for 'chain 'D' and resid 283 through 285' Processing helix chain 'D' and resid 296 through 300 removed outlier: 3.596A pdb=" N ILE D 299 " --> pdb=" O TYR D 296 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG D 300 " --> pdb=" O GLN D 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 296 through 300' Processing helix chain 'D' and resid 331 through 336 Processing sheet with id=AA1, first strand: chain 'E' and resid 62 through 69 removed outlier: 6.308A pdb=" N LEU E 33 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ALA E 65 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL E 35 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL E 67 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE E 37 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU E 69 " --> pdb=" O PHE E 37 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR E 39 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL E 93 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N SER E 36 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA E 95 " --> pdb=" O SER E 36 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR E 38 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ASP E 97 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY E 350 " --> pdb=" O THR E 150 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR E 150 " --> pdb=" O GLY E 350 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU E 352 " --> pdb=" O VAL E 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 272 through 275 Processing sheet with id=AA3, first strand: chain 'C' and resid 18 through 23 removed outlier: 5.161A pdb=" N ARG C 21 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LYS C 11 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL C 9 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER C 58 " --> pdb=" O VAL C 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 190 through 191 removed outlier: 6.507A pdb=" N ILE C 34 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N MET C 208 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL C 36 " --> pdb=" O MET C 208 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN C 215 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N TYR C 209 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ALA C 213 " --> pdb=" O TYR C 209 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 81 Processing sheet with id=AA6, first strand: chain 'C' and resid 241 through 245 removed outlier: 3.581A pdb=" N ILE C 279 " --> pdb=" O PHE C 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 247 through 248 Processing sheet with id=AA8, first strand: chain 'C' and resid 288 through 289 removed outlier: 3.734A pdb=" N GLN C 288 " --> pdb=" O ALA C 370 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 26 through 27 removed outlier: 5.637A pdb=" N LEU D 6 " --> pdb=" O ARG D 62 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG D 62 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N HIS D 8 " --> pdb=" O GLU D 60 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLU D 60 " --> pdb=" O HIS D 8 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 188 through 189 removed outlier: 3.503A pdb=" N LEU D 33 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL D 206 " --> pdb=" O PHE D 32 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE D 34 " --> pdb=" O VAL D 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 79 through 81 Processing sheet with id=AB3, first strand: chain 'D' and resid 257 through 258 removed outlier: 3.553A pdb=" N VAL D 278 " --> pdb=" O ALA D 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 287 through 289 removed outlier: 5.079A pdb=" N VAL D 308 " --> pdb=" O THR D 323 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N THR D 323 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 287 through 289 removed outlier: 5.079A pdb=" N VAL D 308 " --> pdb=" O THR D 323 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N THR D 323 " --> pdb=" O VAL D 308 " (cutoff:3.500A) 635 hydrogen bonds defined for protein. 1806 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: 4.26 Time building geometry restraints manager: 5.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4486 1.34 - 1.46: 2871 1.46 - 1.58: 6449 1.58 - 1.70: 0 1.70 - 1.81: 80 Bond restraints: 13886 Sorted by residual: bond pdb=" C1 GLC F 1 " pdb=" O5 GLC F 1 " ideal model delta sigma weight residual 1.410 1.507 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C3 GLC F 2 " pdb=" O3 GLC F 2 " ideal model delta sigma weight residual 1.410 1.484 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C1 GLC F 2 " pdb=" O5 GLC F 2 " ideal model delta sigma weight residual 1.410 1.483 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C5 GLC F 2 " pdb=" O5 GLC F 2 " ideal model delta sigma weight residual 1.410 1.477 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C5 GLC F 1 " pdb=" O5 GLC F 1 " ideal model delta sigma weight residual 1.410 1.475 -0.065 2.00e-02 2.50e+03 1.07e+01 ... (remaining 13881 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.88: 494 106.88 - 113.69: 7911 113.69 - 120.50: 5420 120.50 - 127.31: 4963 127.31 - 134.12: 156 Bond angle restraints: 18944 Sorted by residual: angle pdb=" N GLN E 76 " pdb=" CA GLN E 76 " pdb=" C GLN E 76 " ideal model delta sigma weight residual 111.28 105.73 5.55 1.09e+00 8.42e-01 2.59e+01 angle pdb=" CA ASP E 43 " pdb=" C ASP E 43 " pdb=" O ASP E 43 " ideal model delta sigma weight residual 121.32 118.15 3.17 1.16e+00 7.43e-01 7.46e+00 angle pdb=" CA ARG E 421 " pdb=" C ARG E 421 " pdb=" O ARG E 421 " ideal model delta sigma weight residual 120.96 117.99 2.97 1.09e+00 8.42e-01 7.40e+00 angle pdb=" O GLN E 76 " pdb=" C GLN E 76 " pdb=" N ARG E 77 " ideal model delta sigma weight residual 122.12 124.89 -2.77 1.06e+00 8.90e-01 6.85e+00 angle pdb=" C PRO E 315 " pdb=" N SER E 316 " pdb=" CA SER E 316 " ideal model delta sigma weight residual 120.89 117.11 3.78 1.50e+00 4.44e-01 6.35e+00 ... (remaining 18939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 7564 17.50 - 35.00: 634 35.00 - 52.50: 74 52.50 - 70.00: 25 70.00 - 87.50: 16 Dihedral angle restraints: 8313 sinusoidal: 3177 harmonic: 5136 Sorted by residual: dihedral pdb=" CA LYS D 11 " pdb=" C LYS D 11 " pdb=" N SER D 12 " pdb=" CA SER D 12 " ideal model delta harmonic sigma weight residual 180.00 154.46 25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA SER E 316 " pdb=" C SER E 316 " pdb=" N ASP E 317 " pdb=" CA ASP E 317 " ideal model delta harmonic sigma weight residual 180.00 158.47 21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA SER E 242 " pdb=" C SER E 242 " pdb=" N VAL E 243 " pdb=" CA VAL E 243 " ideal model delta harmonic sigma weight residual 180.00 161.41 18.59 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 8310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.945: 2251 0.945 - 1.890: 0 1.890 - 2.835: 0 2.835 - 3.780: 0 3.780 - 4.725: 1 Chirality restraints: 2252 Sorted by residual: chirality pdb=" C1 GLC F 2 " pdb=" C2 GLC F 2 " pdb=" O1 GLC F 2 " pdb=" O5 GLC F 2 " both_signs ideal model delta sigma weight residual False 2.33 -2.39 4.73 2.00e-01 2.50e+01 5.58e+02 chirality pdb=" C1 GLC F 1 " pdb=" C2 GLC F 1 " pdb=" O5 GLC F 1 " pdb=" O1 GLC F 2 " both_signs ideal model delta sigma weight residual False 2.40 2.35 0.05 2.00e-02 2.50e+03 5.16e+00 chirality pdb=" CA GLN E 76 " pdb=" N GLN E 76 " pdb=" C GLN E 76 " pdb=" CB GLN E 76 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.30e-01 ... (remaining 2249 not shown) Planarity restraints: 2437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 165 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO A 166 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 166 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 166 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 254 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO C 255 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 255 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 255 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 75 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" C GLU E 75 " -0.028 2.00e-02 2.50e+03 pdb=" O GLU E 75 " 0.011 2.00e-02 2.50e+03 pdb=" N GLN E 76 " 0.010 2.00e-02 2.50e+03 ... (remaining 2434 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 483 2.71 - 3.25: 15049 3.25 - 3.80: 22644 3.80 - 4.35: 28717 4.35 - 4.90: 46789 Nonbonded interactions: 113682 Sorted by model distance: nonbonded pdb=" O LYS E 241 " pdb=" OG1 THR E 245 " model vdw 2.158 2.440 nonbonded pdb=" O ILE A 91 " pdb=" OG SER A 95 " model vdw 2.168 2.440 nonbonded pdb=" OG1 THR E 442 " pdb=" OE1 GLU E 443 " model vdw 2.172 2.440 nonbonded pdb=" OG SER E 215 " pdb=" O ASP E 217 " model vdw 2.175 2.440 nonbonded pdb=" OE1 GLN D 305 " pdb=" OG SER D 366 " model vdw 2.182 2.440 ... (remaining 113677 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 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.720 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 38.960 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 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 : 0.004 0.097 13886 Z= 0.272 Angle : 0.618 8.060 18944 Z= 0.341 Chirality : 0.109 4.725 2252 Planarity : 0.004 0.042 2437 Dihedral : 13.437 87.499 5001 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -3.10 (0.18), residues: 1774 helix: -1.53 (0.16), residues: 817 sheet: -2.26 (0.36), residues: 131 loop : -2.54 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 109 HIS 0.004 0.001 HIS D 286 PHE 0.010 0.001 PHE A 231 TYR 0.016 0.001 TYR E 427 ARG 0.002 0.000 ARG D 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2460 time to fit residues: 51.4206 Evaluate side-chains 105 residues out of total 1423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.637 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 5.9990 chunk 134 optimal weight: 20.0000 chunk 74 optimal weight: 0.0470 chunk 45 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 138 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 160 optimal weight: 8.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN B 52 ASN B 68 ASN E 52 GLN E 55 ASN E 203 ASN E 238 GLN ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN E 353 ASN E 378 ASN E 379 GLN E 402 GLN E 414 GLN C 241 ASN C 266 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 GLN C 347 HIS C 386 ASN D 10 ASN D 48 ASN D 69 ASN D 96 ASN D 134 GLN D 141 GLN D 272 HIS ** D 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13886 Z= 0.202 Angle : 0.604 10.807 18944 Z= 0.302 Chirality : 0.044 0.211 2252 Planarity : 0.004 0.042 2437 Dihedral : 4.863 64.295 1935 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.77 % Allowed : 10.06 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -1.88 (0.19), residues: 1774 helix: -0.41 (0.18), residues: 832 sheet: -1.64 (0.35), residues: 158 loop : -2.05 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 210 HIS 0.019 0.002 HIS D 8 PHE 0.019 0.001 PHE C 379 TYR 0.018 0.001 TYR B 8 ARG 0.009 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 131 average time/residue: 0.2494 time to fit residues: 50.5975 Evaluate side-chains 118 residues out of total 1423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 1.560 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1348 time to fit residues: 3.7395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 chunk 173 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 159 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 HIS ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13886 Z= 0.252 Angle : 0.592 13.408 18944 Z= 0.295 Chirality : 0.043 0.178 2252 Planarity : 0.004 0.039 2437 Dihedral : 4.791 61.711 1935 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.48 % Allowed : 12.59 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -1.38 (0.20), residues: 1774 helix: 0.08 (0.18), residues: 830 sheet: -1.49 (0.34), residues: 173 loop : -1.87 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 109 HIS 0.006 0.001 HIS C 286 PHE 0.013 0.001 PHE C 379 TYR 0.020 0.002 TYR A 140 ARG 0.009 0.000 ARG D 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 134 average time/residue: 0.2370 time to fit residues: 48.8956 Evaluate side-chains 114 residues out of total 1423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 1.594 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1689 time to fit residues: 4.6473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 20.0000 chunk 121 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 0.0000 chunk 108 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 chunk 171 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13886 Z= 0.352 Angle : 0.627 9.577 18944 Z= 0.314 Chirality : 0.045 0.225 2252 Planarity : 0.004 0.038 2437 Dihedral : 4.863 60.415 1935 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.20 % Allowed : 14.91 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.20), residues: 1774 helix: 0.13 (0.18), residues: 837 sheet: -1.39 (0.35), residues: 183 loop : -1.73 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 169 HIS 0.005 0.001 HIS C 286 PHE 0.012 0.001 PHE E 280 TYR 0.022 0.002 TYR E 427 ARG 0.005 0.000 ARG E 421 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 124 average time/residue: 0.2320 time to fit residues: 44.9202 Evaluate side-chains 117 residues out of total 1423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 1.521 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.1333 time to fit residues: 4.6934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 118 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 GLN D 241 ASN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13886 Z= 0.346 Angle : 0.634 11.898 18944 Z= 0.315 Chirality : 0.045 0.185 2252 Planarity : 0.004 0.038 2437 Dihedral : 4.884 59.244 1935 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.76 % Allowed : 15.89 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -1.19 (0.20), residues: 1774 helix: 0.17 (0.18), residues: 840 sheet: -1.24 (0.35), residues: 180 loop : -1.75 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 109 HIS 0.005 0.001 HIS C 286 PHE 0.012 0.001 PHE E 280 TYR 0.022 0.002 TYR E 427 ARG 0.004 0.000 ARG E 421 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 133 average time/residue: 0.2293 time to fit residues: 47.5074 Evaluate side-chains 123 residues out of total 1423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 1.492 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1326 time to fit residues: 5.8662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 100 optimal weight: 0.0170 chunk 42 optimal weight: 0.8980 chunk 171 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 HIS ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13886 Z= 0.153 Angle : 0.577 8.161 18944 Z= 0.286 Chirality : 0.043 0.172 2252 Planarity : 0.004 0.038 2437 Dihedral : 4.559 55.160 1935 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.84 % Allowed : 16.88 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -0.91 (0.20), residues: 1774 helix: 0.47 (0.19), residues: 828 sheet: -1.02 (0.36), residues: 177 loop : -1.69 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 109 HIS 0.004 0.001 HIS C 8 PHE 0.016 0.001 PHE E 280 TYR 0.018 0.001 TYR E 427 ARG 0.003 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 127 average time/residue: 0.2396 time to fit residues: 46.9401 Evaluate side-chains 121 residues out of total 1423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 1.517 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1721 time to fit residues: 4.4156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.646 > 50: distance: 17 - 122: 27.213 distance: 42 - 59: 31.415 distance: 46 - 64: 29.132 distance: 54 - 59: 34.304 distance: 59 - 60: 10.397 distance: 60 - 61: 32.201 distance: 60 - 63: 17.718 distance: 61 - 62: 42.069 distance: 61 - 64: 32.572 distance: 64 - 65: 13.943 distance: 65 - 66: 43.648 distance: 66 - 67: 8.425 distance: 66 - 69: 23.509 distance: 71 - 72: 57.544 distance: 71 - 79: 22.093 distance: 74 - 76: 38.642 distance: 76 - 78: 30.584 distance: 77 - 78: 7.491 distance: 79 - 80: 26.748 distance: 79 - 85: 18.626 distance: 80 - 81: 23.625 distance: 80 - 83: 45.939 distance: 81 - 82: 39.365 distance: 81 - 86: 40.724 distance: 83 - 84: 40.555 distance: 84 - 85: 5.521 distance: 86 - 87: 31.423 distance: 87 - 88: 22.065 distance: 87 - 90: 28.282 distance: 88 - 89: 17.997 distance: 88 - 95: 32.711 distance: 90 - 91: 34.195 distance: 91 - 92: 7.159 distance: 92 - 93: 40.634 distance: 93 - 94: 39.871 distance: 95 - 96: 38.782 distance: 95 - 101: 49.134 distance: 96 - 97: 12.344 distance: 97 - 98: 45.207 distance: 97 - 102: 34.873 distance: 99 - 100: 4.676 distance: 100 - 101: 24.534 distance: 103 - 104: 4.486 distance: 103 - 106: 22.138 distance: 104 - 105: 29.668 distance: 104 - 111: 14.561 distance: 106 - 107: 25.238 distance: 107 - 108: 10.481 distance: 108 - 109: 24.118 distance: 108 - 110: 10.130 distance: 112 - 113: 34.082 distance: 113 - 114: 34.206 distance: 113 - 119: 19.036 distance: 116 - 117: 4.332 distance: 116 - 118: 35.628 distance: 119 - 120: 3.399 distance: 120 - 121: 49.146 distance: 120 - 123: 41.373 distance: 121 - 122: 10.081 distance: 121 - 126: 42.577 distance: 123 - 124: 8.381 distance: 123 - 125: 31.510 distance: 126 - 127: 5.249 distance: 126 - 156: 28.590 distance: 127 - 128: 43.343 distance: 128 - 129: 16.660 distance: 128 - 134: 25.763 distance: 129 - 153: 22.624 distance: 130 - 131: 20.791 distance: 130 - 132: 37.337 distance: 131 - 133: 24.161