Starting phenix.real_space_refine on Sat Mar 16 08:59:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukj_26582/03_2024/7ukj_26582.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukj_26582/03_2024/7ukj_26582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukj_26582/03_2024/7ukj_26582.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukj_26582/03_2024/7ukj_26582.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukj_26582/03_2024/7ukj_26582.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukj_26582/03_2024/7ukj_26582.pdb" } resolution = 3.6 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 8916 2.51 5 N 2420 2.21 5 O 2794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 131": "OD1" <-> "OD2" Residue "B TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 472": "OE1" <-> "OE2" Residue "C PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14196 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4717 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 621, 4701 Classifications: {'peptide': 621} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 595} Conformer: "B" Number of residues, atoms: 621, 4701 Classifications: {'peptide': 621} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 595} bond proxies already assigned to first conformer: 4777 Chain: "B" Number of atoms: 4724 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 619, 4685 Classifications: {'peptide': 619} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 593} Conformer: "B" Number of residues, atoms: 619, 4685 Classifications: {'peptide': 619} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 593} bond proxies already assigned to first conformer: 4738 Chain: "C" Number of atoms: 4755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 622, 4701 Classifications: {'peptide': 622} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 25, 'TRANS': 596} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 622, 4701 Classifications: {'peptide': 622} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 25, 'TRANS': 596} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 4738 Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AGLY A 235 " occ=0.43 ... (6 atoms not shown) pdb=" O BGLY A 235 " occ=0.57 residue: pdb=" N ASER B 234 " occ=0.68 ... (10 atoms not shown) pdb=" OG BSER B 234 " occ=0.32 residue: pdb=" N AGLY B 235 " occ=0.68 ... (6 atoms not shown) pdb=" O BGLY B 235 " occ=0.32 residue: pdb=" N ASER C 234 " occ=0.49 ... (10 atoms not shown) pdb=" OG BSER C 234 " occ=0.51 residue: pdb=" N AGLY C 235 " occ=0.49 ... (6 atoms not shown) pdb=" O BGLY C 235 " occ=0.51 Time building chain proxies: 13.35, per 1000 atoms: 0.94 Number of scatterers: 14196 At special positions: 0 Unit cell: (90.882, 86.394, 184.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2794 8.00 N 2420 7.00 C 8916 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: 5.11 Conformation dependent library (CDL) restraints added in 4.9 seconds 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3422 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 39 sheets defined 7.7% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 105 through 110 Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 154 through 160 removed outlier: 3.774A pdb=" N ASN A 157 " --> pdb=" O HIS A 154 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS A 158 " --> pdb=" O ASP A 155 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 159 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A 160 " --> pdb=" O ASN A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 160' Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.502A pdb=" N ASP A 165 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'B' and resid 110 through 123 Proline residue: B 116 - end of helix Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 153 through 160 removed outlier: 4.498A pdb=" N ALA B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 176 through 190 removed outlier: 3.692A pdb=" N LEU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 46 Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.841A pdb=" N ILE C 119 " --> pdb=" O GLY C 115 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU C 120 " --> pdb=" O PRO C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 Processing helix chain 'C' and resid 134 through 138 Processing helix chain 'C' and resid 153 through 158 removed outlier: 3.754A pdb=" N LYS C 158 " --> pdb=" O HIS C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 167 removed outlier: 3.810A pdb=" N GLY C 167 " --> pdb=" O LEU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 9 removed outlier: 4.082A pdb=" N VAL A 8 " --> pdb=" O THR C 84 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS C 81 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL C 49 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79 removed outlier: 3.604A pdb=" N GLN A 78 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 75 " --> pdb=" O GLN A 78 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL A 66 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 61 removed outlier: 4.634A pdb=" N VAL A 49 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS A 81 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 8 " --> pdb=" O THR A 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AA5, first strand: chain 'A' and resid 194 through 198 removed outlier: 5.779A pdb=" N TYR A 253 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG A 252 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASP A 288 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU A 254 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER A 307 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU A 392 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE A 370 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N MET A 394 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY A 415 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 417 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE A 416 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N SER A 451 " --> pdb=" O PHE A 416 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N PHE A 418 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS A 448 " --> pdb=" O PHE A 479 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N SER A 481 " --> pdb=" O LYS A 448 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL A 450 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 502 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 521 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 207 through 209 removed outlier: 6.011A pdb=" N LEU A 230 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 213 through 215 removed outlier: 5.947A pdb=" N LEU A 241 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 300 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR A 270 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLN A 302 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR A 299 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 324 " --> pdb=" O TYR A 299 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N MET A 301 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLU A 296 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU A 321 " --> pdb=" O GLU A 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 213 through 215 removed outlier: 5.947A pdb=" N LEU A 241 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 300 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR A 270 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLN A 302 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR A 299 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 324 " --> pdb=" O TYR A 299 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N MET A 301 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLY A 349 " --> pdb=" O CYS A 317 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL A 319 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ARG A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU A 321 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N GLN A 353 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N PHE A 323 " --> pdb=" O GLN A 353 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 470 " --> pdb=" O ILE A 436 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 337 through 338 removed outlier: 3.552A pdb=" N ILE A 378 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N CYS A 377 " --> pdb=" O ASP A 400 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 355 through 357 removed outlier: 3.529A pdb=" N GLN A 355 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR A 357 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU A 362 " --> pdb=" O TYR A 357 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 421 through 423 removed outlier: 6.128A pdb=" N SER A 421 " --> pdb=" O HIS A 454 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 484 through 485 Processing sheet with id=AB4, first strand: chain 'A' and resid 555 through 558 Processing sheet with id=AB5, first strand: chain 'B' and resid 73 through 74 removed outlier: 3.555A pdb=" N VAL B 74 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL B 66 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY B 34 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 101 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 59 through 61 removed outlier: 4.168A pdb=" N VAL B 49 " --> pdb=" O VAL B 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AB8, first strand: chain 'B' and resid 196 through 198 removed outlier: 5.716A pdb=" N LEU B 196 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 207 through 209 removed outlier: 3.540A pdb=" N THR B 260 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 213 through 214 removed outlier: 5.759A pdb=" N LEU B 213 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY B 267 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 241 " --> pdb=" O GLY B 267 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA B 298 " --> pdb=" O ASN B 266 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 322 through 323 removed outlier: 6.687A pdb=" N ALA B 383 " --> pdb=" O PHE B 348 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE B 352 " --> pdb=" O TYR B 385 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.801A pdb=" N ALA B 368 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 335 through 338 removed outlier: 6.023A pdb=" N CYS B 335 " --> pdb=" O MET B 376 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE B 378 " --> pdb=" O CYS B 335 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE B 337 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TRP B 422 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE B 423 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N CYS B 483 " --> pdb=" O ILE B 507 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N CYS B 506 " --> pdb=" O TYR B 526 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 390 through 392 removed outlier: 3.860A pdb=" N ASP B 391 " --> pdb=" O ASN B 413 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLY B 415 " --> pdb=" O ASP B 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 554 through 555 Processing sheet with id=AC7, first strand: chain 'B' and resid 558 through 559 Processing sheet with id=AC8, first strand: chain 'C' and resid 30 through 31 removed outlier: 4.611A pdb=" N VAL C 66 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AD1, first strand: chain 'C' and resid 207 through 209 removed outlier: 3.739A pdb=" N THR C 260 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 213 through 215 removed outlier: 7.329A pdb=" N ASN C 266 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU C 300 " --> pdb=" O ASN C 266 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE C 268 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLU C 296 " --> pdb=" O CYS C 317 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU C 321 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LEU C 300 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N PHE C 323 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY C 349 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA C 383 " --> pdb=" O PHE C 348 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N VAL C 408 " --> pdb=" O ASN C 382 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL C 384 " --> pdb=" O VAL C 408 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 221 through 222 removed outlier: 6.479A pdb=" N LEU C 254 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 283 " --> pdb=" O HIS C 306 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N LYS C 308 " --> pdb=" O TYR C 283 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TRP C 285 " --> pdb=" O LYS C 308 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE C 310 " --> pdb=" O TRP C 285 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE C 287 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL C 330 " --> pdb=" O HIS C 306 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS C 308 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C 332 " --> pdb=" O LYS C 308 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE C 310 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 312 through 314 removed outlier: 7.825A pdb=" N CYS C 312 " --> pdb=" O HIS C 336 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N SER C 338 " --> pdb=" O CYS C 312 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA C 314 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N CYS C 335 " --> pdb=" O MET C 376 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE C 378 " --> pdb=" O CYS C 335 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE C 337 " --> pdb=" O ILE C 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 355 through 356 removed outlier: 3.903A pdb=" N GLN C 355 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 389 through 390 removed outlier: 6.304A pdb=" N CYS C 389 " --> pdb=" O ASN C 413 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 416 through 418 removed outlier: 6.514A pdb=" N PHE C 416 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS C 448 " --> pdb=" O PHE C 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 495 through 497 removed outlier: 6.436A pdb=" N ARG C 516 " --> pdb=" O VAL C 495 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 497 " --> pdb=" O ARG C 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 512 through 514 removed outlier: 5.842A pdb=" N LEU C 512 " --> pdb=" O THR C 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 521 through 523 removed outlier: 6.641A pdb=" N VAL C 522 " --> pdb=" O ARG C 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 568 through 570 Processing sheet with id=AE3, first strand: chain 'C' and resid 583 through 584 removed outlier: 4.210A pdb=" N MET C 617 " --> pdb=" O LEU C 584 " (cutoff:3.500A) 241 hydrogen bonds defined for protein. 588 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: 5.19 Time building geometry restraints manager: 5.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4768 1.34 - 1.46: 3270 1.46 - 1.58: 6346 1.58 - 1.70: 0 1.70 - 1.82: 93 Bond restraints: 14477 Sorted by residual: bond pdb=" CA THR B 430 " pdb=" CB THR B 430 " ideal model delta sigma weight residual 1.528 1.562 -0.034 2.61e-02 1.47e+03 1.69e+00 bond pdb=" C VAL C 549 " pdb=" N PRO C 550 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.18e+00 bond pdb=" CG MET A 291 " pdb=" SD MET A 291 " ideal model delta sigma weight residual 1.803 1.776 0.027 2.50e-02 1.60e+03 1.17e+00 bond pdb=" N GLU A 532 " pdb=" CA GLU A 532 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.13e+00 bond pdb=" CB VAL B 74 " pdb=" CG2 VAL B 74 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.11e+00 ... (remaining 14472 not shown) Histogram of bond angle deviations from ideal: 95.59 - 103.28: 118 103.28 - 110.97: 5360 110.97 - 118.66: 6105 118.66 - 126.35: 7970 126.35 - 134.05: 161 Bond angle restraints: 19714 Sorted by residual: angle pdb=" CA GLY C 554 " pdb=" C GLY C 554 " pdb=" N ILE C 555 " ideal model delta sigma weight residual 114.58 117.93 -3.35 8.60e-01 1.35e+00 1.51e+01 angle pdb=" CA MET A 394 " pdb=" CB MET A 394 " pdb=" CG MET A 394 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CB MET A 617 " pdb=" CG MET A 617 " pdb=" SD MET A 617 " ideal model delta sigma weight residual 112.70 121.95 -9.25 3.00e+00 1.11e-01 9.50e+00 angle pdb=" N GLU B 85 " pdb=" CA GLU B 85 " pdb=" CB GLU B 85 " ideal model delta sigma weight residual 113.65 109.15 4.50 1.47e+00 4.63e-01 9.38e+00 angle pdb=" CA MET A 617 " pdb=" CB MET A 617 " pdb=" CG MET A 617 " ideal model delta sigma weight residual 114.10 119.78 -5.68 2.00e+00 2.50e-01 8.08e+00 ... (remaining 19709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 7806 17.83 - 35.65: 624 35.65 - 53.48: 114 53.48 - 71.30: 40 71.30 - 89.13: 17 Dihedral angle restraints: 8601 sinusoidal: 3234 harmonic: 5367 Sorted by residual: dihedral pdb=" CA VAL A 282 " pdb=" C VAL A 282 " pdb=" N TYR A 283 " pdb=" CA TYR A 283 " ideal model delta harmonic sigma weight residual -180.00 -152.75 -27.25 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA ASP C 372 " pdb=" C ASP C 372 " pdb=" N SER C 373 " pdb=" CA SER C 373 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA LEU C 321 " pdb=" C LEU C 321 " pdb=" N HIS C 322 " pdb=" CA HIS C 322 " ideal model delta harmonic sigma weight residual -180.00 -158.87 -21.13 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 8598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1496 0.039 - 0.079: 466 0.079 - 0.118: 253 0.118 - 0.157: 38 0.157 - 0.197: 3 Chirality restraints: 2256 Sorted by residual: chirality pdb=" CG LEU C 512 " pdb=" CB LEU C 512 " pdb=" CD1 LEU C 512 " pdb=" CD2 LEU C 512 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CB ILE C 476 " pdb=" CA ILE C 476 " pdb=" CG1 ILE C 476 " pdb=" CG2 ILE C 476 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CB THR A 249 " pdb=" CA THR A 249 " pdb=" OG1 THR A 249 " pdb=" CG2 THR A 249 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.09e-01 ... (remaining 2253 not shown) Planarity restraints: 2592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 440 " -0.044 5.00e-02 4.00e+02 6.73e-02 7.24e+00 pdb=" N PRO C 441 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 441 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 441 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 115 " -0.043 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO C 116 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 116 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 116 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 145 " -0.039 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO A 146 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.033 5.00e-02 4.00e+02 ... (remaining 2589 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 919 2.73 - 3.27: 15089 3.27 - 3.81: 23416 3.81 - 4.36: 28027 4.36 - 4.90: 48418 Nonbonded interactions: 115869 Sorted by model distance: nonbonded pdb=" NH2 ARG C 339 " pdb=" O SER C 343 " model vdw 2.183 2.520 nonbonded pdb=" NH1 ARG B 365 " pdb=" OD1 ASP B 388 " model vdw 2.242 2.520 nonbonded pdb=" OG ASER B 419 " pdb=" OD1 ASN B 420 " model vdw 2.244 2.440 nonbonded pdb=" OG BSER B 419 " pdb=" OD1 ASN B 420 " model vdw 2.251 2.440 nonbonded pdb=" O PRO A 550 " pdb=" ND2 ASN A 573 " model vdw 2.269 2.520 ... (remaining 115864 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 113 or (resid 114 through 115 and (name N or nam \ e CA or name C or name O )) or resid 116 through 157 or resid 159 through 233 or \ resid 236 through 337 or resid 339 through 344 or resid 346 through 418 or resi \ d 420 through 430 or resid 432 through 438 or resid 440 through 459 or resid 461 \ through 508 or resid 510 through 520 or resid 522 through 555 or resid 557 thro \ ugh 581 or resid 583 through 590 or resid 592 through 603 or resid 605 through 6 \ 20 or resid 622 through 623)) selection = (chain 'B' and (resid 5 through 113 or (resid 114 through 115 and (name N or nam \ e CA or name C or name O )) or resid 116 through 157 or resid 159 through 233 or \ resid 236 through 337 or resid 339 through 344 or resid 346 through 418 or resi \ d 420 through 430 or resid 432 through 438 or resid 440 through 459 or resid 461 \ through 508 or resid 510 through 520 or resid 522 through 555 or resid 557 thro \ ugh 581 or resid 583 through 590 or resid 592 through 603 or resid 605 through 6 \ 20 or resid 622 through 623)) selection = (chain 'C' and (resid 5 through 157 or resid 159 through 233 or resid 236 throug \ h 337 or resid 339 through 344 or resid 346 through 418 or resid 420 through 430 \ or resid 432 through 438 or resid 440 through 459 or resid 461 through 508 or r \ esid 510 through 520 or resid 522 through 555 or resid 557 through 581 or resid \ 583 through 590 or resid 592 through 603 or resid 605 through 620 or resid 622 t \ hrough 623)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.220 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: 0.010 Extract box with map and model: 27.250 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 47.930 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.090 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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 : 0.003 0.035 14477 Z= 0.223 Angle : 0.609 9.245 19714 Z= 0.326 Chirality : 0.048 0.197 2256 Planarity : 0.005 0.067 2592 Dihedral : 14.529 89.126 5179 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.77 % Favored : 87.23 % Rotamer: Outliers : 1.78 % Allowed : 1.14 % Favored : 97.08 % 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: -2.80 (0.19), residues: 1867 helix: 0.35 (0.58), residues: 91 sheet: -2.00 (0.26), residues: 447 loop : -2.09 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 490 HIS 0.014 0.001 HIS A 306 PHE 0.030 0.001 PHE C 477 TYR 0.030 0.001 TYR A 283 ARG 0.010 0.000 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.574 Fit side-chains revert: symmetry clash REVERT: C 291 MET cc_start: 0.7538 (mtp) cc_final: 0.7325 (mtm) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2012 time to fit residues: 17.2923 Evaluate side-chains 39 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 94 optimal weight: 30.0000 chunk 74 optimal weight: 30.0000 chunk 145 optimal weight: 20.0000 chunk 56 optimal weight: 0.3980 chunk 88 optimal weight: 50.0000 chunk 107 optimal weight: 40.0000 chunk 168 optimal weight: 20.0000 overall best weight: 8.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.0537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14477 Z= 0.292 Angle : 0.597 6.951 19714 Z= 0.320 Chirality : 0.048 0.220 2256 Planarity : 0.005 0.065 2592 Dihedral : 5.002 45.282 2014 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.42 % Favored : 86.58 % Rotamer: Outliers : 2.03 % Allowed : 4.51 % Favored : 93.45 % 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: -2.82 (0.19), residues: 1867 helix: 0.47 (0.59), residues: 90 sheet: -2.03 (0.26), residues: 452 loop : -2.11 (0.16), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 490 HIS 0.012 0.001 HIS A 306 PHE 0.011 0.002 PHE B 503 TYR 0.026 0.001 TYR A 283 ARG 0.006 0.000 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 1.526 Fit side-chains REVERT: A 19 MET cc_start: 0.9396 (mmm) cc_final: 0.9141 (mmm) REVERT: B 376 MET cc_start: 0.6432 (ptt) cc_final: 0.6135 (ptt) outliers start: 2 outliers final: 2 residues processed: 44 average time/residue: 0.2021 time to fit residues: 16.4155 Evaluate side-chains 42 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain B residue 405 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 40.0000 chunk 52 optimal weight: 6.9990 chunk 139 optimal weight: 30.0000 chunk 114 optimal weight: 40.0000 chunk 46 optimal weight: 10.0000 chunk 168 optimal weight: 30.0000 chunk 181 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 166 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14477 Z= 0.271 Angle : 0.574 7.161 19714 Z= 0.308 Chirality : 0.048 0.186 2256 Planarity : 0.005 0.064 2592 Dihedral : 4.993 45.821 2014 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.09 % Favored : 86.91 % Rotamer: Outliers : 2.23 % Allowed : 6.29 % Favored : 91.48 % 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: -2.88 (0.19), residues: 1867 helix: 0.42 (0.58), residues: 91 sheet: -2.12 (0.25), residues: 462 loop : -2.13 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 490 HIS 0.011 0.001 HIS A 306 PHE 0.010 0.001 PHE B 503 TYR 0.022 0.001 TYR A 283 ARG 0.006 0.000 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 1.494 Fit side-chains REVERT: A 19 MET cc_start: 0.9405 (mmm) cc_final: 0.9060 (mmm) outliers start: 4 outliers final: 2 residues processed: 43 average time/residue: 0.2013 time to fit residues: 15.9230 Evaluate side-chains 42 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain B residue 405 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 87 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 113 optimal weight: 40.0000 chunk 168 optimal weight: 3.9990 chunk 178 optimal weight: 50.0000 chunk 88 optimal weight: 40.0000 chunk 160 optimal weight: 30.0000 chunk 48 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 ASN B 86 GLN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14477 Z= 0.175 Angle : 0.554 17.159 19714 Z= 0.289 Chirality : 0.047 0.174 2256 Planarity : 0.004 0.063 2592 Dihedral : 4.746 44.816 2014 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.85 % Favored : 88.15 % Rotamer: Outliers : 2.23 % Allowed : 7.57 % Favored : 90.21 % 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: -2.74 (0.19), residues: 1867 helix: 0.58 (0.58), residues: 91 sheet: -1.98 (0.26), residues: 458 loop : -2.06 (0.16), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 490 HIS 0.010 0.001 HIS A 306 PHE 0.010 0.001 PHE C 323 TYR 0.021 0.001 TYR A 283 ARG 0.004 0.000 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 1.515 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 0.1975 time to fit residues: 16.9081 Evaluate side-chains 42 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 405 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 30.0000 chunk 101 optimal weight: 6.9990 chunk 2 optimal weight: 0.0970 chunk 133 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 91 optimal weight: 40.0000 chunk 160 optimal weight: 30.0000 chunk 45 optimal weight: 50.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14477 Z= 0.164 Angle : 0.531 11.476 19714 Z= 0.280 Chirality : 0.047 0.202 2256 Planarity : 0.004 0.062 2592 Dihedral : 4.564 43.024 2014 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.91 % Favored : 88.09 % Rotamer: Outliers : 2.54 % Allowed : 8.01 % Favored : 89.45 % 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: -2.70 (0.19), residues: 1867 helix: 0.57 (0.56), residues: 97 sheet: -1.93 (0.26), residues: 454 loop : -2.05 (0.16), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 490 HIS 0.008 0.001 HIS A 306 PHE 0.012 0.001 PHE A 418 TYR 0.018 0.001 TYR A 283 ARG 0.003 0.000 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 1.668 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 51 average time/residue: 0.2118 time to fit residues: 18.8905 Evaluate side-chains 45 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 30.0000 chunk 35 optimal weight: 40.0000 chunk 104 optimal weight: 30.0000 chunk 44 optimal weight: 20.0000 chunk 178 optimal weight: 30.0000 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 40.0000 chunk 14 optimal weight: 0.9990 chunk 59 optimal weight: 30.0000 chunk 93 optimal weight: 40.0000 overall best weight: 12.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14477 Z= 0.396 Angle : 0.646 11.244 19714 Z= 0.344 Chirality : 0.049 0.185 2256 Planarity : 0.005 0.063 2592 Dihedral : 5.220 47.804 2014 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.25 % Favored : 84.75 % Rotamer: Outliers : 2.80 % Allowed : 8.90 % Favored : 88.30 % 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: -2.94 (0.19), residues: 1867 helix: 0.39 (0.57), residues: 90 sheet: -2.16 (0.25), residues: 452 loop : -2.17 (0.16), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 490 HIS 0.013 0.001 HIS A 306 PHE 0.014 0.002 PHE C 416 TYR 0.022 0.002 TYR A 514 ARG 0.007 0.001 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 1.625 Fit side-chains REVERT: B 220 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8188 (m-40) outliers start: 13 outliers final: 10 residues processed: 51 average time/residue: 0.1902 time to fit residues: 18.0801 Evaluate side-chains 51 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 595 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 130 optimal weight: 0.0030 chunk 150 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 178 optimal weight: 50.0000 chunk 111 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 110 optimal weight: 0.8980 overall best weight: 4.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14477 Z= 0.177 Angle : 0.541 8.926 19714 Z= 0.288 Chirality : 0.047 0.174 2256 Planarity : 0.004 0.063 2592 Dihedral : 4.800 47.450 2014 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 2.67 % Allowed : 10.11 % Favored : 87.22 % 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: -2.79 (0.19), residues: 1867 helix: 0.74 (0.58), residues: 91 sheet: -2.06 (0.25), residues: 459 loop : -2.09 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 490 HIS 0.008 0.001 HIS A 306 PHE 0.011 0.001 PHE C 323 TYR 0.016 0.001 TYR A 283 ARG 0.003 0.000 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 1.584 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 53 average time/residue: 0.1899 time to fit residues: 18.5829 Evaluate side-chains 51 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 595 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 3.9990 chunk 106 optimal weight: 40.0000 chunk 53 optimal weight: 20.0000 chunk 35 optimal weight: 40.0000 chunk 34 optimal weight: 40.0000 chunk 113 optimal weight: 0.0270 chunk 121 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 30.0000 chunk 140 optimal weight: 30.0000 chunk 162 optimal weight: 30.0000 overall best weight: 6.8048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14477 Z= 0.232 Angle : 0.556 8.924 19714 Z= 0.295 Chirality : 0.047 0.175 2256 Planarity : 0.004 0.061 2592 Dihedral : 4.797 46.504 2014 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.72 % Favored : 87.28 % Rotamer: Outliers : 2.67 % Allowed : 10.43 % Favored : 86.90 % 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: -2.80 (0.19), residues: 1867 helix: 0.72 (0.58), residues: 91 sheet: -2.07 (0.25), residues: 459 loop : -2.09 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 490 HIS 0.011 0.001 HIS A 306 PHE 0.010 0.001 PHE B 503 TYR 0.023 0.001 TYR A 514 ARG 0.003 0.000 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 1.631 Fit side-chains REVERT: C 376 MET cc_start: 0.7259 (ptt) cc_final: 0.7004 (ptt) outliers start: 11 outliers final: 11 residues processed: 52 average time/residue: 0.1905 time to fit residues: 18.1400 Evaluate side-chains 53 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 595 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 8.9990 chunk 155 optimal weight: 40.0000 chunk 166 optimal weight: 20.0000 chunk 100 optimal weight: 30.0000 chunk 72 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 150 optimal weight: 50.0000 chunk 157 optimal weight: 40.0000 chunk 165 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14477 Z= 0.231 Angle : 0.559 9.797 19714 Z= 0.297 Chirality : 0.047 0.172 2256 Planarity : 0.004 0.063 2592 Dihedral : 4.820 46.350 2014 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.23 % Favored : 87.77 % Rotamer: Outliers : 2.67 % Allowed : 10.43 % Favored : 86.90 % 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: -2.80 (0.19), residues: 1867 helix: 0.73 (0.58), residues: 91 sheet: -2.08 (0.25), residues: 459 loop : -2.09 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 490 HIS 0.011 0.001 HIS A 306 PHE 0.009 0.001 PHE B 503 TYR 0.015 0.001 TYR A 283 ARG 0.003 0.000 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 1.618 Fit side-chains revert: symmetry clash REVERT: C 376 MET cc_start: 0.7256 (ptt) cc_final: 0.7022 (ptt) outliers start: 11 outliers final: 11 residues processed: 52 average time/residue: 0.1895 time to fit residues: 18.1633 Evaluate side-chains 53 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 595 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 30.0000 chunk 107 optimal weight: 50.0000 chunk 83 optimal weight: 0.2980 chunk 122 optimal weight: 10.0000 chunk 184 optimal weight: 40.0000 chunk 169 optimal weight: 50.0000 chunk 146 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 116 optimal weight: 50.0000 overall best weight: 6.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14477 Z= 0.233 Angle : 0.559 8.634 19714 Z= 0.297 Chirality : 0.047 0.157 2256 Planarity : 0.004 0.062 2592 Dihedral : 4.809 46.400 2014 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.61 % Favored : 87.39 % Rotamer: Outliers : 2.67 % Allowed : 10.55 % Favored : 86.78 % 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: -2.78 (0.19), residues: 1867 helix: 0.73 (0.58), residues: 91 sheet: -2.03 (0.26), residues: 439 loop : -2.10 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 490 HIS 0.011 0.001 HIS A 306 PHE 0.011 0.001 PHE A 418 TYR 0.023 0.001 TYR A 514 ARG 0.003 0.000 ARG B 351 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 1.464 Fit side-chains revert: symmetry clash REVERT: A 19 MET cc_start: 0.9403 (mmm) cc_final: 0.9151 (mmm) REVERT: C 376 MET cc_start: 0.7245 (ptt) cc_final: 0.6999 (ptt) outliers start: 11 outliers final: 11 residues processed: 52 average time/residue: 0.1906 time to fit residues: 18.0275 Evaluate side-chains 53 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 595 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 30.0000 chunk 44 optimal weight: 30.0000 chunk 135 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 40 optimal weight: 30.0000 chunk 146 optimal weight: 9.9990 chunk 61 optimal weight: 0.5980 chunk 150 optimal weight: 40.0000 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** 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 = 0.3668 r_free = 0.3668 target = 0.075417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.051041 restraints weight = 276060.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.054088 restraints weight = 62236.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.055368 restraints weight = 30101.546| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14477 Z= 0.151 Angle : 0.523 8.705 19714 Z= 0.276 Chirality : 0.047 0.153 2256 Planarity : 0.004 0.061 2592 Dihedral : 4.545 44.050 2014 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 2.48 % Allowed : 10.68 % Favored : 86.84 % 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: -2.69 (0.19), residues: 1867 helix: 0.79 (0.57), residues: 97 sheet: -1.95 (0.27), residues: 431 loop : -2.06 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 490 HIS 0.008 0.001 HIS A 306 PHE 0.011 0.001 PHE C 323 TYR 0.016 0.001 TYR A 283 ARG 0.002 0.000 ARG C 516 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2398.83 seconds wall clock time: 48 minutes 30.42 seconds (2910.42 seconds total)