Starting phenix.real_space_refine on Wed Feb 14 20:27:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ram_4780/02_2024/6ram_4780_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ram_4780/02_2024/6ram_4780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ram_4780/02_2024/6ram_4780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ram_4780/02_2024/6ram_4780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ram_4780/02_2024/6ram_4780_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ram_4780/02_2024/6ram_4780_updated.pdb" } resolution = 3.8 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= 0.003 sd= 0.047 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 5 5.49 5 Mg 2 5.21 5 S 25 5.16 5 C 6569 2.51 5 N 1797 2.21 5 O 1788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 373": "OD1" <-> "OD2" Residue "A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 423": "OD1" <-> "OD2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 545": "OE1" <-> "OE2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 93": "OD1" <-> "OD2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 445": "OE1" <-> "OE2" Residue "B TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 508": "OE1" <-> "OE2" Residue "B ASP 540": "OD1" <-> "OD2" Residue "C ASP 30": "OD1" <-> "OD2" Residue "C TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C GLU 89": "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: 10186 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4710 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 24, 'TRANS': 563} Chain: "B" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4519 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 18, 'TRANS': 553} Chain: "C" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 897 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.85, per 1000 atoms: 0.57 Number of scatterers: 10186 At special positions: 0 Unit cell: (102.315, 87.237, 154.011, 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 25 16.00 P 5 15.00 Mg 2 11.99 O 1788 8.00 N 1797 7.00 C 6569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 108 " distance=2.06 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: 3.92 Conformation dependent library (CDL) restraints added in 1.8 seconds 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 9 sheets defined 56.7% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 removed outlier: 3.966A pdb=" N ILE A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 19 " --> pdb=" O PHE A 15 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR A 21 " --> pdb=" O ARG A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 28 removed outlier: 4.927A pdb=" N LEU A 27 " --> pdb=" O PRO A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 44 removed outlier: 3.654A pdb=" N VAL A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 73 through 119 removed outlier: 3.673A pdb=" N LEU A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.689A pdb=" N ARG A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 150 removed outlier: 3.529A pdb=" N THR A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 170 removed outlier: 3.762A pdb=" N LEU A 162 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY A 164 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 166 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 167 " --> pdb=" O GLY A 164 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 170 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 195 removed outlier: 3.871A pdb=" N VAL A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 3.506A pdb=" N THR A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 220 removed outlier: 4.457A pdb=" N GLU A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 229 removed outlier: 4.116A pdb=" N PHE A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 284 removed outlier: 3.720A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TRP A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 260 " --> pdb=" O TRP A 256 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE A 261 " --> pdb=" O PHE A 257 " (cutoff:3.500A) Proline residue: A 262 - end of helix removed outlier: 3.619A pdb=" N ASP A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 303 Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 314 through 331 removed outlier: 3.822A pdb=" N ARG A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 399 through 407 removed outlier: 3.836A pdb=" N VAL A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 429 through 434 Processing helix chain 'A' and resid 450 through 454 Processing helix chain 'A' and resid 463 through 473 Processing helix chain 'A' and resid 476 through 479 No H-bonds generated for 'chain 'A' and resid 476 through 479' Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 492 through 494 No H-bonds generated for 'chain 'A' and resid 492 through 494' Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.744A pdb=" N LEU A 507 " --> pdb=" O GLN A 503 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 543 removed outlier: 3.928A pdb=" N ALA A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 560 Processing helix chain 'A' and resid 579 through 585 Processing helix chain 'A' and resid 588 through 597 removed outlier: 3.529A pdb=" N GLN A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 17 Proline residue: B 15 - end of helix Processing helix chain 'B' and resid 21 through 36 removed outlier: 3.684A pdb=" N TRP B 26 " --> pdb=" O TRP B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 51 Processing helix chain 'B' and resid 59 through 102 removed outlier: 3.565A pdb=" N VAL B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU B 99 " --> pdb=" O ARG B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 removed outlier: 3.885A pdb=" N HIS B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 132 removed outlier: 4.115A pdb=" N ASN B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 155 removed outlier: 3.811A pdb=" N SER B 144 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 151 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR B 155 " --> pdb=" O PHE B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 206 removed outlier: 3.832A pdb=" N LEU B 167 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Proline residue: B 170 - end of helix removed outlier: 4.006A pdb=" N ALA B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 218 through 269 removed outlier: 3.881A pdb=" N LEU B 227 " --> pdb=" O TRP B 223 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 233 " --> pdb=" O ARG B 229 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Proline residue: B 244 - end of helix removed outlier: 3.704A pdb=" N ALA B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 268 " --> pdb=" O GLY B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 316 removed outlier: 4.209A pdb=" N LEU B 285 " --> pdb=" O PHE B 281 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 288 " --> pdb=" O TYR B 284 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TRP B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 4.378A pdb=" N GLY B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TRP B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 377 through 384 removed outlier: 4.197A pdb=" N VAL B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 407 through 410 No H-bonds generated for 'chain 'B' and resid 407 through 410' Processing helix chain 'B' and resid 428 through 432 Processing helix chain 'B' and resid 441 through 450 removed outlier: 3.882A pdb=" N GLU B 445 " --> pdb=" O ARG B 441 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 459 Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 477 through 491 removed outlier: 4.276A pdb=" N LYS B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 519 Processing helix chain 'B' and resid 533 through 537 Processing helix chain 'B' and resid 565 through 574 removed outlier: 3.751A pdb=" N LEU B 572 " --> pdb=" O GLU B 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 353 through 356 removed outlier: 3.920A pdb=" N CYS A 416 " --> pdb=" O ARG A 356 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 564 through 568 removed outlier: 4.245A pdb=" N ARG A 564 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N SER A 549 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU A 391 " --> pdb=" O SER A 549 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE A 551 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N GLY A 393 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A 519 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 358 through 360 removed outlier: 7.992A pdb=" N LEU A 360 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS A 377 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 359 through 361 Processing sheet with id= E, first strand: chain 'B' and resid 549 through 554 removed outlier: 6.933A pdb=" N VAL B 544 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU B 553 " --> pdb=" O ILE B 542 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 542 " --> pdb=" O GLU B 553 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP B 541 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N THR B 526 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE B 369 " --> pdb=" O THR B 526 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU B 528 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N GLY B 371 " --> pdb=" O LEU B 528 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 344 through 346 removed outlier: 7.526A pdb=" N LEU B 346 " --> pdb=" O ARG B 355 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ARG B 355 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.659A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.529A pdb=" N ALA C 92 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 101 through 103 removed outlier: 4.066A pdb=" N ALA C 101 " --> pdb=" O VAL C 109 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1443 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: 2.96 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1611 1.31 - 1.44: 3256 1.44 - 1.57: 5474 1.57 - 1.70: 13 1.70 - 1.83: 45 Bond restraints: 10399 Sorted by residual: bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.01e+01 bond pdb=" C5 ATP B 601 " pdb=" N7 ATP B 601 " ideal model delta sigma weight residual 1.387 1.327 0.060 1.00e-02 1.00e+04 3.54e+01 bond pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " ideal model delta sigma weight residual 1.374 1.321 0.053 1.00e-02 1.00e+04 2.84e+01 bond pdb=" CA GLY B 368 " pdb=" C GLY B 368 " ideal model delta sigma weight residual 1.519 1.484 0.035 7.00e-03 2.04e+04 2.44e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.457 -0.048 1.00e-02 1.00e+04 2.34e+01 ... (remaining 10394 not shown) Histogram of bond angle deviations from ideal: 91.62 - 100.43: 19 100.43 - 109.25: 1569 109.25 - 118.06: 6356 118.06 - 126.88: 6046 126.88 - 135.69: 118 Bond angle restraints: 14108 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 115.99 23.88 1.00e+00 1.00e+00 5.70e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 114.66 22.17 1.00e+00 1.00e+00 4.92e+02 angle pdb=" N VAL B 241 " pdb=" CA VAL B 241 " pdb=" C VAL B 241 " ideal model delta sigma weight residual 111.62 101.60 10.02 7.90e-01 1.60e+00 1.61e+02 angle pdb=" N SER B 558 " pdb=" CA SER B 558 " pdb=" C SER B 558 " ideal model delta sigma weight residual 111.36 100.23 11.13 1.09e+00 8.42e-01 1.04e+02 angle pdb=" N ILE B 473 " pdb=" CA ILE B 473 " pdb=" C ILE B 473 " ideal model delta sigma weight residual 113.53 103.64 9.89 9.80e-01 1.04e+00 1.02e+02 ... (remaining 14103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.89: 5905 18.89 - 37.78: 204 37.78 - 56.66: 50 56.66 - 75.55: 24 75.55 - 94.44: 6 Dihedral angle restraints: 6189 sinusoidal: 2527 harmonic: 3662 Sorted by residual: dihedral pdb=" N ASP B 349 " pdb=" C ASP B 349 " pdb=" CA ASP B 349 " pdb=" CB ASP B 349 " ideal model delta harmonic sigma weight residual 122.80 135.65 -12.85 0 2.50e+00 1.60e-01 2.64e+01 dihedral pdb=" O1B ADP A 701 " pdb=" O3A ADP A 701 " pdb=" PB ADP A 701 " pdb=" PA ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 -154.44 94.44 1 2.00e+01 2.50e-03 2.59e+01 dihedral pdb=" N GLU B 438 " pdb=" C GLU B 438 " pdb=" CA GLU B 438 " pdb=" CB GLU B 438 " ideal model delta harmonic sigma weight residual 122.80 110.37 12.43 0 2.50e+00 1.60e-01 2.47e+01 ... (remaining 6186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1078 0.103 - 0.205: 399 0.205 - 0.308: 93 0.308 - 0.410: 25 0.410 - 0.513: 12 Chirality restraints: 1607 Sorted by residual: chirality pdb=" CA ASN B 123 " pdb=" N ASN B 123 " pdb=" C ASN B 123 " pdb=" CB ASN B 123 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.58e+00 chirality pdb=" CA GLU A 533 " pdb=" N GLU A 533 " pdb=" C GLU A 533 " pdb=" CB GLU A 533 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" CA GLN A 441 " pdb=" N GLN A 441 " pdb=" C GLN A 441 " pdb=" CB GLN A 441 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.61e+00 ... (remaining 1604 not shown) Planarity restraints: 1784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 223 " 0.051 2.00e-02 2.50e+03 2.56e-02 1.64e+01 pdb=" CG TRP B 223 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TRP B 223 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP B 223 " -0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP B 223 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 223 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 223 " -0.034 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 223 " 0.028 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 223 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP B 223 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 52 " 0.053 2.00e-02 2.50e+03 2.50e-02 1.57e+01 pdb=" CG TRP A 52 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 52 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 52 " -0.023 2.00e-02 2.50e+03 pdb=" NE1 TRP A 52 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 52 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 52 " -0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 52 " 0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 52 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP A 52 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 216 " -0.019 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C LEU B 216 " 0.068 2.00e-02 2.50e+03 pdb=" O LEU B 216 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU B 217 " -0.023 2.00e-02 2.50e+03 ... (remaining 1781 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 462 2.71 - 3.26: 10060 3.26 - 3.80: 15437 3.80 - 4.35: 20837 4.35 - 4.90: 33397 Nonbonded interactions: 80193 Sorted by model distance: nonbonded pdb=" O2B ADP A 701 " pdb="MG MG A 702 " model vdw 2.162 2.170 nonbonded pdb=" OG1 THR A 400 " pdb="MG MG A 702 " model vdw 2.173 2.170 nonbonded pdb=" OE1 GLN A 441 " pdb="MG MG A 702 " model vdw 2.233 2.170 nonbonded pdb=" O2B ATP B 601 " pdb="MG MG B 602 " model vdw 2.273 2.170 nonbonded pdb=" O1G ATP B 601 " pdb="MG MG B 602 " model vdw 2.316 2.170 ... (remaining 80188 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 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: 0.700 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: 3.850 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 30.090 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 : 0.016 0.071 10399 Z= 1.074 Angle : 1.964 23.885 14108 Z= 1.407 Chirality : 0.119 0.513 1607 Planarity : 0.012 0.082 1784 Dihedral : 11.725 94.441 3839 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.82 % Favored : 96.94 % Rotamer: Outliers : 0.10 % Allowed : 2.96 % Favored : 96.95 % Cbeta Deviations : 0.60 % 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: -2.86 (0.20), residues: 1275 helix: -1.94 (0.16), residues: 745 sheet: -0.77 (0.42), residues: 132 loop : -1.78 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.008 TRP A 52 HIS 0.006 0.001 HIS B 400 PHE 0.044 0.007 PHE B 313 TYR 0.049 0.006 TYR A 277 ARG 0.005 0.000 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 328 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ILE cc_start: 0.9395 (mm) cc_final: 0.9150 (mm) REVERT: A 160 PHE cc_start: 0.7924 (m-80) cc_final: 0.7686 (m-80) REVERT: A 303 LEU cc_start: 0.9286 (tp) cc_final: 0.9051 (tp) REVERT: A 309 ASP cc_start: 0.8722 (t0) cc_final: 0.8380 (t70) REVERT: A 321 MET cc_start: 0.8433 (tpt) cc_final: 0.8184 (tpt) REVERT: A 359 TRP cc_start: 0.7904 (m100) cc_final: 0.6882 (m100) REVERT: A 372 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7913 (tptm) REVERT: A 376 LEU cc_start: 0.8173 (mp) cc_final: 0.7903 (mm) REVERT: A 391 LEU cc_start: 0.9224 (mp) cc_final: 0.8647 (tt) REVERT: A 503 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8162 (tp40) REVERT: A 538 GLU cc_start: 0.8616 (tt0) cc_final: 0.8318 (tp30) REVERT: A 554 HIS cc_start: 0.6726 (m90) cc_final: 0.5875 (m-70) REVERT: B 21 ARG cc_start: 0.8232 (ttp-110) cc_final: 0.7516 (ptm160) REVERT: B 125 ASP cc_start: 0.6470 (m-30) cc_final: 0.6157 (m-30) REVERT: B 191 GLN cc_start: 0.8573 (tp40) cc_final: 0.8209 (tm-30) REVERT: B 282 ASN cc_start: 0.9411 (t0) cc_final: 0.8906 (t0) REVERT: B 299 MET cc_start: 0.8777 (mmm) cc_final: 0.8475 (mmp) REVERT: B 359 LEU cc_start: 0.8936 (tp) cc_final: 0.8703 (tt) REVERT: B 365 MET cc_start: 0.7839 (ttp) cc_final: 0.7447 (tmm) REVERT: B 505 VAL cc_start: 0.9116 (t) cc_final: 0.8908 (p) REVERT: C 80 HIS cc_start: 0.7781 (m-70) cc_final: 0.6543 (m-70) outliers start: 1 outliers final: 0 residues processed: 328 average time/residue: 0.2997 time to fit residues: 126.8630 Evaluate side-chains 198 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.7980 chunk 96 optimal weight: 0.3980 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 115 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS B 120 ASN B 123 ASN C 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10399 Z= 0.229 Angle : 0.694 9.580 14108 Z= 0.350 Chirality : 0.042 0.175 1607 Planarity : 0.005 0.048 1784 Dihedral : 6.599 71.614 1485 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.34 % Allowed : 11.82 % Favored : 84.84 % 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: -1.30 (0.22), residues: 1275 helix: -0.50 (0.18), residues: 769 sheet: -0.84 (0.45), residues: 114 loop : -1.30 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 290 HIS 0.005 0.001 HIS B 454 PHE 0.024 0.002 PHE A 88 TYR 0.018 0.002 TYR A 589 ARG 0.009 0.001 ARG A 569 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 227 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9257 (mt) cc_final: 0.8804 (tt) REVERT: A 94 GLU cc_start: 0.7920 (tp30) cc_final: 0.7592 (tp30) REVERT: A 118 MET cc_start: 0.8970 (mmp) cc_final: 0.8442 (mmp) REVERT: A 160 PHE cc_start: 0.7749 (m-80) cc_final: 0.7527 (m-80) REVERT: A 305 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8170 (tp40) REVERT: A 309 ASP cc_start: 0.8348 (t0) cc_final: 0.7947 (t0) REVERT: A 359 TRP cc_start: 0.7976 (m100) cc_final: 0.7404 (m100) REVERT: A 376 LEU cc_start: 0.8298 (mp) cc_final: 0.8056 (mm) REVERT: A 444 PHE cc_start: 0.7236 (t80) cc_final: 0.6088 (t80) REVERT: A 569 ARG cc_start: 0.7408 (mtt90) cc_final: 0.7043 (mtt90) REVERT: B 132 MET cc_start: 0.8970 (tmm) cc_final: 0.8644 (tmm) REVERT: B 185 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8685 (ttm110) REVERT: B 255 PHE cc_start: 0.8669 (t80) cc_final: 0.8235 (t80) REVERT: B 282 ASN cc_start: 0.8987 (t0) cc_final: 0.8756 (t0) REVERT: B 299 MET cc_start: 0.8727 (mmm) cc_final: 0.8425 (mmp) REVERT: B 301 LEU cc_start: 0.8629 (tt) cc_final: 0.8374 (tp) REVERT: C 20 LEU cc_start: 0.8816 (tp) cc_final: 0.8417 (tp) REVERT: C 51 ILE cc_start: 0.8880 (tp) cc_final: 0.8644 (tp) REVERT: C 86 LEU cc_start: 0.8816 (mt) cc_final: 0.8318 (mt) REVERT: C 103 LEU cc_start: 0.8276 (mp) cc_final: 0.7596 (tp) REVERT: C 107 ARG cc_start: 0.7501 (mmm160) cc_final: 0.6833 (ttt-90) outliers start: 35 outliers final: 20 residues processed: 246 average time/residue: 0.2551 time to fit residues: 84.6372 Evaluate side-chains 187 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 165 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 108 CYS Chi-restraints excluded: chain C residue 122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 115 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10399 Z= 0.202 Angle : 0.661 9.594 14108 Z= 0.322 Chirality : 0.040 0.153 1607 Planarity : 0.004 0.042 1784 Dihedral : 5.777 55.980 1481 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.62 % Allowed : 13.82 % Favored : 82.55 % 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: -0.59 (0.23), residues: 1275 helix: 0.19 (0.18), residues: 767 sheet: -0.51 (0.42), residues: 137 loop : -1.35 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 290 HIS 0.007 0.001 HIS C 80 PHE 0.019 0.001 PHE A 317 TYR 0.028 0.001 TYR B 92 ARG 0.009 0.001 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 185 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9183 (mt) cc_final: 0.8822 (tt) REVERT: A 36 LEU cc_start: 0.8848 (tt) cc_final: 0.8538 (tp) REVERT: A 40 THR cc_start: 0.9077 (m) cc_final: 0.8762 (p) REVERT: A 72 LEU cc_start: 0.7830 (mm) cc_final: 0.7492 (mm) REVERT: A 94 GLU cc_start: 0.7919 (tp30) cc_final: 0.7700 (tp30) REVERT: A 145 ASN cc_start: 0.8684 (m-40) cc_final: 0.8199 (m110) REVERT: A 302 GLN cc_start: 0.8153 (tt0) cc_final: 0.7841 (tm-30) REVERT: A 308 GLN cc_start: 0.7601 (mt0) cc_final: 0.7268 (mt0) REVERT: A 309 ASP cc_start: 0.8186 (t0) cc_final: 0.7822 (t0) REVERT: A 359 TRP cc_start: 0.8153 (m100) cc_final: 0.7346 (m100) REVERT: A 376 LEU cc_start: 0.8297 (mp) cc_final: 0.8038 (mm) REVERT: A 417 VAL cc_start: 0.8991 (OUTLIER) cc_final: 0.8771 (p) REVERT: B 132 MET cc_start: 0.8974 (tmm) cc_final: 0.8613 (tmm) REVERT: B 281 PHE cc_start: 0.9030 (t80) cc_final: 0.8742 (t80) REVERT: B 282 ASN cc_start: 0.9058 (t0) cc_final: 0.8762 (t0) REVERT: B 316 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8444 (mt) REVERT: B 523 LYS cc_start: 0.8130 (pttm) cc_final: 0.7881 (pttm) REVERT: C 20 LEU cc_start: 0.8810 (tp) cc_final: 0.8295 (tp) REVERT: C 45 ARG cc_start: 0.8427 (mtm110) cc_final: 0.8026 (mtm110) REVERT: C 107 ARG cc_start: 0.7467 (mmm160) cc_final: 0.7025 (ttt-90) outliers start: 38 outliers final: 19 residues processed: 212 average time/residue: 0.2388 time to fit residues: 70.0111 Evaluate side-chains 177 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 156 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 HIS B 280 GLN B 419 GLN B 538 HIS ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10399 Z= 0.335 Angle : 0.698 8.800 14108 Z= 0.344 Chirality : 0.043 0.164 1607 Planarity : 0.004 0.049 1784 Dihedral : 5.762 59.651 1481 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.00 % Allowed : 15.92 % Favored : 80.08 % 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: -0.32 (0.23), residues: 1275 helix: 0.43 (0.19), residues: 758 sheet: -0.20 (0.45), residues: 121 loop : -1.32 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 446 HIS 0.007 0.002 HIS C 80 PHE 0.021 0.002 PHE A 70 TYR 0.027 0.002 TYR B 92 ARG 0.014 0.001 ARG A 569 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 163 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.9169 (m) cc_final: 0.8893 (p) REVERT: A 72 LEU cc_start: 0.8001 (mm) cc_final: 0.7610 (mm) REVERT: A 94 GLU cc_start: 0.7966 (tp30) cc_final: 0.7631 (tp30) REVERT: A 145 ASN cc_start: 0.8758 (m-40) cc_final: 0.8152 (m110) REVERT: A 146 GLN cc_start: 0.8135 (mt0) cc_final: 0.7902 (mp10) REVERT: A 302 GLN cc_start: 0.8103 (tt0) cc_final: 0.7886 (tm-30) REVERT: A 309 ASP cc_start: 0.8378 (t0) cc_final: 0.7942 (t0) REVERT: A 359 TRP cc_start: 0.8228 (m100) cc_final: 0.7527 (m100) REVERT: A 417 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8772 (p) REVERT: B 16 TYR cc_start: 0.8753 (m-80) cc_final: 0.8525 (m-10) REVERT: B 154 MET cc_start: 0.8739 (mmm) cc_final: 0.8105 (mmm) REVERT: B 282 ASN cc_start: 0.9094 (t0) cc_final: 0.8788 (t0) REVERT: B 365 MET cc_start: 0.8531 (tmm) cc_final: 0.8207 (tmm) REVERT: B 523 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8074 (pttm) REVERT: C 13 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7102 (tp40) REVERT: C 20 LEU cc_start: 0.9076 (tp) cc_final: 0.8832 (tp) outliers start: 42 outliers final: 26 residues processed: 192 average time/residue: 0.2284 time to fit residues: 61.9487 Evaluate side-chains 183 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 155 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 243 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 HIS B 287 GLN B 419 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10399 Z= 0.254 Angle : 0.644 10.322 14108 Z= 0.312 Chirality : 0.041 0.169 1607 Planarity : 0.004 0.042 1784 Dihedral : 5.524 56.249 1481 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.00 % Allowed : 17.45 % Favored : 78.55 % 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: -0.07 (0.23), residues: 1275 helix: 0.66 (0.19), residues: 759 sheet: -0.16 (0.46), residues: 126 loop : -1.29 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 446 HIS 0.005 0.001 HIS B 246 PHE 0.015 0.001 PHE A 15 TYR 0.024 0.001 TYR B 92 ARG 0.005 0.000 ARG A 569 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 170 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.9203 (m) cc_final: 0.8931 (p) REVERT: A 72 LEU cc_start: 0.7961 (mm) cc_final: 0.7628 (mm) REVERT: A 94 GLU cc_start: 0.7987 (tp30) cc_final: 0.7609 (tp30) REVERT: A 145 ASN cc_start: 0.8792 (m-40) cc_final: 0.8191 (m110) REVERT: A 302 GLN cc_start: 0.8099 (tt0) cc_final: 0.7897 (tm-30) REVERT: A 391 LEU cc_start: 0.9122 (mp) cc_final: 0.8788 (mt) REVERT: B 112 LYS cc_start: 0.8765 (mmmt) cc_final: 0.7996 (mttp) REVERT: B 132 MET cc_start: 0.8998 (ttp) cc_final: 0.8778 (tmm) REVERT: B 154 MET cc_start: 0.8730 (mmm) cc_final: 0.8098 (mmm) REVERT: B 282 ASN cc_start: 0.9069 (t0) cc_final: 0.8666 (t0) REVERT: B 365 MET cc_start: 0.8499 (tmm) cc_final: 0.8028 (tmm) REVERT: B 523 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8142 (pttm) REVERT: C 13 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7310 (tp40) REVERT: C 20 LEU cc_start: 0.9136 (tp) cc_final: 0.8909 (tp) REVERT: C 46 GLU cc_start: 0.8009 (pm20) cc_final: 0.7794 (pm20) outliers start: 42 outliers final: 32 residues processed: 198 average time/residue: 0.2269 time to fit residues: 63.2068 Evaluate side-chains 184 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 151 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 122 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN B 123 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 HIS ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10399 Z= 0.183 Angle : 0.613 9.075 14108 Z= 0.294 Chirality : 0.040 0.272 1607 Planarity : 0.004 0.037 1784 Dihedral : 5.277 52.314 1481 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.96 % Allowed : 18.78 % Favored : 78.27 % 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: 0.31 (0.23), residues: 1275 helix: 1.02 (0.19), residues: 758 sheet: -0.10 (0.47), residues: 125 loop : -1.22 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 359 HIS 0.005 0.001 HIS B 246 PHE 0.015 0.001 PHE A 15 TYR 0.016 0.001 TYR B 92 ARG 0.003 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 163 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.9196 (m) cc_final: 0.8917 (p) REVERT: A 72 LEU cc_start: 0.7905 (mm) cc_final: 0.7584 (mm) REVERT: A 94 GLU cc_start: 0.7974 (tp30) cc_final: 0.7622 (tp30) REVERT: A 145 ASN cc_start: 0.8786 (m-40) cc_final: 0.8469 (m-40) REVERT: A 302 GLN cc_start: 0.8083 (tt0) cc_final: 0.7876 (tm-30) REVERT: A 391 LEU cc_start: 0.9106 (mp) cc_final: 0.8781 (mt) REVERT: B 112 LYS cc_start: 0.8794 (mmmt) cc_final: 0.8090 (mttp) REVERT: B 130 ARG cc_start: 0.8499 (tmm-80) cc_final: 0.8070 (tmm-80) REVERT: B 132 MET cc_start: 0.8944 (ttp) cc_final: 0.8595 (tmm) REVERT: B 154 MET cc_start: 0.8687 (mmm) cc_final: 0.8109 (mmm) REVERT: B 253 MET cc_start: 0.8638 (mmm) cc_final: 0.8375 (mmp) REVERT: B 281 PHE cc_start: 0.8758 (t80) cc_final: 0.7452 (t80) REVERT: B 282 ASN cc_start: 0.9024 (t0) cc_final: 0.8587 (t0) REVERT: B 365 MET cc_start: 0.8461 (tmm) cc_final: 0.7990 (tmm) REVERT: C 13 GLN cc_start: 0.7848 (mm-40) cc_final: 0.6999 (tp40) REVERT: C 20 LEU cc_start: 0.9158 (tp) cc_final: 0.8940 (tp) REVERT: C 39 GLN cc_start: 0.7846 (tm-30) cc_final: 0.7566 (tm-30) REVERT: C 103 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8333 (tp) REVERT: C 113 TYR cc_start: 0.7274 (m-80) cc_final: 0.7051 (m-80) outliers start: 31 outliers final: 21 residues processed: 186 average time/residue: 0.2383 time to fit residues: 61.3007 Evaluate side-chains 177 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 HIS ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10399 Z= 0.224 Angle : 0.625 8.964 14108 Z= 0.302 Chirality : 0.040 0.161 1607 Planarity : 0.004 0.036 1784 Dihedral : 5.224 53.641 1481 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.15 % Allowed : 19.45 % Favored : 77.41 % 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: 0.34 (0.23), residues: 1275 helix: 1.00 (0.19), residues: 776 sheet: -0.11 (0.47), residues: 120 loop : -1.18 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 359 HIS 0.005 0.001 HIS B 246 PHE 0.027 0.001 PHE B 38 TYR 0.023 0.001 TYR B 92 ARG 0.009 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 161 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.9229 (m) cc_final: 0.8961 (p) REVERT: A 94 GLU cc_start: 0.7972 (tp30) cc_final: 0.7593 (tp30) REVERT: A 365 LYS cc_start: 0.8580 (ttmt) cc_final: 0.7868 (mtmt) REVERT: A 391 LEU cc_start: 0.9127 (mp) cc_final: 0.8820 (mt) REVERT: A 492 GLU cc_start: 0.8260 (pt0) cc_final: 0.8023 (pm20) REVERT: A 493 ARG cc_start: 0.7898 (tpt90) cc_final: 0.7573 (tpp-160) REVERT: B 40 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8139 (tt) REVERT: B 131 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8441 (mm-30) REVERT: B 132 MET cc_start: 0.9036 (ttp) cc_final: 0.8724 (tmm) REVERT: B 154 MET cc_start: 0.8696 (mmm) cc_final: 0.8137 (mmm) REVERT: B 253 MET cc_start: 0.8643 (mmm) cc_final: 0.8398 (mmp) REVERT: B 281 PHE cc_start: 0.8772 (t80) cc_final: 0.7609 (t80) REVERT: B 282 ASN cc_start: 0.9051 (t0) cc_final: 0.8638 (t0) REVERT: B 365 MET cc_start: 0.8464 (tmm) cc_final: 0.7860 (tmm) REVERT: B 508 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8547 (pm20) REVERT: C 20 LEU cc_start: 0.9179 (tp) cc_final: 0.8949 (tp) REVERT: C 39 GLN cc_start: 0.7842 (tm-30) cc_final: 0.7428 (tm-30) REVERT: C 107 ARG cc_start: 0.7663 (ttt90) cc_final: 0.7157 (ttt-90) REVERT: C 113 TYR cc_start: 0.7329 (m-80) cc_final: 0.7107 (m-80) outliers start: 33 outliers final: 22 residues processed: 187 average time/residue: 0.2283 time to fit residues: 59.5250 Evaluate side-chains 176 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 36 optimal weight: 0.0040 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 308 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 HIS B 282 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10399 Z= 0.182 Angle : 0.631 9.554 14108 Z= 0.299 Chirality : 0.039 0.153 1607 Planarity : 0.004 0.044 1784 Dihedral : 5.054 51.315 1481 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.76 % Allowed : 20.59 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.24), residues: 1275 helix: 1.20 (0.19), residues: 773 sheet: 0.10 (0.47), residues: 119 loop : -1.14 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 262 HIS 0.005 0.001 HIS B 246 PHE 0.015 0.001 PHE A 15 TYR 0.021 0.001 TYR B 92 ARG 0.006 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 174 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.9218 (m) cc_final: 0.8936 (p) REVERT: A 94 GLU cc_start: 0.7935 (tp30) cc_final: 0.7561 (tp30) REVERT: A 182 LEU cc_start: 0.8512 (tp) cc_final: 0.8180 (tt) REVERT: A 365 LYS cc_start: 0.8357 (ttmt) cc_final: 0.8031 (mtmt) REVERT: A 384 ARG cc_start: 0.8629 (tpt170) cc_final: 0.8119 (mmm160) REVERT: A 391 LEU cc_start: 0.9121 (mp) cc_final: 0.8806 (mt) REVERT: A 492 GLU cc_start: 0.8146 (pt0) cc_final: 0.7886 (pm20) REVERT: A 508 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8043 (p) REVERT: B 38 PHE cc_start: 0.8688 (t80) cc_final: 0.8464 (t80) REVERT: B 40 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8050 (tt) REVERT: B 112 LYS cc_start: 0.8740 (mmmt) cc_final: 0.7908 (mttp) REVERT: B 130 ARG cc_start: 0.8394 (tmm-80) cc_final: 0.7933 (tmm-80) REVERT: B 132 MET cc_start: 0.9001 (ttp) cc_final: 0.8739 (tmm) REVERT: B 154 MET cc_start: 0.8640 (mmm) cc_final: 0.8044 (mmm) REVERT: B 281 PHE cc_start: 0.8721 (t80) cc_final: 0.7559 (t80) REVERT: B 282 ASN cc_start: 0.8989 (t0) cc_final: 0.8579 (t0) REVERT: B 365 MET cc_start: 0.8378 (tmm) cc_final: 0.7938 (tmm) REVERT: B 508 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8544 (pm20) REVERT: C 20 LEU cc_start: 0.9168 (tp) cc_final: 0.8946 (tp) REVERT: C 39 GLN cc_start: 0.7885 (tm-30) cc_final: 0.7385 (tm-30) REVERT: C 43 LYS cc_start: 0.8406 (ptpp) cc_final: 0.8076 (ptpp) REVERT: C 65 LYS cc_start: 0.8975 (pttp) cc_final: 0.8598 (ptpt) REVERT: C 107 ARG cc_start: 0.7530 (ttt90) cc_final: 0.7177 (ttt-90) REVERT: C 113 TYR cc_start: 0.7188 (m-80) cc_final: 0.6954 (m-80) outliers start: 29 outliers final: 22 residues processed: 198 average time/residue: 0.2251 time to fit residues: 62.6844 Evaluate side-chains 185 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 108 CYS Chi-restraints excluded: chain C residue 122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 103 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 HIS ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10399 Z= 0.196 Angle : 0.645 10.726 14108 Z= 0.304 Chirality : 0.039 0.154 1607 Planarity : 0.004 0.057 1784 Dihedral : 4.982 51.858 1481 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.86 % Allowed : 20.97 % Favored : 76.17 % 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: 0.57 (0.24), residues: 1275 helix: 1.24 (0.19), residues: 768 sheet: 0.11 (0.47), residues: 119 loop : -1.22 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 290 HIS 0.005 0.001 HIS B 246 PHE 0.019 0.001 PHE A 15 TYR 0.020 0.001 TYR B 92 ARG 0.005 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 167 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.9219 (m) cc_final: 0.8945 (p) REVERT: A 94 GLU cc_start: 0.8026 (tp30) cc_final: 0.7647 (tp30) REVERT: A 182 LEU cc_start: 0.8490 (tp) cc_final: 0.8165 (tt) REVERT: A 305 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7963 (tp40) REVERT: A 365 LYS cc_start: 0.8449 (ttmt) cc_final: 0.8189 (ttmt) REVERT: A 384 ARG cc_start: 0.8613 (tpt170) cc_final: 0.8120 (mmm160) REVERT: A 391 LEU cc_start: 0.9126 (mp) cc_final: 0.8803 (mt) REVERT: A 492 GLU cc_start: 0.8271 (pt0) cc_final: 0.8025 (pm20) REVERT: A 508 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8059 (p) REVERT: B 40 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8032 (tt) REVERT: B 130 ARG cc_start: 0.8478 (tmm-80) cc_final: 0.7989 (tmm-80) REVERT: B 132 MET cc_start: 0.9012 (ttp) cc_final: 0.8760 (tmm) REVERT: B 154 MET cc_start: 0.8661 (mmm) cc_final: 0.8273 (mmm) REVERT: B 282 ASN cc_start: 0.8970 (t0) cc_final: 0.8534 (t0) REVERT: B 359 LEU cc_start: 0.9095 (tp) cc_final: 0.8817 (tt) REVERT: B 365 MET cc_start: 0.8434 (tmm) cc_final: 0.7897 (tmm) REVERT: B 508 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8556 (pm20) REVERT: C 20 LEU cc_start: 0.9192 (tp) cc_final: 0.8591 (tp) REVERT: C 39 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7478 (tm-30) REVERT: C 43 LYS cc_start: 0.8412 (ptpp) cc_final: 0.8056 (ptpp) REVERT: C 107 ARG cc_start: 0.7680 (ttt90) cc_final: 0.7288 (ttt-90) outliers start: 30 outliers final: 21 residues processed: 189 average time/residue: 0.2360 time to fit residues: 62.9461 Evaluate side-chains 181 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 HIS ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10399 Z= 0.294 Angle : 0.699 12.096 14108 Z= 0.333 Chirality : 0.041 0.162 1607 Planarity : 0.004 0.063 1784 Dihedral : 5.164 54.221 1481 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.86 % Allowed : 21.26 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.24), residues: 1275 helix: 1.16 (0.19), residues: 764 sheet: 0.09 (0.47), residues: 119 loop : -1.25 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 36 HIS 0.006 0.001 HIS B 246 PHE 0.023 0.002 PHE A 70 TYR 0.023 0.001 TYR B 92 ARG 0.005 0.000 ARG C 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 159 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.9263 (m) cc_final: 0.9012 (p) REVERT: A 94 GLU cc_start: 0.7992 (tp30) cc_final: 0.7590 (tp30) REVERT: A 145 ASN cc_start: 0.8808 (m-40) cc_final: 0.8484 (m-40) REVERT: A 305 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7796 (tp-100) REVERT: A 347 ARG cc_start: 0.7582 (mmt-90) cc_final: 0.6859 (tmm-80) REVERT: A 365 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8329 (mtmt) REVERT: A 391 LEU cc_start: 0.9160 (mp) cc_final: 0.8864 (mt) REVERT: B 40 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8108 (tt) REVERT: B 130 ARG cc_start: 0.8579 (tmm-80) cc_final: 0.8003 (tmm-80) REVERT: B 132 MET cc_start: 0.9038 (ttp) cc_final: 0.8733 (tmm) REVERT: B 154 MET cc_start: 0.8723 (mmm) cc_final: 0.8405 (mmm) REVERT: B 186 ARG cc_start: 0.8649 (mpt-90) cc_final: 0.8384 (mpt-90) REVERT: B 282 ASN cc_start: 0.9011 (t0) cc_final: 0.8572 (t0) REVERT: B 365 MET cc_start: 0.8467 (tmm) cc_final: 0.7892 (tmm) REVERT: C 20 LEU cc_start: 0.9249 (tp) cc_final: 0.8605 (tp) REVERT: C 39 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7247 (tm-30) REVERT: C 43 LYS cc_start: 0.8375 (ptpp) cc_final: 0.7951 (ptpp) REVERT: C 107 ARG cc_start: 0.7646 (ttt90) cc_final: 0.7218 (ttt-90) outliers start: 30 outliers final: 22 residues processed: 181 average time/residue: 0.2331 time to fit residues: 58.8041 Evaluate side-chains 178 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.5980 chunk 107 optimal weight: 0.0970 chunk 30 optimal weight: 0.2980 chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 HIS ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.096503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.077578 restraints weight = 25777.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.080343 restraints weight = 13673.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.082207 restraints weight = 8937.470| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.5929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10399 Z= 0.178 Angle : 0.660 10.948 14108 Z= 0.308 Chirality : 0.039 0.157 1607 Planarity : 0.004 0.053 1784 Dihedral : 4.977 51.014 1481 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.91 % Allowed : 22.02 % Favored : 76.07 % 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: 0.59 (0.24), residues: 1275 helix: 1.26 (0.19), residues: 762 sheet: 0.31 (0.49), residues: 119 loop : -1.26 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 14 HIS 0.005 0.001 HIS B 246 PHE 0.020 0.001 PHE A 15 TYR 0.018 0.001 TYR B 92 ARG 0.007 0.000 ARG A 569 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2245.98 seconds wall clock time: 41 minutes 24.80 seconds (2484.80 seconds total)