Starting phenix.real_space_refine on Wed Feb 14 07:48:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdv_14671/02_2024/7zdv_14671_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdv_14671/02_2024/7zdv_14671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdv_14671/02_2024/7zdv_14671.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdv_14671/02_2024/7zdv_14671.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdv_14671/02_2024/7zdv_14671_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdv_14671/02_2024/7zdv_14671_neut_updated.pdb" } resolution = 3.05 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= 0.006 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 3 5.49 5 Mg 1 5.21 5 S 28 5.16 5 C 5685 2.51 5 N 1566 2.21 5 O 1594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 2": "NH1" <-> "NH2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 159": "OD1" <-> "OD2" Residue "C TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C ARG 223": "NH1" <-> "NH2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C GLU 367": "OE1" <-> "OE2" Residue "C ASP 391": "OD1" <-> "OD2" Residue "C GLU 396": "OE1" <-> "OE2" Residue "C ARG 422": "NH1" <-> "NH2" Residue "C PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 444": "OE1" <-> "OE2" Residue "C ARG 451": "NH1" <-> "NH2" Residue "C ASP 461": "OD1" <-> "OD2" Residue "C ARG 473": "NH1" <-> "NH2" Residue "C GLU 503": "OE1" <-> "OE2" Residue "C ARG 522": "NH1" <-> "NH2" Residue "C GLU 552": "OE1" <-> "OE2" Residue "C ARG 562": "NH1" <-> "NH2" Residue "C ARG 565": "NH1" <-> "NH2" Residue "C TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D GLU 8": "OE1" <-> "OE2" Residue "D ARG 11": "NH1" <-> "NH2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D ARG 105": "NH1" <-> "NH2" Residue "D ASP 132": "OD1" <-> "OD2" Residue "D TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 139": "NH1" <-> "NH2" Residue "D PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 189": "OD1" <-> "OD2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D ARG 193": "NH1" <-> "NH2" Residue "D PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D ASP 234": "OD1" <-> "OD2" Residue "D ARG 236": "NH1" <-> "NH2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D ASP 306": "OD1" <-> "OD2" Residue "D ASP 322": "OD1" <-> "OD2" Residue "D PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D GLU 354": "OE1" <-> "OE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 378": "NH1" <-> "NH2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D GLU 419": "OE1" <-> "OE2" Residue "D ARG 422": "NH1" <-> "NH2" Residue "D ASP 441": "OD1" <-> "OD2" Residue "D GLU 454": "OE1" <-> "OE2" Residue "D ASP 460": "OD1" <-> "OD2" Residue "D ARG 485": "NH1" <-> "NH2" Residue "D ARG 493": "NH1" <-> "NH2" Residue "D ASP 517": "OD1" <-> "OD2" Residue "D GLU 526": "OE1" <-> "OE2" Residue "D ARG 534": "NH1" <-> "NH2" Residue "D ASP 549": "OD1" <-> "OD2" Residue "D ASP 558": "OD1" <-> "OD2" Residue "D ARG 566": "NH1" <-> "NH2" Residue "D TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 586": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8877 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 4292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4292 Classifications: {'peptide': 555} Link IDs: {'PTRANS': 17, 'TRANS': 537} Chain breaks: 2 Chain: "D" Number of atoms: 4585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4585 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'peptide': 586, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 27, 'TRANS': 558, None: 2} Not linked: pdbres="ILE D 588 " pdbres=" MG D 601 " Not linked: pdbres=" MG D 601 " pdbres="ANP D 602 " Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 5.14, per 1000 atoms: 0.58 Number of scatterers: 8877 At special positions: 0 Unit cell: (123.039, 75.33, 112.158, 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 28 16.00 P 3 15.00 Mg 1 11.99 O 1594 8.00 N 1566 7.00 C 5685 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: 3.89 Conformation dependent library (CDL) restraints added in 1.9 seconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 4 sheets defined 62.6% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'C' and resid 2 through 49 Proline residue: C 6 - end of helix removed outlier: 3.913A pdb=" N ALA C 9 " --> pdb=" O PRO C 6 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG C 13 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS C 15 " --> pdb=" O LYS C 12 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N TRP C 16 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU C 18 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER C 19 " --> pdb=" O TRP C 16 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU C 20 " --> pdb=" O MET C 17 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C 21 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU C 24 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR C 28 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C 30 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER C 32 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY C 34 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU C 35 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR C 37 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 38 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER C 39 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY C 40 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU C 43 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 45 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 46 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 54 No H-bonds generated for 'chain 'C' and resid 52 through 54' Processing helix chain 'C' and resid 59 through 104 removed outlier: 3.589A pdb=" N TYR C 78 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 103 " --> pdb=" O THR C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 136 removed outlier: 3.786A pdb=" N LEU C 133 " --> pdb=" O THR C 129 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TYR C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LEU C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 157 removed outlier: 3.776A pdb=" N PHE C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 175 removed outlier: 3.674A pdb=" N THR C 165 " --> pdb=" O THR C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 216 removed outlier: 4.393A pdb=" N SER C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N THR C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 195 " --> pdb=" O ASN C 191 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN C 210 " --> pdb=" O TRP C 206 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ALA C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N GLU C 212 " --> pdb=" O GLN C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 268 removed outlier: 3.580A pdb=" N GLN C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY C 268 " --> pdb=" O TRP C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 292 removed outlier: 3.590A pdb=" N PHE C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLU C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 318 removed outlier: 3.985A pdb=" N GLY C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN C 306 " --> pdb=" O GLN C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 386 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 412 No H-bonds generated for 'chain 'C' and resid 409 through 412' Processing helix chain 'C' and resid 430 through 434 Processing helix chain 'C' and resid 443 through 452 Processing helix chain 'C' and resid 456 through 459 No H-bonds generated for 'chain 'C' and resid 456 through 459' 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 490 removed outlier: 3.903A pdb=" N ARG C 482 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 520 removed outlier: 3.532A pdb=" N SER C 511 " --> pdb=" O ALA C 507 " (cutoff:3.500A) removed outlier: 4.381A 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 569 removed outlier: 3.733A pdb=" N PHE C 569 " --> pdb=" O ARG C 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 565 through 569' Processing helix chain 'D' and resid 4 through 17 Processing helix chain 'D' and resid 21 through 53 removed outlier: 3.661A pdb=" N GLY D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 63 through 108 removed outlier: 3.694A pdb=" N ILE D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 116 removed outlier: 4.566A 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: 3.779A pdb=" N MET D 133 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N HIS D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASP D 135 " --> pdb=" O ASP D 131 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N TYR D 136 " --> pdb=" O ASP D 132 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR D 137 " --> pdb=" O MET D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 161 removed outlier: 4.200A 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 190 removed outlier: 3.713A pdb=" N LEU D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.750A 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: 3.990A pdb=" N GLY D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP D 189 " --> pdb=" O MET D 185 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D 190 " --> pdb=" O GLY D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 200 Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 212 through 216 Processing helix chain 'D' and resid 225 through 272 removed outlier: 4.104A pdb=" N GLU D 241 " --> pdb=" O GLN D 237 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU D 248 " --> pdb=" O ARG D 244 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 309 Proline residue: D 298 - end of helix removed outlier: 4.031A pdb=" N PHE D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 311 through 328 removed outlier: 3.642A pdb=" N ALA D 315 " --> pdb=" O TYR D 311 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER D 323 " --> pdb=" O GLY D 319 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 397 Processing helix chain 'D' and resid 413 through 415 No H-bonds generated for 'chain 'D' and resid 413 through 415' Processing helix chain 'D' and resid 418 through 424 removed outlier: 4.150A pdb=" N LYS D 423 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N HIS D 424 " --> pdb=" O SER D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 445 removed outlier: 3.520A pdb=" N VAL D 443 " --> pdb=" O LEU D 439 " (cutoff:3.500A) 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 481 through 483 No H-bonds generated for 'chain 'D' and resid 481 through 483' Processing helix chain 'D' and resid 488 through 501 removed outlier: 3.527A pdb=" N ARG D 493 " --> pdb=" O GLY D 489 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA D 495 " --> pdb=" O ALA D 491 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG D 498 " --> pdb=" O VAL D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 531 removed outlier: 4.465A pdb=" N GLN D 522 " --> pdb=" O ALA D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 571 Processing helix chain 'D' and resid 576 through 586 removed outlier: 3.724A pdb=" N ARG D 584 " --> pdb=" O LEU D 580 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN D 585 " --> pdb=" O LEU D 581 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU D 586 " --> pdb=" O ALA D 582 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 339 through 342 removed outlier: 3.622A pdb=" N ARG C 342 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C 396 " --> pdb=" O ARG C 342 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 543 through 545 Processing sheet with id= C, first strand: chain 'D' and resid 370 through 373 Processing sheet with id= D, first strand: chain 'D' and resid 552 through 556 removed outlier: 4.037A pdb=" N VAL D 552 " --> pdb=" O ARG D 378 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR D 537 " --> pdb=" O ALA D 379 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N LEU D 381 " --> pdb=" O THR D 537 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N MET D 539 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N GLY D 383 " --> pdb=" O MET D 539 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU D 507 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL D 540 " --> pdb=" O LEU D 507 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU D 509 " --> pdb=" O VAL D 540 " (cutoff:3.500A) 458 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: 2.80 Time building geometry restraints manager: 4.06 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: 1847 1.33 - 1.45: 1994 1.45 - 1.57: 5149 1.57 - 1.69: 5 1.69 - 1.81: 55 Bond restraints: 9050 Sorted by residual: bond pdb=" O3A ANP D 602 " pdb=" PB ANP D 602 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.15e+01 bond pdb=" N3B ANP D 602 " pdb=" PG ANP D 602 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" O5' ANP D 602 " pdb=" PA ANP D 602 " ideal model delta sigma weight residual 1.655 1.578 0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" N GLN D 302 " pdb=" CA GLN D 302 " ideal model delta sigma weight residual 1.461 1.488 -0.027 9.20e-03 1.18e+04 8.36e+00 bond pdb=" N GLN D 473 " pdb=" CA GLN D 473 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.29e-02 6.01e+03 7.84e+00 ... (remaining 9045 not shown) Histogram of bond angle deviations from ideal: 99.73 - 106.64: 248 106.64 - 113.55: 5081 113.55 - 120.45: 3726 120.45 - 127.36: 3139 127.36 - 134.27: 105 Bond angle restraints: 12299 Sorted by residual: angle pdb=" N PRO D 448 " pdb=" CA PRO D 448 " pdb=" CB PRO D 448 " ideal model delta sigma weight residual 103.51 110.11 -6.60 9.60e-01 1.09e+00 4.73e+01 angle pdb=" PB ANP D 602 " pdb=" N3B ANP D 602 " pdb=" PG ANP D 602 " ideal model delta sigma weight residual 126.95 107.42 19.53 3.00e+00 1.11e-01 4.24e+01 angle pdb=" N ASN C 191 " pdb=" CA ASN C 191 " pdb=" C ASN C 191 " ideal model delta sigma weight residual 113.18 105.90 7.28 1.21e+00 6.83e-01 3.62e+01 angle pdb=" N ALA C 389 " pdb=" CA ALA C 389 " pdb=" C ALA C 389 " ideal model delta sigma weight residual 111.28 105.59 5.69 1.09e+00 8.42e-01 2.73e+01 angle pdb=" N GLN C 202 " pdb=" CA GLN C 202 " pdb=" C GLN C 202 " ideal model delta sigma weight residual 113.23 108.21 5.02 1.24e+00 6.50e-01 1.64e+01 ... (remaining 12294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 4865 17.66 - 35.32: 444 35.32 - 52.98: 72 52.98 - 70.64: 16 70.64 - 88.30: 17 Dihedral angle restraints: 5414 sinusoidal: 2142 harmonic: 3272 Sorted by residual: dihedral pdb=" CA PRO C 296 " pdb=" C PRO C 296 " pdb=" N VAL C 297 " pdb=" CA VAL C 297 " ideal model delta harmonic sigma weight residual -180.00 -163.03 -16.97 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ASN C 273 " pdb=" C ASN C 273 " pdb=" N ALA C 274 " pdb=" CA ALA C 274 " ideal model delta harmonic sigma weight residual 180.00 163.58 16.42 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" C GLN D 430 " pdb=" N GLN D 430 " pdb=" CA GLN D 430 " pdb=" CB GLN D 430 " ideal model delta harmonic sigma weight residual -122.60 -114.46 -8.14 0 2.50e+00 1.60e-01 1.06e+01 ... (remaining 5411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1222 0.061 - 0.121: 192 0.121 - 0.181: 18 0.181 - 0.242: 1 0.242 - 0.302: 2 Chirality restraints: 1435 Sorted by residual: chirality pdb=" CA GLN D 430 " pdb=" N GLN D 430 " pdb=" C GLN D 430 " pdb=" CB GLN D 430 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.29e+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 -2.63 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA PRO D 448 " pdb=" N PRO D 448 " pdb=" C PRO D 448 " pdb=" CB PRO D 448 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1432 not shown) Planarity restraints: 1565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 190 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C GLN C 190 " -0.039 2.00e-02 2.50e+03 pdb=" O GLN C 190 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN C 191 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 427 " 0.011 2.00e-02 2.50e+03 1.11e-02 3.07e+00 pdb=" CG TRP D 427 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP D 427 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP D 427 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 427 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 427 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 427 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 427 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 427 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 427 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 201 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C GLN C 201 " -0.029 2.00e-02 2.50e+03 pdb=" O GLN C 201 " 0.011 2.00e-02 2.50e+03 pdb=" N GLN C 202 " 0.010 2.00e-02 2.50e+03 ... (remaining 1562 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 65 2.57 - 3.16: 7204 3.16 - 3.74: 13677 3.74 - 4.32: 19913 4.32 - 4.90: 32788 Nonbonded interactions: 73647 Sorted by model distance: nonbonded pdb=" OG SER D 390 " pdb="MG MG D 601 " model vdw 1.993 2.170 nonbonded pdb="MG MG D 601 " pdb=" O3G ANP D 602 " model vdw 2.002 2.170 nonbonded pdb="MG MG D 601 " pdb=" O1B ANP D 602 " model vdw 2.079 2.170 nonbonded pdb=" OE1 GLN D 129 " pdb=" OG SER D 323 " model vdw 2.157 2.440 nonbonded pdb=" NH1 ARG C 431 " pdb=" OD2 ASP C 443 " model vdw 2.196 2.520 ... (remaining 73642 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: 1.220 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: 5.320 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 27.840 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 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 : 0.006 0.143 9050 Z= 0.370 Angle : 0.738 19.529 12299 Z= 0.407 Chirality : 0.045 0.302 1435 Planarity : 0.004 0.041 1565 Dihedral : 14.827 88.301 3302 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.11 % Allowed : 0.44 % Favored : 99.46 % 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: -2.81 (0.23), residues: 1133 helix: -2.29 (0.17), residues: 683 sheet: -1.18 (0.76), residues: 49 loop : -0.72 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 427 HIS 0.007 0.001 HIS C 94 PHE 0.009 0.001 PHE D 371 TYR 0.014 0.001 TYR D 88 ARG 0.006 0.000 ARG C 522 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 1.134 Fit side-chains REVERT: C 160 PHE cc_start: 0.7661 (m-80) cc_final: 0.7191 (m-80) REVERT: C 364 ASN cc_start: 0.8404 (m-40) cc_final: 0.7888 (m110) REVERT: C 390 TRP cc_start: 0.8477 (OUTLIER) cc_final: 0.7729 (p90) REVERT: C 422 ARG cc_start: 0.8085 (tpt90) cc_final: 0.7178 (tmt170) REVERT: C 541 GLN cc_start: 0.7793 (mm110) cc_final: 0.7536 (tp40) REVERT: D 560 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7527 (ttp-110) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.3112 time to fit residues: 44.1791 Evaluate side-chains 92 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 390 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.0470 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 ASN C 202 GLN C 208 GLN C 248 GLN C 302 GLN ** C 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 GLN D 237 GLN D 370 ASN D 456 GLN D 473 GLN D 522 GLN D 543 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9050 Z= 0.195 Angle : 0.605 8.285 12299 Z= 0.300 Chirality : 0.040 0.184 1435 Planarity : 0.005 0.038 1565 Dihedral : 8.173 98.054 1276 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.54 % Allowed : 4.47 % Favored : 94.99 % 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: -1.15 (0.24), residues: 1133 helix: -0.61 (0.19), residues: 688 sheet: -0.92 (0.70), residues: 48 loop : -0.73 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 81 HIS 0.004 0.001 HIS C 132 PHE 0.013 0.001 PHE D 32 TYR 0.021 0.001 TYR D 88 ARG 0.008 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 0.993 Fit side-chains REVERT: C 160 PHE cc_start: 0.7654 (m-80) cc_final: 0.7233 (m-80) REVERT: C 364 ASN cc_start: 0.8424 (m-40) cc_final: 0.7959 (m110) REVERT: C 422 ARG cc_start: 0.8013 (tpt90) cc_final: 0.7120 (tmt170) REVERT: D 115 GLN cc_start: 0.8023 (mm110) cc_final: 0.7801 (pp30) REVERT: D 522 GLN cc_start: 0.7233 (mp-120) cc_final: 0.7000 (mp10) REVERT: D 560 ARG cc_start: 0.7881 (ttp80) cc_final: 0.7514 (ttp-110) outliers start: 5 outliers final: 5 residues processed: 116 average time/residue: 0.3038 time to fit residues: 45.6387 Evaluate side-chains 101 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 427 TRP Chi-restraints excluded: chain D residue 533 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 85 optimal weight: 0.0040 chunk 69 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 ASN D 424 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9050 Z= 0.231 Angle : 0.572 6.963 12299 Z= 0.280 Chirality : 0.041 0.169 1435 Planarity : 0.004 0.035 1565 Dihedral : 6.886 90.016 1276 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.98 % Allowed : 9.04 % Favored : 89.98 % 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: -0.15 (0.25), residues: 1133 helix: 0.33 (0.20), residues: 678 sheet: -0.71 (0.71), residues: 48 loop : -0.56 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 81 HIS 0.005 0.001 HIS C 94 PHE 0.012 0.001 PHE C 181 TYR 0.022 0.001 TYR D 88 ARG 0.007 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 1.020 Fit side-chains REVERT: C 160 PHE cc_start: 0.7666 (m-80) cc_final: 0.7293 (m-80) REVERT: C 364 ASN cc_start: 0.8349 (m-40) cc_final: 0.7926 (m110) REVERT: C 422 ARG cc_start: 0.8018 (tpt90) cc_final: 0.7107 (tmt170) REVERT: D 522 GLN cc_start: 0.7372 (mp-120) cc_final: 0.7104 (mp-120) REVERT: D 560 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7533 (ttp-110) outliers start: 9 outliers final: 5 residues processed: 106 average time/residue: 0.2964 time to fit residues: 40.4747 Evaluate side-chains 95 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.9990 chunk 77 optimal weight: 0.2980 chunk 53 optimal weight: 0.0270 chunk 11 optimal weight: 0.0070 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9050 Z= 0.136 Angle : 0.496 6.807 12299 Z= 0.246 Chirality : 0.038 0.164 1435 Planarity : 0.003 0.036 1565 Dihedral : 6.239 83.819 1276 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.09 % Allowed : 10.46 % Favored : 88.45 % 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: 0.54 (0.25), residues: 1133 helix: 0.94 (0.21), residues: 678 sheet: -0.21 (0.73), residues: 47 loop : -0.41 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 81 HIS 0.002 0.001 HIS C 94 PHE 0.009 0.001 PHE D 32 TYR 0.020 0.001 TYR D 88 ARG 0.010 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.084 Fit side-chains REVERT: C 160 PHE cc_start: 0.7611 (m-80) cc_final: 0.7342 (m-80) REVERT: C 422 ARG cc_start: 0.7961 (tpt90) cc_final: 0.7119 (tmt170) REVERT: C 530 THR cc_start: 0.8444 (p) cc_final: 0.8048 (t) REVERT: D 522 GLN cc_start: 0.7491 (mp-120) cc_final: 0.7221 (mp-120) REVERT: D 560 ARG cc_start: 0.7832 (ttp80) cc_final: 0.7409 (ttp-110) outliers start: 10 outliers final: 7 residues processed: 113 average time/residue: 0.2959 time to fit residues: 43.2728 Evaluate side-chains 103 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 0.1980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9050 Z= 0.255 Angle : 0.551 7.050 12299 Z= 0.269 Chirality : 0.041 0.154 1435 Planarity : 0.004 0.036 1565 Dihedral : 6.122 84.377 1276 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.63 % Allowed : 11.00 % Favored : 87.36 % 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: 0.55 (0.25), residues: 1133 helix: 0.95 (0.20), residues: 679 sheet: 0.04 (0.75), residues: 45 loop : -0.47 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 81 HIS 0.006 0.001 HIS C 94 PHE 0.014 0.001 PHE C 181 TYR 0.021 0.001 TYR D 88 ARG 0.010 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 1.085 Fit side-chains REVERT: C 160 PHE cc_start: 0.7644 (m-80) cc_final: 0.7363 (m-80) REVERT: C 422 ARG cc_start: 0.7987 (tpt90) cc_final: 0.7120 (tmt170) REVERT: C 530 THR cc_start: 0.8601 (p) cc_final: 0.8152 (t) REVERT: D 522 GLN cc_start: 0.7503 (mp-120) cc_final: 0.7226 (mp-120) REVERT: D 525 MET cc_start: 0.8633 (mmp) cc_final: 0.8197 (mmt) REVERT: D 560 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7469 (ttp-110) outliers start: 15 outliers final: 12 residues processed: 104 average time/residue: 0.2961 time to fit residues: 40.3076 Evaluate side-chains 106 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9050 Z= 0.282 Angle : 0.568 7.095 12299 Z= 0.279 Chirality : 0.042 0.219 1435 Planarity : 0.004 0.036 1565 Dihedral : 6.050 85.790 1276 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.42 % Allowed : 12.09 % Favored : 86.49 % 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 (0.25), residues: 1133 helix: 0.90 (0.20), residues: 685 sheet: 0.14 (0.77), residues: 45 loop : -0.54 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 81 HIS 0.007 0.001 HIS C 94 PHE 0.015 0.001 PHE C 181 TYR 0.022 0.001 TYR D 88 ARG 0.007 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 1.005 Fit side-chains REVERT: C 160 PHE cc_start: 0.7635 (m-80) cc_final: 0.7353 (m-80) REVERT: C 364 ASN cc_start: 0.8365 (m-40) cc_final: 0.8093 (m110) REVERT: C 422 ARG cc_start: 0.8004 (tpt90) cc_final: 0.7130 (tmt170) REVERT: C 530 THR cc_start: 0.8689 (p) cc_final: 0.8237 (t) REVERT: D 522 GLN cc_start: 0.7449 (mp-120) cc_final: 0.7168 (mp-120) REVERT: D 556 MET cc_start: 0.7826 (ptp) cc_final: 0.7489 (ptp) REVERT: D 560 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7520 (ttp-110) outliers start: 13 outliers final: 11 residues processed: 105 average time/residue: 0.2810 time to fit residues: 38.4925 Evaluate side-chains 105 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9050 Z= 0.177 Angle : 0.515 6.957 12299 Z= 0.255 Chirality : 0.039 0.211 1435 Planarity : 0.003 0.036 1565 Dihedral : 5.890 84.713 1276 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.31 % Allowed : 12.64 % Favored : 86.06 % 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: 0.86 (0.25), residues: 1133 helix: 1.22 (0.20), residues: 680 sheet: 0.28 (0.77), residues: 45 loop : -0.41 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 81 HIS 0.004 0.001 HIS C 94 PHE 0.011 0.001 PHE C 181 TYR 0.020 0.001 TYR D 88 ARG 0.006 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 1.029 Fit side-chains REVERT: C 160 PHE cc_start: 0.7623 (m-80) cc_final: 0.7381 (m-80) REVERT: C 422 ARG cc_start: 0.8021 (tpt90) cc_final: 0.7166 (tmt170) REVERT: C 530 THR cc_start: 0.8629 (p) cc_final: 0.8204 (t) REVERT: D 522 GLN cc_start: 0.7478 (mp-120) cc_final: 0.7186 (mp-120) REVERT: D 560 ARG cc_start: 0.7878 (ttp80) cc_final: 0.7488 (ttp-110) outliers start: 12 outliers final: 11 residues processed: 106 average time/residue: 0.2928 time to fit residues: 40.6305 Evaluate side-chains 108 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.9980 chunk 32 optimal weight: 0.0070 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 0.0370 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9050 Z= 0.162 Angle : 0.499 6.942 12299 Z= 0.248 Chirality : 0.039 0.206 1435 Planarity : 0.004 0.039 1565 Dihedral : 5.740 83.656 1276 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.31 % Allowed : 12.85 % Favored : 85.84 % 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: 1.09 (0.26), residues: 1133 helix: 1.41 (0.20), residues: 681 sheet: 0.01 (0.74), residues: 48 loop : -0.28 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 81 HIS 0.003 0.001 HIS C 94 PHE 0.011 0.001 PHE C 181 TYR 0.020 0.001 TYR D 88 ARG 0.009 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 0.990 Fit side-chains REVERT: C 160 PHE cc_start: 0.7596 (m-80) cc_final: 0.7392 (m-80) REVERT: C 422 ARG cc_start: 0.7993 (tpt90) cc_final: 0.7139 (tmt170) REVERT: C 530 THR cc_start: 0.8484 (p) cc_final: 0.8097 (t) REVERT: D 522 GLN cc_start: 0.7469 (mp-120) cc_final: 0.7184 (mp-120) REVERT: D 560 ARG cc_start: 0.7862 (ttp80) cc_final: 0.7465 (ttp-110) outliers start: 12 outliers final: 10 residues processed: 110 average time/residue: 0.2786 time to fit residues: 40.0114 Evaluate side-chains 108 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.0870 chunk 104 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9050 Z= 0.182 Angle : 0.510 6.990 12299 Z= 0.253 Chirality : 0.039 0.196 1435 Planarity : 0.004 0.038 1565 Dihedral : 5.691 83.438 1276 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.53 % Allowed : 12.96 % Favored : 85.51 % 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: 1.08 (0.26), residues: 1133 helix: 1.40 (0.20), residues: 683 sheet: 0.03 (0.74), residues: 48 loop : -0.30 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 81 HIS 0.004 0.001 HIS C 94 PHE 0.011 0.001 PHE C 181 TYR 0.020 0.001 TYR D 88 ARG 0.008 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 1.037 Fit side-chains REVERT: C 422 ARG cc_start: 0.8000 (tpt90) cc_final: 0.7131 (tmt170) REVERT: C 530 THR cc_start: 0.8556 (p) cc_final: 0.8137 (t) REVERT: D 522 GLN cc_start: 0.7451 (mp-120) cc_final: 0.7178 (mp-120) REVERT: D 560 ARG cc_start: 0.7873 (ttp80) cc_final: 0.7474 (ttp-110) outliers start: 14 outliers final: 12 residues processed: 107 average time/residue: 0.2776 time to fit residues: 38.6872 Evaluate side-chains 106 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.0270 chunk 74 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9050 Z= 0.186 Angle : 0.511 6.988 12299 Z= 0.252 Chirality : 0.040 0.195 1435 Planarity : 0.004 0.038 1565 Dihedral : 5.663 83.078 1276 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.31 % Allowed : 13.29 % Favored : 85.40 % 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: 1.10 (0.25), residues: 1133 helix: 1.43 (0.20), residues: 682 sheet: 0.01 (0.76), residues: 48 loop : -0.29 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 81 HIS 0.004 0.001 HIS C 94 PHE 0.013 0.001 PHE C 164 TYR 0.020 0.001 TYR D 88 ARG 0.008 0.000 ARG D 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 1.000 Fit side-chains REVERT: C 422 ARG cc_start: 0.8003 (tpt90) cc_final: 0.7128 (tmt170) REVERT: C 530 THR cc_start: 0.8567 (p) cc_final: 0.8133 (t) REVERT: D 522 GLN cc_start: 0.7444 (mp-120) cc_final: 0.7167 (mp-120) REVERT: D 556 MET cc_start: 0.7904 (ptp) cc_final: 0.7569 (ptp) REVERT: D 560 ARG cc_start: 0.7884 (ttp80) cc_final: 0.7476 (ttp-110) outliers start: 12 outliers final: 12 residues processed: 101 average time/residue: 0.2910 time to fit residues: 38.4815 Evaluate side-chains 106 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.0670 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.149250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.103221 restraints weight = 9895.417| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.77 r_work: 0.2814 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9050 Z= 0.210 Angle : 0.520 7.041 12299 Z= 0.256 Chirality : 0.040 0.194 1435 Planarity : 0.004 0.038 1565 Dihedral : 5.633 83.009 1276 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.53 % Allowed : 13.07 % Favored : 85.40 % 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: 1133 helix: 1.39 (0.20), residues: 682 sheet: -0.05 (0.76), residues: 48 loop : -0.29 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 81 HIS 0.005 0.001 HIS C 94 PHE 0.012 0.001 PHE C 181 TYR 0.020 0.001 TYR D 88 ARG 0.008 0.000 ARG D 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2080.37 seconds wall clock time: 38 minutes 17.25 seconds (2297.25 seconds total)