Starting phenix.real_space_refine on Thu Jan 18 17:27:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdk_14652/01_2024/7zdk_14652_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdk_14652/01_2024/7zdk_14652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdk_14652/01_2024/7zdk_14652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdk_14652/01_2024/7zdk_14652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdk_14652/01_2024/7zdk_14652_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdk_14652/01_2024/7zdk_14652_updated.pdb" } resolution = 3.01 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= 0.007 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 30 5.16 5 C 5804 2.51 5 N 1600 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 126": "OD1" <-> "OD2" Residue "C TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C ASP 220": "OD1" <-> "OD2" Residue "C TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 316": "OD1" <-> "OD2" Residue "C GLU 323": "OE1" <-> "OE2" Residue "C PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C GLU 350": "OE1" <-> "OE2" Residue "C ASP 401": "OD1" <-> "OD2" Residue "C GLU 409": "OE1" <-> "OE2" Residue "C ARG 422": "NH1" <-> "NH2" Residue "C ASP 432": "OD1" <-> "OD2" Residue "C ARG 452": "NH1" <-> "NH2" Residue "C GLU 470": "OE1" <-> "OE2" Residue "C ARG 481": "NH1" <-> "NH2" Residue "C GLU 500": "OE1" <-> "OE2" Residue "C GLU 503": "OE1" <-> "OE2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "C ARG 534": "NH1" <-> "NH2" Residue "C ARG 538": "NH1" <-> "NH2" Residue "C PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 558": "OE1" <-> "OE2" Residue "C ARG 565": "NH1" <-> "NH2" Residue "C TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D GLU 8": "OE1" <-> "OE2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ASP 104": "OD1" <-> "OD2" Residue "D ASP 135": "OD1" <-> "OD2" Residue "D TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D ARG 236": "NH1" <-> "NH2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D GLU 275": "OE1" <-> "OE2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D ASP 306": "OD1" <-> "OD2" Residue "D TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ASP 346": "OD1" <-> "OD2" Residue "D GLU 353": "OE1" <-> "OE2" Residue "D PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 378": "NH1" <-> "NH2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "D GLU 412": "OE1" <-> "OE2" Residue "D ASP 415": "OD1" <-> "OD2" Residue "D GLU 419": "OE1" <-> "OE2" Residue "D ARG 422": "NH1" <-> "NH2" Residue "D ASP 441": "OD1" <-> "OD2" Residue "D GLU 452": "OE1" <-> "OE2" Residue "D GLU 454": "OE1" <-> "OE2" Residue "D ASP 460": "OD1" <-> "OD2" Residue "D PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 481": "OD1" <-> "OD2" Residue "D ARG 493": "NH1" <-> "NH2" Residue "D ASP 510": "OD1" <-> "OD2" Residue "D GLU 511": "OE1" <-> "OE2" Residue "D GLU 526": "OE1" <-> "OE2" Residue "D ARG 534": "NH1" <-> "NH2" Residue "D ASP 551": "OD1" <-> "OD2" Residue "D ASP 558": "OD1" <-> "OD2" Residue "D ARG 566": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 9089 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4433 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 18, 'TRANS': 554} Chain: "D" Number of atoms: 4592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4592 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 27, 'TRANS': 560} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.33, per 1000 atoms: 0.59 Number of scatterers: 9089 At special positions: 0 Unit cell: (117.18, 80.352, 114.669, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 6 15.00 Mg 2 11.99 O 1647 8.00 N 1600 7.00 C 5804 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 Time building additional restraints: 3.74 Conformation dependent library (CDL) restraints added in 1.9 seconds 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 4 sheets defined 62.2% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'C' and resid 5 through 8 No H-bonds generated for 'chain 'C' and resid 5 through 8' Processing helix chain 'C' and resid 15 through 49 Processing helix chain 'C' and resid 59 through 104 removed outlier: 3.556A pdb=" N ARG C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 136 removed outlier: 3.513A pdb=" N LEU C 120 " --> pdb=" O GLN C 116 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN C 121 " --> pdb=" O GLY C 117 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU C 133 " --> pdb=" O THR C 129 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N TYR C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 158 removed outlier: 3.849A pdb=" N PHE C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 175 removed outlier: 3.612A pdb=" N THR C 165 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE C 169 " --> pdb=" O THR C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 184 Processing helix chain 'C' and resid 186 through 208 Processing helix chain 'C' and resid 210 through 215 Processing helix chain 'C' and resid 219 through 268 removed outlier: 3.586A pdb=" N LEU C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY C 268 " --> pdb=" O TRP C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.680A pdb=" N VAL C 284 " --> pdb=" O ALA C 281 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE C 285 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU C 288 " --> pdb=" O PHE C 285 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA C 290 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE C 291 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 318 removed outlier: 4.335A pdb=" N GLY C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 300 " --> pdb=" O PRO C 296 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLN C 302 " --> pdb=" O THR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 386 removed outlier: 3.665A pdb=" N GLN C 385 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 386 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 409 through 415 Processing helix chain 'C' and resid 430 through 435 Processing helix chain 'C' and resid 443 through 452 Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 477 through 491 removed outlier: 3.675A pdb=" N LEU C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 520 removed outlier: 3.675A pdb=" N GLN C 512 " --> pdb=" O THR C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 561 Processing helix chain 'C' and resid 565 through 571 Processing helix chain 'D' and resid 3 through 53 removed outlier: 3.556A pdb=" N GLU D 8 " --> pdb=" O SER D 4 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN D 15 " --> pdb=" O ARG D 11 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ILE D 19 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER D 20 " --> pdb=" O GLN D 16 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ARG D 22 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TRP D 23 " --> pdb=" O ILE D 19 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 109 removed outlier: 4.120A pdb=" N LEU D 63 " --> pdb=" O GLU D 60 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU D 64 " --> pdb=" O ALA D 61 " (cutoff:3.500A) Proline residue: D 65 - end of helix removed outlier: 3.719A pdb=" N LEU D 71 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU D 75 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL D 79 " --> pdb=" O ARG D 76 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 80 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL D 86 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY D 87 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN D 92 " --> pdb=" O HIS D 89 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE D 96 " --> pdb=" O HIS D 93 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE D 98 " --> pdb=" O ARG D 95 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG D 99 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 103 " --> pdb=" O ARG D 100 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP D 104 " --> pdb=" O GLN D 101 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN D 107 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN D 108 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA D 109 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 116 removed outlier: 4.501A pdb=" N GLY D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 128 through 138 removed outlier: 3.789A pdb=" N MET D 133 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N HIS D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASP D 135 " --> pdb=" O ASP D 131 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TYR D 136 " --> pdb=" O ASP D 132 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR D 137 " --> pdb=" O MET D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 161 removed outlier: 3.670A pdb=" N VAL D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Proline residue: D 151 - end of helix Proline residue: D 160 - end of helix Processing helix chain 'D' and resid 163 through 202 removed outlier: 3.605A pdb=" N THR D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Proline residue: D 174 - end of helix Proline residue: D 177 - end of helix removed outlier: 3.683A pdb=" N ASP D 189 " --> pdb=" O MET D 185 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA D 197 " --> pdb=" O ARG D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 212 through 217 Processing helix chain 'D' and resid 221 through 273 removed outlier: 3.784A pdb=" N GLU D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU D 241 " --> pdb=" O GLN D 237 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D 248 " --> pdb=" O ARG D 244 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 309 Proline residue: D 298 - end of helix removed outlier: 4.098A pdb=" N PHE D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Proline residue: D 303 - end of helix removed outlier: 3.538A pdb=" N THR D 309 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 329 removed outlier: 4.223A pdb=" N GLN D 316 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY D 319 " --> pdb=" O GLN D 316 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA D 320 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE D 327 " --> pdb=" O LEU D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 396 Processing helix chain 'D' and resid 418 through 424 removed outlier: 3.904A pdb=" N LYS D 423 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS D 424 " --> pdb=" O SER D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 452 through 461 Processing helix chain 'D' and resid 474 through 476 No H-bonds generated for 'chain 'D' and resid 474 through 476' Processing helix chain 'D' and resid 488 through 500 Processing helix chain 'D' and resid 518 through 533 removed outlier: 4.329A pdb=" N LEU D 533 " --> pdb=" O ASN D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 572 removed outlier: 3.739A pdb=" N VAL D 572 " --> pdb=" O ALA D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 582 Processing sheet with id= A, first strand: chain 'C' and resid 339 through 342 Processing sheet with id= B, first strand: chain 'C' and resid 549 through 554 removed outlier: 6.966A pdb=" N VAL C 544 " --> pdb=" O ILE C 551 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLN C 553 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE C 542 " --> pdb=" O GLN C 553 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ILE C 543 " --> pdb=" O HIS C 368 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ALA C 370 " --> pdb=" O ILE C 543 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N MET C 545 " --> pdb=" O ALA C 370 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU C 372 " --> pdb=" O MET C 545 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL C 526 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE C 371 " --> pdb=" O VAL C 526 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET C 528 " --> pdb=" O ILE C 371 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 371 through 373 removed outlier: 3.532A pdb=" N PHE D 371 " --> pdb=" O ALA D 352 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 560 through 565 removed outlier: 6.816A pdb=" N VAL D 555 " --> pdb=" O ILE D 562 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN D 564 " --> pdb=" O ILE D 553 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE D 553 " --> pdb=" O GLN D 564 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL D 552 " --> pdb=" O ARG D 378 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N THR D 537 " --> pdb=" O ALA D 379 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU D 381 " --> pdb=" O THR D 537 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N MET D 539 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N GLY D 383 " --> pdb=" O MET D 539 " (cutoff:3.500A) 487 hydrogen bonds defined for protein. 1302 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: 2.72 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2482 1.33 - 1.45: 1557 1.45 - 1.57: 5163 1.57 - 1.69: 10 1.69 - 1.81: 57 Bond restraints: 9269 Sorted by residual: bond pdb=" N3B ANP D 602 " pdb=" PG ANP D 602 " ideal model delta sigma weight residual 1.795 1.626 0.169 2.00e-02 2.50e+03 7.12e+01 bond pdb=" N3B ANP C 602 " pdb=" PG ANP C 602 " ideal model delta sigma weight residual 1.795 1.628 0.167 2.00e-02 2.50e+03 6.99e+01 bond pdb=" O3A ANP C 602 " pdb=" PB ANP C 602 " ideal model delta sigma weight residual 1.700 1.596 0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" O3A ANP D 602 " pdb=" PB ANP D 602 " ideal model delta sigma weight residual 1.700 1.602 0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" N GLU C 500 " pdb=" CA GLU C 500 " ideal model delta sigma weight residual 1.458 1.488 -0.030 7.40e-03 1.83e+04 1.69e+01 ... (remaining 9264 not shown) Histogram of bond angle deviations from ideal: 98.59 - 105.73: 203 105.73 - 112.88: 5022 112.88 - 120.02: 3248 120.02 - 127.16: 4014 127.16 - 134.30: 117 Bond angle restraints: 12604 Sorted by residual: angle pdb=" N GLU C 515 " pdb=" CA GLU C 515 " pdb=" C GLU C 515 " ideal model delta sigma weight residual 111.36 105.54 5.82 1.09e+00 8.42e-01 2.86e+01 angle pdb=" C GLU C 500 " pdb=" CA GLU C 500 " pdb=" CB GLU C 500 " ideal model delta sigma weight residual 111.00 114.48 -3.48 8.70e-01 1.32e+00 1.60e+01 angle pdb=" N TYR C 11 " pdb=" CA TYR C 11 " pdb=" C TYR C 11 " ideal model delta sigma weight residual 112.89 108.04 4.85 1.24e+00 6.50e-01 1.53e+01 angle pdb=" N LYS C 12 " pdb=" CA LYS C 12 " pdb=" C LYS C 12 " ideal model delta sigma weight residual 111.28 107.08 4.20 1.09e+00 8.42e-01 1.48e+01 angle pdb=" N ARG D 11 " pdb=" CA ARG D 11 " pdb=" C ARG D 11 " ideal model delta sigma weight residual 111.82 107.40 4.42 1.16e+00 7.43e-01 1.45e+01 ... (remaining 12599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.57: 5037 19.57 - 39.13: 412 39.13 - 58.70: 71 58.70 - 78.27: 26 78.27 - 97.83: 18 Dihedral angle restraints: 5564 sinusoidal: 2233 harmonic: 3331 Sorted by residual: dihedral pdb=" CA LEU D 209 " pdb=" C LEU D 209 " pdb=" N ARG D 210 " pdb=" CA ARG D 210 " ideal model delta harmonic sigma weight residual 180.00 154.97 25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" O2' ANP D 602 " pdb=" C2' ANP D 602 " pdb=" C3' ANP D 602 " pdb=" O3' ANP D 602 " ideal model delta sinusoidal sigma weight residual 47.90 -49.93 97.83 1 3.00e+01 1.11e-03 1.21e+01 dihedral pdb=" C1' ANP D 602 " pdb=" C2' ANP D 602 " pdb=" C3' ANP D 602 " pdb=" O3' ANP D 602 " ideal model delta sinusoidal sigma weight residual 164.59 69.72 94.87 1 3.00e+01 1.11e-03 1.16e+01 ... (remaining 5561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1348 0.089 - 0.179: 103 0.179 - 0.268: 8 0.268 - 0.357: 0 0.357 - 0.446: 2 Chirality restraints: 1461 Sorted by residual: chirality pdb=" C3' ANP C 602 " pdb=" C2' ANP C 602 " pdb=" C4' ANP C 602 " pdb=" O3' ANP C 602 " both_signs ideal model delta sigma weight residual False -2.36 -2.80 0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" C3' ANP D 602 " pdb=" C2' ANP D 602 " pdb=" C4' ANP D 602 " pdb=" O3' ANP D 602 " both_signs ideal model delta sigma weight residual False -2.36 -2.80 0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" CA VAL D 428 " pdb=" N VAL D 428 " pdb=" C VAL D 428 " pdb=" CB VAL D 428 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1458 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 428 " 0.012 2.00e-02 2.50e+03 2.55e-02 6.51e+00 pdb=" C VAL D 428 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL D 428 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY D 429 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 497 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" C LEU C 497 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU C 497 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU C 498 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 511 " 0.027 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO D 512 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 512 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 512 " 0.022 5.00e-02 4.00e+02 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1446 2.75 - 3.29: 8920 3.29 - 3.83: 14932 3.83 - 4.36: 19300 4.36 - 4.90: 32306 Nonbonded interactions: 76904 Sorted by model distance: nonbonded pdb=" OG1 THR D 438 " pdb=" OD1 ASP D 441 " model vdw 2.219 2.440 nonbonded pdb="MG MG D 601 " pdb=" O1G ANP D 602 " model vdw 2.220 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1B ANP C 602 " model vdw 2.222 2.170 nonbonded pdb=" OG SER C 380 " pdb="MG MG C 601 " model vdw 2.223 2.170 nonbonded pdb="MG MG C 601 " pdb=" O2G ANP C 602 " model vdw 2.224 2.170 ... (remaining 76899 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 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: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 5.340 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 28.550 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 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 0.169 9269 Z= 0.443 Angle : 0.783 11.363 12604 Z= 0.460 Chirality : 0.051 0.446 1461 Planarity : 0.004 0.040 1604 Dihedral : 16.142 97.831 3416 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: -1.50 (0.23), residues: 1157 helix: -1.19 (0.18), residues: 723 sheet: 0.39 (0.63), residues: 62 loop : -0.40 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 81 HIS 0.004 0.001 HIS C 14 PHE 0.014 0.002 PHE D 467 TYR 0.012 0.002 TYR D 88 ARG 0.008 0.001 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.947 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.3275 time to fit residues: 47.6381 Evaluate side-chains 104 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 0.0770 chunk 104 optimal weight: 0.9990 overall best weight: 0.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 GLN D 2 ASN D 302 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9269 Z= 0.220 Angle : 0.584 8.076 12604 Z= 0.295 Chirality : 0.041 0.154 1461 Planarity : 0.005 0.041 1604 Dihedral : 10.130 76.356 1329 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.74 % Allowed : 6.15 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.24), residues: 1157 helix: 0.19 (0.19), residues: 718 sheet: 0.46 (0.60), residues: 62 loop : -0.29 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 427 HIS 0.003 0.001 HIS C 14 PHE 0.016 0.001 PHE C 164 TYR 0.011 0.001 TYR C 98 ARG 0.003 0.000 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 1.015 Fit side-chains REVERT: D 154 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8642 (mt) REVERT: D 240 MET cc_start: 0.8500 (mmm) cc_final: 0.8117 (mmm) outliers start: 7 outliers final: 5 residues processed: 115 average time/residue: 0.3247 time to fit residues: 47.8852 Evaluate side-chains 109 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 453 GLN D 482 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9269 Z= 0.249 Angle : 0.545 6.928 12604 Z= 0.273 Chirality : 0.040 0.157 1461 Planarity : 0.004 0.041 1604 Dihedral : 8.043 69.513 1329 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.59 % Allowed : 8.38 % Favored : 90.03 % 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: 0.48 (0.24), residues: 1157 helix: 0.77 (0.19), residues: 716 sheet: 0.27 (0.59), residues: 62 loop : -0.36 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 81 HIS 0.003 0.001 HIS C 14 PHE 0.013 0.001 PHE D 467 TYR 0.010 0.001 TYR C 98 ARG 0.003 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 1.001 Fit side-chains REVERT: D 154 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8752 (mt) REVERT: D 240 MET cc_start: 0.8575 (mmm) cc_final: 0.8227 (mmm) outliers start: 15 outliers final: 12 residues processed: 116 average time/residue: 0.3058 time to fit residues: 45.9651 Evaluate side-chains 116 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9269 Z= 0.282 Angle : 0.543 7.090 12604 Z= 0.272 Chirality : 0.041 0.176 1461 Planarity : 0.004 0.041 1604 Dihedral : 7.222 74.546 1329 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.70 % Allowed : 9.44 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1157 helix: 0.95 (0.19), residues: 716 sheet: 0.22 (0.58), residues: 62 loop : -0.36 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 81 HIS 0.004 0.001 HIS D 93 PHE 0.015 0.001 PHE D 467 TYR 0.011 0.001 TYR D 88 ARG 0.004 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 1.056 Fit side-chains REVERT: D 11 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6994 (ttt180) REVERT: D 240 MET cc_start: 0.8605 (mmm) cc_final: 0.8247 (mmm) REVERT: D 277 ASP cc_start: 0.6628 (t0) cc_final: 0.6350 (t0) outliers start: 16 outliers final: 12 residues processed: 114 average time/residue: 0.2900 time to fit residues: 43.0124 Evaluate side-chains 118 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 546 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.0070 chunk 1 optimal weight: 0.1980 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 99 optimal weight: 0.0770 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 HIS ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9269 Z= 0.143 Angle : 0.464 6.366 12604 Z= 0.237 Chirality : 0.038 0.143 1461 Planarity : 0.004 0.042 1604 Dihedral : 6.496 75.039 1329 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.38 % Allowed : 10.71 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1157 helix: 1.33 (0.20), residues: 714 sheet: 0.46 (0.62), residues: 61 loop : -0.35 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 81 HIS 0.003 0.000 HIS C 85 PHE 0.010 0.001 PHE D 467 TYR 0.011 0.001 TYR C 98 ARG 0.004 0.000 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 0.928 Fit side-chains REVERT: C 538 ARG cc_start: 0.8585 (mmm-85) cc_final: 0.8378 (mmm-85) REVERT: D 11 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6884 (ttt180) REVERT: D 207 ASP cc_start: 0.7354 (t0) cc_final: 0.7148 (t0) REVERT: D 240 MET cc_start: 0.8623 (mmm) cc_final: 0.8235 (mmm) outliers start: 13 outliers final: 9 residues processed: 118 average time/residue: 0.3019 time to fit residues: 46.1537 Evaluate side-chains 114 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 111 optimal weight: 0.0470 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9269 Z= 0.214 Angle : 0.492 6.402 12604 Z= 0.248 Chirality : 0.039 0.152 1461 Planarity : 0.004 0.041 1604 Dihedral : 6.391 77.112 1329 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.12 % Allowed : 10.82 % Favored : 87.06 % 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: 1.06 (0.25), residues: 1157 helix: 1.35 (0.20), residues: 710 sheet: 0.44 (0.62), residues: 61 loop : -0.36 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 427 HIS 0.003 0.001 HIS C 85 PHE 0.012 0.001 PHE D 467 TYR 0.011 0.001 TYR C 98 ARG 0.004 0.000 ARG C 522 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 1.037 Fit side-chains REVERT: D 11 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6886 (ttt180) REVERT: D 207 ASP cc_start: 0.7427 (t0) cc_final: 0.7209 (t0) outliers start: 20 outliers final: 16 residues processed: 114 average time/residue: 0.2880 time to fit residues: 42.6956 Evaluate side-chains 118 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 546 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 0.0770 chunk 81 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 110 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9269 Z= 0.165 Angle : 0.469 6.353 12604 Z= 0.238 Chirality : 0.038 0.140 1461 Planarity : 0.004 0.041 1604 Dihedral : 6.252 78.629 1329 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.91 % Allowed : 11.13 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.25), residues: 1157 helix: 1.48 (0.20), residues: 710 sheet: 0.53 (0.62), residues: 61 loop : -0.33 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 427 HIS 0.003 0.001 HIS C 85 PHE 0.011 0.001 PHE D 467 TYR 0.011 0.001 TYR C 98 ARG 0.004 0.000 ARG C 522 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 0.991 Fit side-chains REVERT: D 11 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6878 (ttt180) REVERT: D 207 ASP cc_start: 0.7444 (t0) cc_final: 0.7222 (t0) outliers start: 18 outliers final: 15 residues processed: 116 average time/residue: 0.2825 time to fit residues: 42.7378 Evaluate side-chains 116 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 581 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9269 Z= 0.191 Angle : 0.481 6.394 12604 Z= 0.244 Chirality : 0.039 0.152 1461 Planarity : 0.004 0.040 1604 Dihedral : 6.193 81.527 1329 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.12 % Allowed : 11.24 % Favored : 86.64 % 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: 1.24 (0.25), residues: 1157 helix: 1.49 (0.20), residues: 712 sheet: 0.54 (0.62), residues: 61 loop : -0.28 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 427 HIS 0.003 0.001 HIS C 85 PHE 0.011 0.001 PHE D 467 TYR 0.011 0.001 TYR C 98 ARG 0.003 0.000 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 1.013 Fit side-chains REVERT: D 11 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6926 (ttt180) REVERT: D 207 ASP cc_start: 0.7373 (t0) cc_final: 0.7160 (t0) outliers start: 20 outliers final: 16 residues processed: 113 average time/residue: 0.2979 time to fit residues: 43.7530 Evaluate side-chains 118 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 581 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9269 Z= 0.183 Angle : 0.480 6.297 12604 Z= 0.243 Chirality : 0.039 0.148 1461 Planarity : 0.004 0.040 1604 Dihedral : 6.149 83.939 1329 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.91 % Allowed : 11.56 % Favored : 86.53 % 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: 1.31 (0.25), residues: 1157 helix: 1.55 (0.20), residues: 711 sheet: 0.55 (0.62), residues: 61 loop : -0.27 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 427 HIS 0.003 0.001 HIS C 85 PHE 0.011 0.001 PHE D 467 TYR 0.011 0.001 TYR C 98 ARG 0.004 0.000 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 1.092 Fit side-chains REVERT: D 207 ASP cc_start: 0.7432 (t0) cc_final: 0.7219 (t0) outliers start: 18 outliers final: 15 residues processed: 111 average time/residue: 0.3045 time to fit residues: 43.5722 Evaluate side-chains 113 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 546 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 91 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9269 Z= 0.189 Angle : 0.488 8.323 12604 Z= 0.245 Chirality : 0.039 0.152 1461 Planarity : 0.004 0.040 1604 Dihedral : 6.121 88.099 1329 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.70 % Allowed : 11.98 % Favored : 86.32 % 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: 1.33 (0.25), residues: 1157 helix: 1.55 (0.20), residues: 713 sheet: 0.60 (0.62), residues: 61 loop : -0.24 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 427 HIS 0.003 0.001 HIS C 85 PHE 0.011 0.001 PHE D 467 TYR 0.011 0.001 TYR C 98 ARG 0.004 0.000 ARG D 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 1.074 Fit side-chains REVERT: C 360 SER cc_start: 0.8868 (OUTLIER) cc_final: 0.8648 (t) REVERT: D 207 ASP cc_start: 0.7384 (t0) cc_final: 0.7172 (t0) outliers start: 16 outliers final: 15 residues processed: 110 average time/residue: 0.3152 time to fit residues: 44.5757 Evaluate side-chains 111 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 546 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.0370 chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 0.0670 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN D 108 GLN D 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.115334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.093376 restraints weight = 11001.581| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.49 r_work: 0.2851 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9269 Z= 0.163 Angle : 0.475 7.910 12604 Z= 0.239 Chirality : 0.038 0.139 1461 Planarity : 0.004 0.040 1604 Dihedral : 5.993 87.273 1329 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.70 % Allowed : 12.20 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1157 helix: 1.62 (0.20), residues: 714 sheet: 0.70 (0.62), residues: 61 loop : -0.23 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 427 HIS 0.004 0.001 HIS C 85 PHE 0.010 0.001 PHE C 291 TYR 0.011 0.001 TYR C 98 ARG 0.003 0.000 ARG D 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2186.59 seconds wall clock time: 40 minutes 13.57 seconds (2413.57 seconds total)